Mercurial > repos > galaxyp > openms
changeset 2:cf0d72c7b482 draft
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--- a/README.md Wed Dec 19 00:33:53 2012 -0500 +++ b/README.md Fri May 10 17:31:05 2013 -0400 @@ -1,4 +1,25 @@ -TODO: Document this tool repository. +# OpenMS + +If there is a tool that is part of OpenMS but not available here, let +John Chilton (jmchilton@gmail.com) and he will try to add it. + +These tools require Galaxy to be equipped with common proteomic +datatypes. These can be obtained by installing Ira Cooke's ProtK via +the tool shed or merging the changesets from the following repository +into your Galaxy instance: + + https://bitbucket.org/galaxyp/galaxy-dist-proteomics + +# Installing + +These tools all require OpenMS (at least version 1.10) and may require +other dependencies (such as PepNovo for instance). + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. + # Obtaining Tools Repositories for all Galaxy-P tools can be found at
--- a/README_REPO.md Wed Dec 19 00:33:53 2012 -0500 +++ b/README_REPO.md Fri May 10 17:31:05 2013 -0400 @@ -1,9 +1,7 @@ # OpenMS -This repository is in an early alpha state and many OpenMS tools are -not yet available or are largely untested. If there is a tool that is -part of OpenMS but not available here, let John Chilton -(jmchilton@gmail.com) and he will try to add it. +If there is a tool that is part of OpenMS but not available here, let +John Chilton (jmchilton@gmail.com) and he will try to add it. These tools require Galaxy to be equipped with common proteomic datatypes. These can be obtained by installing Ira Cooke's ProtK via @@ -14,12 +12,11 @@ # Installing -These tools all require OpenMS and may require other dependencies -(such as PepNovo for instance). +These tools all require OpenMS (at least version 1.10) and may require +other dependencies (such as PepNovo for instance). For Galaxy-P we are installing this tool via CloudBioLinux -(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio\ -_proteomics.py). While +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While this fabric script may not be exactly appropriate for your environment it may serve as a template for how to install this software.
--- a/baseline_filter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/baseline_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Executes the top-hat filter to remove the baseline of an MS experiment. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'BaselineFilter' --config $config </command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_mods_loc.py Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,23 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET + +tree = ET.parse('unimod.xml') +ns = '{http://www.unimod.org/xmlns/schema/unimod_2}' +modifications_el = tree.getroot().find('%smodifications' % ns) + + +def to_label(title, site): + return "%s (%s)" % (title, site) + + +labels = [] +for mod in modifications_el.findall('%smod' % ns): + for specificity in mod.findall('%sspecificity' % ns): + title = mod.get('title') + site = specificity.get('site') + labels.append(to_label(title, site)) + +with open("openms_mods.loc", "w") as output: + for mod in sorted(labels, key=str.lower): + output.write("%s\n" % mod)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compnovo.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,69 @@ +<tool id="compnovo" version="0.1.0" name="CompNovo (OpenMS)"> + <description> + Performs a de novo peptide identification using the CompNovo engine. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + #if str($mode) == "cid" + #set $executable = "CompNovoCID" + #else + #set $executable = "CompNovo" + #end if + openms_wrapper.py --executable '$executable' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${input1} +out=${out} +#set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods]) +#if $fixed_mods_str +algorithm!fixed_modifications=$fixed_mods_str +#end if +#set $variable_mods_str=",".join([str($variable_mod.fixed_mod) for $variable_mod in $variable_mods]) +#if $variable_mods_str +algorithm!variable_modifications=$variable_mods_str +#end if +</configfile> + </configfiles> + <inputs> + <param name="input1" type="data" format="mzml" label="Input peak list" /> + <param name="mode" type="select" label="Mode"> + <option value="cid">CID-only</option> + <option value="cidetd">CID/ETD</option> + </param> + <repeat name="fixed_mods" title="Fixed Modification"> + <param name="fixed_mod" type="select" label="Fixed Modification"> + <options from_file="openms_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </repeat> + <repeat name="variable_mods" title="Variable Modification"> + <param name="variable_mod" type="select" label="Variable Modification"> + <options from_file="openms_mods.loc"> + <column name="name" index="0"/> + <column name="value" index="0" /> + </options> + </param> + </repeat> + </inputs> + <outputs> + <data format="idxml" name="out" /> + </outputs> + <help> +**What it does** + +De novo peptide sequencing of mass spectrometry data. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, et al.: De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 2009, 30:3736-3747.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consensus_extract_features.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,37 @@ +<tool id="openms_consensus_extract_features" version="0.1.0" name="Extract Consensus Features"> + <description> + Extracts one map of features from a consensus file. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FileFilter' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +in_type=consensusXML +out=$output +out_type=featureXML +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Input" type="data" format="consensusxml" /> + <param name="map" label="Map" type="integer" value="0" help="First map if 0, then 1, etc..." /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consensus_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,36 @@ +<tool id="openms_consensus_filter" version="0.1.0" name="Consensus Filter"> + <description> + Filters consensus results by different criteria. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FileFilter' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +in_type=consensusXML +out=$output +out_type=consensusXML +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Input" type="data" format="consensusxml" /> + </inputs> + <outputs> + <data format="consensusxml" name="output" /> + </outputs> + <help> +**What it does** + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consensus_id.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,42 @@ +<tool id="openms_consensus_id" version="0.1.0" name="Consensus ID"> + <description> + Computes a consensus identification from peptide identification engines. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'ConsensusID' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${input1} +out=${out} +</configfile> + </configfiles> + <inputs> + <param format="idxml,consensusxml,featurexml" name="input1" type="data" label="idXML Input" /> + <!-- Add options --> + </inputs> + <outputs> + <data format="input" name="out" metadata_source="input1" /> + </outputs> + <help> +**What it does** + +This implementation (for PEPMatrix and PEPIons) is described in + +Nahnsen S, Bertsch A, Rahnenfuehrer J, Nordheim A, Kohlbacher O +Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification +Journal of Proteome Research (2011), DOI: 10.1021/pr2002879 +The input file can contain several searches, e.g., from several identification engines. In order to use the PEPMatrix or the PEPIons algorithm, posterior error probabilities (PEPs) need to be calculated using the IDPosteriorErrorProbability tool for all individual search engines. After PEP calculation, the different search engine results have to be combined using IDMerger. Identification runs can be mapped to featureXML and consensusXML with the IDMapper tool. The merged file can now be fed into into the ConsensusID tool. For the statistical assessment of the results it is recommended to use target-decoy databases for peptide identifications. The false discovery rates (FDRs) can be calculated using the FalseDiscoveryRate tool. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/decoy_database.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,53 @@ +<tool id="openms_decoy_database" version="0.1.0" name="Decoy Database Creator"> + <description> + Create decoy protein/peptide databases from normal ones. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'DecoyDatabase' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${in} +out=${out} +decoy_string=${decoy_string} +decoy_string_position=${decoy_string_position} +append=${append} +shuffle=${shuffle} +</configfile> + </configfiles> + <inputs> + <param format="fasta" name="in" type="data" label="Input database"/> + <param name="decoy_string" type="text" value="_rev" label="Decoy string"/> + <param name="decoy_string_position" type="select" label="Decoy Position"> + <option value="suffix" selected="true">Suffix</option> + <option value="prefix">Prefix</option> + </param> + <param type="boolean" name="append" label="Append to original database" checked="true" /> + <param type="select" name="shuffle" label="Decoy type"> + <option value="false" selected="true">Reverse</option> + <option value="true">Shuffle</option> + </param> + </inputs> + <outputs> + <data format="fasta" name="out" /> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="Error creating decoy database." /> + </stdio> + <help> +**What it does** + +Create decoy protein/peptide databases from normal ones. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/false_discovery_rate.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,73 @@ +<tool id="openms_false_discvoerage_rate" version="0.1.0" name="False Discovery Rate"> + <description> + Tool to estimate the false discovery rate on peptide and protein level. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FalseDiscoveryRate' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +#if $input.type == "combined" +in=$input1 +algorithm!decoy_string=$input.decoy_string +#else +fwd_in=$input.forward_input +rev_in=$input.forward_input +#end if +out=$output +algorithm!q_value=$q_value +algorithm!use_all_hits=$use_all_hits +algorithm!split_charge_variants=$split_charge_variants +algorithm!add_decoy_peptides=$add_decoy_peptides +</configfile> + </configfiles> + <inputs> + <conditional name="input"> + <param name="type" label="Input Type" type="select"> + <option value="combined">One search against combined target/decoy database</option> + <option value="separate">Two searches from separate target and decoy databases.</option> + </param> + <when value="combined"> + <param name="input1" label="Identification Input" type="data" format="idxml" /> + <param name="decoy_string" type="text" value="_rev" label="Decoy string"/> + </when> + <when value="separate"> + <param name="forward_input" label="Forward Identification Input" type="data" format="idxml" /> + <param name="reverse_input" label="Reverse Identification Input" type="data" format="idxml" /> + </when> + </conditional> + <param name="q_value" label="Compute Q-Value" type="boolean" truevalue="true" falsevalue="false" checked="true" help="If 'true', the q-values will be calculated instead of the FDRs." /> + <param name="use_all_hits" label="Use All Hits" type="boolean" truevalue="true" falsevalue="false" help="If 'true' not only the first hit, but all are used (peptides only)." /> + <param name="split_charge_variants" label="Split Charge Variants" type="boolean" truevalue="true" falsevalue="false" help="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." checked="false" /> + <param name="add_decoy_peptides" type="boolean" label="Add Decoy Peptides" help="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." truevalue="true" falsevalue="false" checked="false" /> + + </inputs> + <outputs> + <data format="idxml" name="output" /> + </outputs> + <help> +**What it does** + +This TOPP tool can calculate the false discovery rate (FDR) given a forward and backward search (or one run on a combined database). Most useful is this on protein level, however, it also can be applied to peptides. + +The false discovery rate is defined as the number of false discoveries (the hits in the reversed search) over the number of false and correct discoveries (the hits in both databases) with a score better than a given threshold. + +Prerequisites: + +When using a combined database of forward and reverse hits (thus only using one search run per ID engine), then use PeptideIndexer to index an idXML file generated by a search engine adapter, e.g. MascotAdapter. This will allow us to discern which peptides are from the target vs. decoy database. +When no decoy hits were found you will get a warning saying something like: +"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!" +This should be a serious concern, since the target/decoy annotation in a previous step has probably a misconfigured database (see PeptideIndexer). + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,39 @@ +<tool id="openms_feature_filter" version="0.1.0" name="Feature Filter"> + <description> + Filters feature results by different criteria. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FileFilter' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +in_type=featureXML +out=$output +out_type=featureXML +feature!q=${min_quality or ''}:${max_quality or ''} +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Input" type="data" format="featurexml" /> + <param name="min_quality" label="Minimum Quality" help="Leave empty to specify no minimum." value="" default="" type="float" /> + <param name="max_quality" label="Maximum Quality" help="Leave empty to specify no maximum." value="" default="" type="float" /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_finder_centroided.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,83 @@ +<tool id="openms_feature_finder_centroided" version="0.1.0" name="Feature Finder (Centroided)"> + <description> + The feature detection application for quantitation (centroided). + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureFinderCentroided' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +algorithm!intensity!bins=$bins +algorithm!mass_trace!mz_tolerance=$trace_mz_tolerance +algorithm!mass_trace!min_spectra=$min_spectra +algorithm!mass_trace!max_missing=$max_missing +algorithm!seed!min_score=$seed_min_score +algorithm!feature!min_score=$feature_min_score +algorithm!feature!reported_mz=$reported_mz +algorithm!isotopic_pattern!mz_tolerance=$isotopic_mz_tolerance +algorithm!isotopic_pattern!charge_low=$charge_low +algorithm!isotopic_pattern!charge_high=$charge_high +#if $advanced_isotopic_pattern.specify +algorithm!isotopic_pattern!abundance_12C=$abundance_12C +algorithm!isotopic_pattern!abundance_14N=$abundance_14N +#end if +</configfile> + </configfiles> + <inputs> + <param name="input1" label="mzML Input" type="data" format="mzml" /> + <param name="bins" label="Bins" type="integer" help="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is. This parameter should be decreased, if the algorithm is used on small regions of a map." value="10" /> + <param name="trace_mz_tolerance" type="float" label="m/z Tolerance (Trace)" help="Tolerated m/z deviation of peaks belonging to the same mass trace. It should be larger than the m/z resolution of the instument. This value must be smaller than that 1/charge_high!" value="0.03" /> + <param name="min_spectra" label="Minimum Number of Spectra" help="Number of spectra that have to show a similar peak mass in a mass trace." value="10" type="integer" /> + <param name="max_missing" label="Max Missing" help="Number of consecutive spectra where a high mass deviation or missing peak is acceptable. This parameter should be well below 'min_spectra'!" value="1" type="integer" /> + <param name="seed_min_score" label="Seed Minimum Score" help="Minimum seed score a peak has to reach to be used as seed. The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." type="float" value="0.8" /> + <param name="feature_min_score" label="Feature Minimum Score" help="Feature score threshold for a feature to be reported. The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." value="0.7" type="float" /> + <param name="reported_mz" label="Reported m/z" help="The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." type="select"> + <option value="monoisotopic">monoisotopic</option> + <option value="average">average</option> + <option value="maximum">maximum</option> + </param> + <param name="charge_low" label="Minimum Charge" type="integer" value="1" /> + <param name="charge_high" label="Maximum Charge" type="integer" value="4" /> + <param name="isotopic_mz_tolerance" label="m/z Tolerance (Isotopic Pattern)" type="float" value="0.03" help="Tolerated m/z deviation from the theoretical isotopic pattern. It should be larger than the m/z resolution of the instument. This value must be smaller than that 1/charge_high!" /> + <conditional name="advanced_isotopic_pattern"> + <param type="boolean" name="specify" label="Specify Advanced Isotopic Pattern Parameters" /> + <when value="true"> + <param name="abundance_12C" label="12C Abundance" type="float" value="98.93" help="Rel. abundance of the light carbon. Modify if labeled." /> + <param name="abundance_14N" label="14N Abundance" type="float" value="99.632" help="Rel. abundance of the light nitrogen. Modify if labeled." /> + </when> + <when value="false"> + </when> + </conditional> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +The mapping is based on retention times and mass-to-charge values. Roughly, a peptide identification is assigned to a (consensus) feature if its position lies within the boundaries of the feature or close enough to the feature centroid. Peptide identifications that don't match anywhere are still recorded in the resulting map, as "unassigned peptides". Protein identifications are annotated to the whole map, i.e. not to any particular (consensus) feature. + +In all cases, tolerance in RT and m/z dimension is applied according to the parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value. + +If several features or consensus features overlap the position of a peptide identification (taking the allowed tolerances into account), the identification is annotated to all of them. + +Annotation of feature maps (featureXML input): +If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls (of individual mass traces, if available) by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if feature:use_centroid_rt or feature:use_centroid_mz are true. + +Annotation of consensus maps (consensusXML input): +Peptide positions are always matched against centroid positions. By default, the consensus centroids are used. However, if consensusfeature:use_subelements is set, the centroids of sub-features are considered instead. In this case, a peptide identification is mapped to a consensus feature if any of its sub-features matches. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_finder_isotope_wavelet.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,41 @@ +<tool id="openms_feature_finder_isotope_wavelet" version="0.1.0" name="Feature Finder (Isotope Wavelet)"> + <description> + The feature detection application for quantitation. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureFinderIsotopeWavelet' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +</configfile> + </configfiles> + <inputs> + <param name="input1" label="mzML Input" type="data" format="mzml" /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide. + +The algorithm identifies pronounced regions of the data around so-called seeds. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions. + +Note: +that the wavelet transform is very slow on high-resolution spectra (i.e. FT, Orbitrap). We recommend to use a noise or intensity filter to remove spurious points first and to speed-up the feature detection process. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_finder_metabo.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,36 @@ +<tool id="openms_feature_finder_metabo" version="0.1.0" name="Feature Finder (Metabolites)"> + <description> + Assembles metabolite features from singleton mass traces. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureFinderMetabo' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +</configfile> + </configfiles> + <inputs> + <param name="input1" label="mzML Input" type="data" format="mzml" /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +Mass traces alone would allow for further analyzes such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied with satellite C13 peaks and thus may render the analysis more difficult. FeatureFinderMetabo fulfills a further data reduction step by assembling compatible mass traces to metabolite features (that is, mass traces all stemming from one metabolite). To this end, multiple metabolite hypotheses are formulated and scored according to how well differences in RT and m/z or intensity ratios match to those of theoretical isotope patterns. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_finder_mrm.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,36 @@ +<tool id="openms_feature_finder_mrm" version="0.1.0" name="Feature Finder (MRM)"> + <description> + The feature detection application for quantitation. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureFinderMRM' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +</configfile> + </configfiles> + <inputs> + <param name="input1" label="mzML Input" type="data" format="mzml" /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_finder_raw.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,44 @@ +<tool id="openms_feature_finder_raw" version="0.1.0" name="Feature Finder (Raw)"> + <description> + Identifies peptide features in raw (i.e. profile) LC-MS data. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureFinderRaw' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +sample!charge=${min_charge}:${max_charge} +sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide} +algorithm!rt_threshold=$rt_threshold +algorithm!rt_min=$rt_min +algorithm!intensity_cutoff=$intensity_cutoff +algorithm!intensity_correlation=$intensity_correlation +algorithm!model_deviation=$model_deviation +</configfile> + </configfiles> + <inputs> + <param name="input1" label="mzML Input" type="data" format="mzml" /> + <expand macro="raw_feature_finder_params" /> + </inputs> + <outputs> + <data format="featurexml" name="output" /> + </outputs> + <help> +**What it does** + +FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_linker_labeled.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,38 @@ +<tool id="openms_feature_linker_labeled" version="0.1.0" name="Feature Linker (Labeled)"> + <description> + Groups corresponding isotope-labeled features in a feature map. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureLinkedLabeled' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Input Features" type="data" format="featurexml" /> + </inputs> + <outputs> + <data format="consensusxml" name="output" /> + </outputs> + <help> +**What it does** + +This tool provides an algorithm for grouping corresponding features in isotope-labeled experiments. For more details and algorithm-specific parameters (set in the ini file) see "Detailed Description" in the algorithm documentation. + +FeatureLinkerLabeled takes one feature map (featureXML file) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_linker_unlabeled.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,51 @@ +<tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Labeled)"> + <description> + Groups corresponding features from multiple maps. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureLinkedUnlabeled' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +</configfile> + </configfiles> + <inputs> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="featurexml">Features (FeatureXML)</option> + <option value="consensusxml">Consensus (ConsensusXML)</option> + </param> + <when value="featurexml"> + <param format="featurexml" name="input1" type="data" label="Input Features" /> + </when> + <when value="consensusxml"> + <param format="consensusxml" name="input1" type="data" label="Input Consensus" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="consensusxml" name="output" /> + </outputs> + <help> +**What it does** + +This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation or the INI file table below. + +FeatureLinkerUnlabeled takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools. + +Advanced users can convert the consensusXML generated by this tool to EDTA using FileConverter and plot the distribution of distances in RT (or m/z) between different input files (can be done in Excel). The distribution should be Gaussian-like with very few points beyond the tails. Points far away from the Gaussian indicate a too wide tolerance. A Gaussian with its left/right tail trimmed indicates a too narrow tolerance. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/file_info.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/file_info.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Shows basic information about the file, such as data ranges and file type. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'FileInfo' --config $config </command>
--- a/high_res_precursosr_mass_corrector.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/high_res_precursosr_mass_corrector.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> precursor m/z correction on picked (centroided) high resolution data. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <configfiles> <configfile name="config">[simple_options] in=${input}
--- a/id_file_converter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/id_file_converter.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Converts identification engine file formats. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'IDFileConverter' --config $config </command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/id_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,48 @@ +<tool id="openms_id_filter" version="0.1.0" name="ID Filter"> + <description> + Filters protein identification engine results by different criteria. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'IDFilter' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +score!pep=$peptide_score +score!prot=$protein_score +thresh!pep=$peptide_threshold +thresh!prot=$protein_threshold +best!n_peptide_hits=$n_peptide_hits +best!n_protein_hits=$n_protein_hits +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Input" type="data" format="idxml" /> + <param name="n_peptide_hits" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). " value="0" type="integer" /> + <param name="n_protein_hits" label="Keep only the 'n' highest scoring protein hits per spectrum (for n>0). " value="0" type="integer" /> + <param name="peptide_score" label="Peptide Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" /> + <param name="protein_score" label="Protein Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" /> + <param name="peptide_threshold" label="Peptide Threshold" help="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" /> + <param name="protein_threshold" label="Protein Threshold" help="Keep a protein hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" /> + </inputs> + <outputs> + <data format="idxml" name="output" /> + </outputs> + <help> +**What it does** + +This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/id_mapper.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,90 @@ +<tool id="openms_id_mapper" version="0.1.0" name="ID Mapper"> + <description> + Assigns protein/peptide identifications to features or consensus features. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'IDMapper' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +id=$id_input +in=$type.map_input +#set $input_type = str($type.input_type) +#if $input_type == "consensusxml" +consensusfeature!use_subelements=$type.use_subelements +#end if +#if $input_type == "featurexml" +feature!use_centroid_rt=$type.use_centroid_rt +feature!use_centroid_mz=$type.use_centroid_mz +#end if +out=$map_output +rt_tolerance=$rt_tolerance +mz_tolerance=$mz_tolerance +mz_measure=$mz_measure +mz_reference=$mz_reference +ignore_charge=$ignore_charge +</configfile> + </configfiles> + <inputs> + <param name="id_input" label="Protein/Peptide Identifications Input" type="data" format="idxml" /> + <conditional name="type"> + <param name="input_type" type="select" label="Map Input Type"> + <option value="consensusxml">Consensus</option> + <option value="featurexml">Feature</option> + </param> + <when value="consensusxml"> + <param format="consensusxml" name="map_input" type="data" label="Input Consensus File"/> + <param name="use_subelements" label="Use Sub-features" help="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." truevalue="true" falsevalue="false" type="boolean" /> + </when> + <when value="featurexml"> + <param format="featurexml" name="map_input" type="data" label="Input Feature File"/> + <param name="use_centroid_rt" label="Use Centroid RT" help="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." truevalue="true" falsevalue="false" type="boolean" /> + <param name="use_centroid_mz" label="Use Centroid m/z" help="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces. (If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" truevalue="true" falsevalue="false" type="boolean" /> + </when> + </conditional> + <param name="rt_tolerance" value="5" label="RT Tolerance (seconds)" type="float" /> + <param name="mz_tolerance" value="20" label="m/z Tolerance" type="float" /> + <param name="mz_measure" label="m/z Tolerance Units" type="select"> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param name="mz_reference" label="m/z Reference" type="select" help="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> + <option value="precursor">precursor</option> + <option value="peptide">peptide</option> + </param> + <param name="ignore_charge" label="Ignore Charge" help="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." truevalue="true" falsevalue="false" type="boolean" /> + </inputs> + <outputs> + <data format="consensusxml" name="map_output"> + <change_format> + <when input="input_type" value="featurexml" format="featurexml" /> + </change_format> + </data> + </outputs> + <help> +**What it does** + +The mapping is based on retention times and mass-to-charge values. Roughly, a peptide identification is assigned to a (consensus) feature if its position lies within the boundaries of the feature or close enough to the feature centroid. Peptide identifications that don't match anywhere are still recorded in the resulting map, as "unassigned peptides". Protein identifications are annotated to the whole map, i.e. not to any particular (consensus) feature. + +In all cases, tolerance in RT and m/z dimension is applied according to the parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value. + +If several features or consensus features overlap the position of a peptide identification (taking the allowed tolerances into account), the identification is annotated to all of them. + +Annotation of feature maps (featureXML input): +If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls (of individual mass traces, if available) by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if feature:use_centroid_rt or feature:use_centroid_mz are true. + +Annotation of consensus maps (consensusXML input): +Peptide positions are always matched against centroid positions. By default, the consensus centroids are used. However, if consensusfeature:use_subelements is set, the centroids of sub-features are considered instead. In this case, a peptide identification is mapped to a consensus feature if any of its sub-features matches. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/id_merger.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/id_merger.xml Fri May 10 17:31:05 2013 -0400 @@ -2,27 +2,23 @@ <description> Merges several idXML files into one idXML file. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'IDMerger' --config $config </command> <configfiles> <configfile name="config">[simple_options] -#set $in_str = "" -#for $input in $inputs -#set $in_str = $input.input + " " $in_str -#end for -in="${in_str}" +in=${",".join(map(str, $inputs))} out=${out} annotate_file_origin=${annotate_file_origin} </configfile> </configfiles> <inputs> - <repeat name="inputs"> - <param format="idxml" name="input" type="data" label="idXML Input"/> - </repeat> + <param format="idxml" name="inputs" type="data" label="idXML Inputs" multiple="true" /> <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." /> </inputs> <outputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/id_posterior_error_probability.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,45 @@ +<tool id="openms_id_posterior_error_probability" version="0.1.0" name="ID Posterior Error Probability"> + <description> + Tool to estimate the probability of peptide hits to be incorrectly assigned. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'IDPosteriorErrorProbability' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${input1} +out=${out} +split_charge=${split_charge} +top_hits_only=${top_hits_only} +</configfile> + </configfiles> + <inputs> + <param format="idxml" name="input1" type="data" label="idXML Input" /> + <param name="split_charge" type="boolean" label="Split Charge" help="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." checked="false" truevalue="true" falsevalue="false" /> + <param name="top_hits_only" type="boolean" label="Use Only Top Hits" help="If set only the top hits of every PeptideIdentification will be used" checked="false" truevalue="true" falsevalue="false" /> + <!-- TODO: Advanced Options --> + </inputs> + <outputs> + <data format="idxml" name="out" /> + </outputs> + <help> +**What it does** + +By default an estimation is performed using the (inverse) Gumbel distribution for incorrectly assigned sequences and a Gaussian distribution for correctly assigned sequences. The probabilities are calculated by using Bayes' law, similar to PeptideProphet. Alternatively, a second Gaussian distribution can be used for incorrectly assigned sequences. At the moment, IDPosteriorErrorProbability is able to handle X!Tandem, Mascot, MyriMatch and OMSSA scores. + +No target/decoy information needs to be provided, since the model fits are done on the mixed distribution. + +In order to validate the computed probabilities one can adjust the fit_algorithm subsection. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/idxml_exporter.py Wed Dec 19 00:33:53 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -from xml.sax import make_parser, ContentHandler -from optparse import OptionParser - - -def main(): - (options, _) = _parse_args() - with open(options.output, "w") as out: - parser = make_parser() - handler = _get_handler(options, out) - parser.setContentHandler(handler) - parser.parse(open(options.input, "r")) - - -def _get_handler(option, out): - return PeptideHandler(out) - - -class PeptideHandler(ContentHandler): - record_values = { - "IdentificationRun": ["search_engine"], - "PeptideIdentification": ["score_type", "significance_threshold", "MZ", "RT"], - "PeptideHit": ["score", "sequence", "charge"], - } - - def __init__(self, output): - self.output = output - - def __record_values(self, keys, attrs): - for key in keys: - setattr(self, key, attrs.get(key, None)) - - def startElement(self, name, attrs): - self._set_attributes(name, attrs) - - def endElement(self, name): - if name == "PeptideHit": - self._write_peptide() - # reset values for element - self._set_attributes(name, {}) - - def _write_peptide(self): - col_keys = ["score", "peptide", "score_type", "charge", "MZ", "RT"] - row_values = self._get_values(col_keys) - row = "\t".join(row_values) - self._write_line(row) - - def _write_line(self, line): - self.output.write(line) - self.output.write("\n") - - def _get_values(self, keys): - return [getattr(self, key, "") for key in keys] - - def _set_attributes(self, name, attrs): - for element_name, element_attributes in self.record_values.iteritems(): - if name == element_name: - self.__record_values(element_attributes, attrs) - - -def _parse_args(): - parser = OptionParser() - parser.add_option("--input", dest="input") - parser.add_option("--output", dest="output") - parser.add_option("--type", dest="type", choices=["peptide"]) - return parser.parse_args() - -if __name__ == "__main__": - main()
--- a/idxml_to_peptides.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/idxml_to_peptides.xml Fri May 10 17:31:05 2013 -0400 @@ -1,11 +1,13 @@ <tool id="openms_idxml_to_peptides" version="0.1.0" name="Export peptide report from idXML "> <description> </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> - idxml_exporter.py --type peptide --in ${in} --out ${out} + openms_exporter.py --type peptide --in ${in} --out ${out} </command> <inputs> <param format="idxml" name="in" type="data" label="Input Identification File"/>
--- a/idxml_to_tabular.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/idxml_to_tabular.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Converts identification engine file formats. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'TextExporter' --config $config </command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isobaric_analyzer.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,112 @@ +<tool id="isobaric_analyzer" version="0.1.0" name="SILACAnalyzer"> + <description> + Extracts and normalizes iTRAQ/TMT information from an MS experiment. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + #set $label_type = str($type.label_type) + #if $label_type == "tmt-6plex" + #set $program = "TMTAnalyzer" + #else + #set $program = "ITRAQAnalyzer" + #end if + openms_wrapper.py + --executable '$program' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$out +Extraction!reporter_mass_shift=$reporter_mass_shift +Extraction!select_activation=$select_activation +Quantification!isotope_correction=$isotope_correction +Quantification!do_normalization=$do_normalization +Quantification!channel_reference=$type.channel_reference +</configfile> + </configfiles> + <inputs> + <param name="input1" type="data" format="mzml" label="Input peak list" /> + <conditional name="type"> + <param name="label_type" type="select" label="Labels"> + <option value="4plex">iTRAQ 4-Plex</option> + <option value="8plex">iTRAQ 8-Plex</option> + <option value="tmt-6plex">TMT 6-plex</option> + </param> + <when value="4plex"> + <param name="channel_reference" type="select" label="Reference Channel"> + <option value="114">114</option> + <option value="115">115</option> + <option value="116">116</option> + <option value="117">117</option> + </param> + </when> + <when value="8plex"> + <param name="channel_reference" type="select" label="Reference Channel"> + <option value="113">113</option> + <option value="114">114</option> + <option value="115">115</option> + <option value="116">116</option> + <option value="117">117</option> + <option value="118">118</option> + <option value="119">119</option> + <option value="121">121</option> + </param> + </when> + <when value="tmt-6plex"> + <param name="channel_reference" type="select" label="Reference Channel"> + <option value="126">126</option> + <option value="127">127</option> + <option value="128">128</option> + <option value="129">129</option> + <option value="130">130</option> + <option value="131">131</option> + </param> + </when> + </conditional> + <param name="select_activation" type="select" label="Select Activation" help="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering."> + <option value="">(Leave empty,use all MSn.)</option> + <option value="Collision-induced dissociation">Collision-induced dissociation</option> + <option value="Post-source decay">Post-source decay</option> + <option value="Plasma desorption">Plasma desorption</option> + <option value="Surface-induced dissociation">Surface-induced dissociation</option> + <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> + <option value="Electron capture dissociation">Electron capture dissociation</option> + <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> + <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> + <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option> + <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> + <option value="Photodissociation">Photodissociation</option> + <option value="Electron transfer dissociation">Electron transfer dissociation</option> + </param> + <param name="reporter_mass_shift" label="Reporter Mass Shift" value="0.1" type="float" /> + <param name="isotope_correction" type="boolean" label="Isotope Correctoin" help="" truevalue="true" falsevalue="false" /> + <param name="do_normalization" type="boolean" label="Normalize" help="" truevalue="true" falsevalue="false" /> + </inputs> + <outputs> + <data format="consensusxml" name="out" /> + </outputs> + <help> +**What it does** + +Extract the iTRAQ reporter ion intensities (4plex or 8plex) from raw MS2 data, does isotope corrections and stores the resulting quantitation as consensusXML, where each consensus centroid corresponds to one iTRAQ MS2 scan (e.g., HCD). The position of the centroid is the precursor position, its sub-elements are the channels (thus having m/z's of 113-121). + +Isotope correction is done using non-negative least squares (NNLS), i.e., + +Minimize ||Ax - b||, subject to x >= 0, where b is the vector of observed reporter intensities (with 'contaminating' isotope species), A is a correction matrix (as supplied by the manufacturer AB Sciex) and x is the desired vector of corrected (real) reporter intensities. Other software solves this problem using an inverse matrix multiplication, but this can yield entries in x which are negative. In a real sample, this solution cannot possibly be true, so usually negative values (= negative reporter intensities) are set to 0. However, a negative result usually means, that noise was not accounted for thus we use NNLS to get a non-negative solution, without the need to truncate negative values. In (the usual) case that inverse matrix multiplication yields only positive values, our NNLS will give the exact same optimal solution. + +The correction matrices can be found (and changed) in the INI file. However, these matrices for both 4plex and 8plex are now stable, and every kit delivered should have the same isotope correction values. Thus, there should be no need to change them, but feel free to compare the values in the INI file with your kit's Certificate. + +After this quantitation step, you might want to annotate the consensus elements with the respective identifications, obtained from an identification pipeline. Note that quantification is solely on peptide level at this stage. In order to obtain protein quantifications, you can try TextExporter to obtain a simple text format which you can feed to other software tools (e.g., R), or you can try ProteinQuantifier. + + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,83 @@ +<macros> + <macro name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error running OpenMS tool." /> + </stdio> + </macro> + <macro name="requires"> + <requirements> + <requirement type="package">openms</requirement> + <yield /> + </requirements> + </macro> + <macro name="sampling_rate_param"> + <param name="sampling_rate_param" label="Sampling Rate" help="New sampling rate in m/z dimension." value="0.1" type="float" /> + </macro> + <macro name="id_inputs"> + <param name="input1" label="Input Peak List (mzML)" type="data" format="mzml" /> + <param name="database" label="Database" type="data" format="fasta" /> + </macro> + <macro name="id_outputs"> + <outputs> + <data format="idxml" name="out" /> + </outputs> + </macro> + <macro name="precursor_mass_tolerance_param"> + <param name="precursor_mass_tolerance" label="Precursor Mass Tolerance" value="1.5" type="float" /> + </macro> + <macro name="precursor_mass_tolerance_unit_param"> + <param name="precursor_mass_tolerance_unit" label="Precursor Mass Tolerance Units" type="select"> + <option value="Da" selected="true">Daltons</option> + <option value="ppm">ppm</option> + </param> + </macro> + <macro name="fragment_mass_tolerance_param"> + <param name="fragment_mass_tolerance" label="Fragment Mass Tolerance" value="0.3" type="float" /> + </macro> + <macro name="fragment_mass_tolerance_unit_param"> + <param name="fragment_mass_tolerance_unit" label="Fragment Mass Tolerance Units" type="select"> + <option value="Da" selected="true">Daltons</option> + <option value="ppm">ppm</option> + </param> + </macro> + <macro name="fixed_modifications_param"> + <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true"> + <options from_file="openms_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </macro> + <macro name="variable_modifications_param"> + <param name="variable_modifications" type="select" label="Variable Modification" multiple="true"> + <options from_file="openms_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </macro> + <macro name="precursor_charge_params"> + <param name="min_precursor_charge" label="Minimum Precursor Charge" value="1" type="integer" /> + <param name="max_precursor_charge" label="Maximum Precursor Charge" value="4" type="integer" /> + </macro> + <macro name="raw_feature_finder_params"> + <param name="rt_threshold" type="float" value="30" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." /> + <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." /> + <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." /> + <param name="intensity_correlation" type="float" value="0.7" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." /> + <param name="model_deviation" type="float" value="3" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." /> + <param name="min_charge" type="integer" value="2" label="Minimum Charge" /> + <param name="max_charge" type="integer" value="4" label="Maximum Charge" /> + <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" /> + <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" /> + </macro> + <macro name="map_input"> + </macro> + <macro name="map_output"> + <data format="consensusxml" name="map_output"> + <change_format> + <when input="input_type" value="featurexml" format="featurexml" /> + </change_format> + </data> + </macro> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/myrimatch_adapter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,86 @@ +<tool id="myrimatch_adapter" version="0.1.0" name="MyriMatch (OpenMS)"> + <description> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires"> + <requirement type="package">myrimatch</requirement> + </expand> + <command interpreter="python"> + openms_wrapper.py + --executable '__SHELL__' --config $setup + --executable 'MyriMatchAdapter' --config $config + </command> + <configfiles> + <configfile name="setup"> + ln -s $input1 'input.mzML'; ln -s $database 'db.fasta' + </configfile> + <configfile name="config">[simple_options] +in=input.mzML +database=db.fasta +out=$out +myrimatch_executable=@WHICH(myrimatch)@ +threads=4 +variable_modifications=${variable_modifications or ''} +fixed_modifications=${fixed_modifications or ''} +precursor_mass_tolerance=$precursor_mass_tolerance +precursor_mass_tolerance_unit=$precursor_mass_tolerance_unit +fragment_mass_tolerance=$fragment_mass_tolerance +fragment_mass_tolerance_unit=$fragment_mass_tolerance_unit +min_precursor_charge=$min_precursor_charge +max_precursor_charge=$max_precursor_charge +MaxDynamicMods=$max_dynamic_mods +TicCutoffPercentage=$tic_cutoff_percentage +NumChargeStates=$num_charge_states +CleavageRules=$cleavage_rules +MinTerminiCleavages=$min_termini_cleavages +MaxMissedCleavages=$max_missed_cleavages +</configfile> + </configfiles> + <inputs> + <expand macro="id_inputs" /> + <expand macro="fixed_modifications_param" /> + <expand macro="variable_modifications_param" /> + <expand macro="precursor_mass_tolerance_param" /> + <expand macro="precursor_mass_tolerance_unit_param" /> + <!-- TODO: precursor_mass_tolerance_avg --> + <expand macro="fragment_mass_tolerance_param" /> + <expand macro="fragment_mass_tolerance_unit_param" /> + <expand macro="precursor_charge_params" /> + <param name="max_dynamic_mods" label="Maximum Number of Dynamic Modifications" help="This parameter sets the maximum number of modified residues that may be in any candidate sequence." type="integer" value="2" /> + <param name="cleavage_rules" label="Cleavage Rules" type="select"> + <option selected="true" value="Trypsin">Trypsin</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="PepsinA">PepsinA</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="NoEnzyme">NoEnzyme</option> + </param> + <param name="min_termini_cleavages" type="select" label="Minimum Number of Termini Cleavages" help=" By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest."> + <option value="0">0</option> + <option value="1">1</option> + <option value="2" type="selected">2</option> + </param> + <param name="max_missed_cleavages" type="integer" value="-1" label="Maximum Number of Missed Cleavages" help="By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages. A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages." /> + <param name="tic_cutoff_percentage" label="Total Ion Current Cutoff Percentage" help="Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter." type="float" value="0.98" /> + <param name="num_charge_states" label="Number of Charge States" help="The number of charge states that MyriMatch will handle during all stages of the program." type="integer" value="3" /> + </inputs> + <expand macro="id_outputs" /> + <help> +**What it does** + + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/noise_filter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/noise_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Utilize a filter to reduce the noise in an MS experiment. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> #if $filter.type == "gaussian" #set $filter_exec = "NoiseFilterGaussian"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omssa_adapter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,92 @@ +<tool id="omssa_adapter" version="0.1.0" name="OMSSA (OpenMS)"> + <description> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires"> + <requirement type="package">omssa</requirement> + <!--<requirement type="package">blast</requirement> --> + </expand> + <command interpreter="python"> + openms_wrapper.py + --executable '__SHELL__' --config $setup + --executable 'OMSSAAdapter' --config $config + </command> + <configfiles> + <configfile name="setup"> + ln -s $database db.fasta; makeblastdb -dbtype prot -parse_seqids -in 'db.fasta' + </configfile> + <configfile name="config">[simple_options] +in=$input1 +out=$out +database=db.fasta.psq +omssa_executable=@WHICH(omssacl)@ +variable_modifications=${variable_modifications or ''} +fixed_modifications=${fixed_modifications or ''} +precursor_mass_tolerance=$precursor_mass_tolerance +#if $precursor_mass_tolerance_unit == "ppm" +precursor_mass_tolerance_unit_ppm=true +#end if +fragment_mass_tolerance=$fragment_mass_tolerance +min_precursor_charge=$min_precursor_charge +max_precursor_charge=$max_precursor_charge +v=$v +e=$e +hl=$hl +he=$he +threads=4 +</configfile> + </configfiles> + <inputs> + <expand macro="id_inputs" /> + <expand macro="fixed_modifications_param" /> + <expand macro="variable_modifications_param" /> + <expand macro="precursor_mass_tolerance_param" /> + <expand macro="precursor_mass_tolerance_unit_param" /> + <expand macro="fragment_mass_tolerance_param" /> + <expand macro="precursor_charge_params" /> + <param name="v" label="Maximum Number of Missed Cleavages" value="1" type="integer" /> + <param name="e" label="Enzyme" type="select"> + <option value="0" selected="true">Trypsin</option> + <option value="1">Arg-C</option> + <option value="2">CNBr</option> + <option value="3">Chymotrypsin (FYWL)</option> + <option value="4">Formic Acid</option> + <option value="5">Lys-C</option> + <option value="6">Lys-C, no P rule</option> + <option value="7">Pepsin A</option> + <option value="8">Trypsin+CNBr</option> + <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> + <option value="10">Trypsin, no P rule</option> + <option value="11">Whole protein</option> + <option value="12">Asp-N</option> + <option value="13">Glu-C</option> + <option value="14">Asp-N+Glu-C</option> + <option value="15">Top-Down</option> + <option value="16">Semi-Tryptic</option> + <option value="17">No Enzyme</option> + <option value="18">Chymotrypsin, no P rule (FYWL)</option> + <option value="19">Asp-N (DE)</option> + <option value="20">Glu-C (DE)</option> + <option value="21">Lys-N (K)</option> + <option value="22">Thermolysin, no P rule</option> + <option value="23">Semi-Chymotrypsin (FYWL)</option> + <option value="24">Semi-Glu-C</option> + </param> + <param name="hl" label="Maximum Hits Per Spectrum" type="integer" value="30" /> + <param name="he" label="Maximum Hits Per Spectrum" type="float" value="1000" help="The maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported. " /> + </inputs> + <expand macro="id_outputs" /> + <help> +**What it does** + + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/openms_exporter.py Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,104 @@ +from xml.sax import make_parser, ContentHandler +from optparse import OptionParser + + +def main(): + (options, _) = _parse_args() + with open(options.output, "w") as out: + parser = make_parser() + handler = _get_handler(options)(out) + parser.setContentHandler(handler) + parser.parse(open(options.input, "r")) + + +def _get_handler(options): + return handlers[options.type] + + +class OpenMsContentHandler(ContentHandler): + + def __record_values(self, keys, attrs): + for key in keys: + setattr(self, key, attrs.get(key, None)) + + def _get_values(self, keys): + return [getattr(self, key, "") for key in keys] + + def _set_attributes(self, name, attrs): + for element_name, element_attributes in self.record_values.iteritems(): + if name == element_name: + self.__record_values(element_attributes, attrs) + + def _write_line(self, line): + self.output.write(line) + self.output.write("\n") + + def startElement(self, name, attrs): + self._set_attributes(name, attrs) + + def _handleElement(self, name): + pass + + def endElement(self, name): + self._handleElement(name) + self._set_attributes(name, {}) + + def _write_row(self, col_keys): + row_values = self._get_values(col_keys) + row = "\t".join(row_values) + self._write_line(row) + + +class FeatureHullHandler(OpenMsContentHandler): + record_values = { + "feature": ["id"], + "convexhull": ["nr"], + "pt": ["x", "y"] + } + + def __init__(self, output): + self.output = output + + def _handleElement(self, name): + if name == "pt": + self._write_point() + + def _write_point(self): + col_keys = ["id", "nr", "x", "y"] + self._write_row(col_keys) + + +class PeptideHandler(OpenMsContentHandler): + record_values = { + "IdentificationRun": ["search_engine"], + "PeptideIdentification": ["score_type", "significance_threshold", "MZ", "RT"], + "PeptideHit": ["score", "sequence", "charge"], + } + + def __init__(self, output): + self.output = output + + def _handleElement(self, name): + if name == "PeptideHit": + self._write_peptide() + + def _write_peptide(self): + col_keys = ["score", "sequence", "score_type", "charge", "MZ", "RT"] + self._write_row(col_keys) + + +handlers = { + "peptide": PeptideHandler, + "feature_hull": FeatureHullHandler, +} + + +def _parse_args(): + parser = OptionParser() + parser.add_option("--input", dest="input") + parser.add_option("--output", dest="output") + parser.add_option("--type", dest="type", choices=["peptide", "feature_hull"]) + return parser.parse_args() + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/openms_mods.loc Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,928 @@ +15dB-biotin (C) +2HPG (R) +3sulfo (N-term) +4-ONE (C) +4-ONE (H) +4-ONE (K) +4-ONE+Delta:H(-2)O(-1) (C) +4-ONE+Delta:H(-2)O(-1) (H) +4-ONE+Delta:H(-2)O(-1) (K) +a-type-ion (C-term) +AccQTag (K) +AccQTag (N-term) +Acetyl (C) +Acetyl (H) +Acetyl (K) +Acetyl (N-term) +Acetyl (N-term) +Acetyl (S) +Acetyl (T) +Acetyl (Y) +Acetyl:2H(3) (K) +Acetyl:2H(3) (N-term) +ADP-Ribosyl (C) +ADP-Ribosyl (E) +ADP-Ribosyl (N) +ADP-Ribosyl (R) +ADP-Ribosyl (S) +AEBS (H) +AEBS (K) +AEBS (N-term) +AEBS (S) +AEBS (Y) +AEC-MAEC (S) +AEC-MAEC (T) +AEC-MAEC:2H(4) (S) +AEC-MAEC:2H(4) (T) +Ala->Asp (A) +Ala->Glu (A) +Ala->Gly (A) +Ala->Pro (A) +Ala->Ser (A) +Ala->Thr (A) +Ala->Val (A) +Amidated (C-term) +Amidated (C-term) +Amidine (K) +Amidine (N-term) +Amidino (C) +Amino (Y) +Ammonia-loss (C) +Ammonia-loss (N) +Ammonia-loss (S) +Ammonia-loss (T) +Archaeol (C) +Arg->Cys (R) +Arg->Gln (R) +Arg->GluSA (R) +Arg->Gly (R) +Arg->His (R) +Arg->Ile (R) +Arg->Lys (R) +Arg->Met (R) +Arg->Npo (R) +Arg->Orn (R) +Arg->Pro (R) +Arg->Ser (R) +Arg->Thr (R) +Arg->Trp (R) +Arg2PG (R) +Argbiotinhydrazide (R) +Asn->Asp (N) +Asn->His (N) +Asn->Ile (N) +Asn->Lys (N) +Asn->Ser (N) +Asn->Thr (N) +Asn->Tyr (N) +Asp->Ala (D) +Asp->Asn (D) +Asp->Glu (D) +Asp->Gly (D) +Asp->His (D) +Asp->Tyr (D) +Asp->Val (D) +BADGE (C) +BDMAPP (H) +BDMAPP (K) +BDMAPP (N-term) +BDMAPP (W) +BDMAPP (Y) +Benzoyl (K) +Benzoyl (N-term) +BHT (C) +BHT (H) +BHT (K) +BHTOH (C) +BHTOH (H) +BHTOH (K) +Biotin (K) +Biotin (N-term) +Biotin-HPDP (C) +Biotin-PEO-Amine (C-term) +Biotin-PEO-Amine (D) +Biotin-PEO-Amine (E) +Biotin-PEO4-hydrazide (C-term) +Biotin-phenacyl (C) +Biotin-phenacyl (H) +Biotin-phenacyl (S) +BisANS (K) +BMOE (C) +Bodipy (C) +Bromo (F) +Bromo (H) +Bromo (W) +Bromobimane (C) +C8-QAT (K) +C8-QAT (N-term) +CAF (N-term) +CAMthiopropanoyl (K) +CAMthiopropanoyl (N-term) +Can-FP-biotin (S) +Can-FP-biotin (T) +Can-FP-biotin (Y) +Carbamidomethyl (C) +Carbamidomethyl (D) +Carbamidomethyl (E) +Carbamidomethyl (H) +Carbamidomethyl (K) +Carbamidomethyl (N-term) +Carbamyl (C) +Carbamyl (K) +Carbamyl (M) +Carbamyl (N-term) +Carbamyl (R) +Carboxy (D) +Carboxy (E) +Carboxy (K) +Carboxy (M) +Carboxy (W) +Carboxy->Thiocarboxy (G) +Carboxyethyl (K) +Carboxymethyl (C) +Carboxymethyl (K) +Carboxymethyl (N-term) +Carboxymethyl (W) +Carboxymethyl:13C(2) (C) +Cation:Cu[I] (C-term) +Cation:Cu[I] (D) +Cation:Cu[I] (E) +Cation:K (C-term) +Cation:K (D) +Cation:K (E) +Cation:Na (C-term) +Cation:Na (D) +Cation:Na (E) +cGMP (C) +cGMP+RMP-loss (C) +CHDH (D) +Cholesterol (C-term) +CLIP_TRAQ_1 (K) +CLIP_TRAQ_1 (N-term) +CLIP_TRAQ_1 (Y) +CLIP_TRAQ_2 (K) +CLIP_TRAQ_2 (N-term) +CLIP_TRAQ_2 (Y) +CLIP_TRAQ_3 (K) +CLIP_TRAQ_3 (N-term) +CLIP_TRAQ_3 (Y) +CLIP_TRAQ_4 (K) +CLIP_TRAQ_4 (N-term) +CLIP_TRAQ_4 (Y) +CoenzymeA (C) +Crotonaldehyde (C) +Crotonaldehyde (H) +Crotonaldehyde (K) +CuSMo (C) +Cy3b-maleimide (C) +Cyano (C) +CyDye-Cy3 (C) +CyDye-Cy5 (C) +Cys->Arg (C) +Cys->Dha (C) +Cys->Gly (C) +Cys->Oxoalanine (C) +Cys->Phe (C) +Cys->PyruvicAcid (C) +Cys->Ser (C) +Cys->Trp (C) +Cys->Tyr (C) +Cysteinyl (C) +Cytopiloyne (C) +Cytopiloyne (K) +Cytopiloyne (N-term) +Cytopiloyne (P) +Cytopiloyne (R) +Cytopiloyne (S) +Cytopiloyne (Y) +Cytopiloyne+water (C) +Cytopiloyne+water (K) +Cytopiloyne+water (N-term) +Cytopiloyne+water (R) +Cytopiloyne+water (S) +Cytopiloyne+water (T) +Cytopiloyne+water (Y) +DAET (S) +DAET (T) +Dansyl (K) +Dansyl (N-term) +Deamidated (F) +Deamidated (N) +Deamidated (Q) +Deamidated (R) +Deamidated:18O(1) (N) +Deamidated:18O(1) (Q) +Decanoyl (S) +Decanoyl (T) +Dehydrated (C) +Dehydrated (D) +Dehydrated (N) +Dehydrated (Q) +Dehydrated (S) +Dehydrated (T) +Dehydrated (Y) +Dehydro (C) +Delta:H(1)O(-1)18O(1) (N) +Delta:H(2)C(2) (H) +Delta:H(2)C(2) (K) +Delta:H(2)C(3) (K) +Delta:H(2)C(3)O(1) (K) +Delta:H(2)C(3)O(1) (R) +Delta:H(2)C(5) (K) +Delta:H(4)C(2) (H) +Delta:H(4)C(2) (K) +Delta:H(4)C(2)O(-1)S(1) (S) +Delta:H(4)C(3) (H) +Delta:H(4)C(3) (K) +Delta:H(4)C(3)O(1) (C) +Delta:H(4)C(3)O(1) (H) +Delta:H(4)C(3)O(1) (K) +Delta:H(4)C(6) (K) +Delta:H(5)C(2) (P) +Delta:H(6)C(6)O(1) (K) +Delta:H(8)C(6)O(2) (K) +Delta:Hg(1) (C) +Delta:S(-1)Se(1) (C) +Delta:S(-1)Se(1) (M) +Delta:Se(1) (C) +Deoxy (D) +Deoxy (S) +Deoxy (T) +DeStreak (C) +Dethiomethyl (M) +DFDNB (K) +DFDNB (N) +DFDNB (Q) +DFDNB (R) +dHex (S) +dHex (T) +dHex(1)Hex(3)HexNAc(4) (N) +dHex(1)Hex(4)HexNAc(4) (N) +dHex(1)Hex(5)HexNAc(4) (N) +DHP (C) +Diacylglycerol (C) +Dibromo (Y) +Didehydro (K) +Didehydro (S) +Didehydro (T) +Didehydro (Y) +Didehydroretinylidene (K) +Diethyl (K) +Diethyl (N-term) +Dihydroxyimidazolidine (R) +Diiodo (Y) +Diironsubcluster (C) +Diisopropylphosphate (S) +Diisopropylphosphate (T) +Diisopropylphosphate (Y) +Dimethyl (K) +Dimethyl (N) +Dimethyl (N-term) +Dimethyl (P) +Dimethyl (R) +Dimethyl:2H(4) (K) +Dimethyl:2H(4) (N-term) +Dimethyl:2H(4) (N-term) +Dimethyl:2H(4)13C(2) (K) +Dimethyl:2H(4)13C(2) (N-term) +Dimethyl:2H(6)13C(2) (R) +DimethylpyrroleAdduct (K) +Dioxidation (C) +Dioxidation (F) +Dioxidation (K) +Dioxidation (M) +Dioxidation (P) +Dioxidation (R) +Dioxidation (W) +Dioxidation (Y) +Diphthamide (H) +Dipyrrolylmethanemethyl (C) +dNIC (N-term) +DTBP (K) +DTBP (N) +DTBP (N-term) +DTBP (Q) +DTBP (R) +DTT_C (C) +DTT_C:2H(6) (C) +DTT_ST (S) +DTT_ST (T) +DTT_ST:2H(6) (S) +DTT_ST:2H(6) (T) +EDT-iodoacetyl-PEO-biotin (S) +EDT-iodoacetyl-PEO-biotin (T) +EDT-maleimide-PEO-biotin (S) +EDT-maleimide-PEO-biotin (T) +EQAT (C) +EQAT:2H(5) (C) +EQIGG (K) +ESP (K) +ESP (N-term) +ESP:2H(10) (K) +ESP:2H(10) (N-term) +Ethanedithiol (S) +Ethanedithiol (T) +Ethanolamine (C-term) +Ethanolamine (D) +Ethanolamine (E) +Ethanolyl (C) +Ethyl (E) +Ethyl (K) +Ethyl (N-term) +Ethyl (N-term) +ExacTagAmine (K) +ExacTagThiol (C) +FAD (C) +FAD (H) +FAD (Y) +Farnesyl (C) +Fluorescein (C) +Fluoro (F) +Fluoro (W) +Fluoro (Y) +FMN (S) +FMN (T) +FMNC (C) +FMNH (C) +FMNH (H) +FNEM (C) +Formyl (K) +Formyl (N-term) +Formyl (N-term) +Formyl (S) +Formyl (T) +FormylMet (N-term) +FP-Biotin (S) +FP-Biotin (T) +FP-Biotin (Y) +FTC (C) +FTC (K) +FTC (P) +FTC (R) +FTC (S) +G-H1 (R) +GeranylGeranyl (C) +GIST-Quat (K) +GIST-Quat (N-term) +GIST-Quat:2H(3) (K) +GIST-Quat:2H(3) (N-term) +GIST-Quat:2H(6) (K) +GIST-Quat:2H(6) (N-term) +GIST-Quat:2H(9) (K) +GIST-Quat:2H(9) (N-term) +Gln->Arg (Q) +Gln->Glu (Q) +Gln->His (Q) +Gln->Leu (Q) +Gln->Lys (Q) +Gln->Pro (Q) +Gln->pyro-Glu (Q) +Glu (C-term) +Glu (E) +Glu->Ala (E) +Glu->Asp (E) +Glu->Gln (E) +Glu->Gly (E) +Glu->Lys (E) +Glu->pyro-Glu (E) +Glu->Val (E) +Glucosylgalactosyl (K) +Glucuronyl (N-term) +Glucuronyl (S) +GluGlu (C-term) +GluGlu (E) +GluGluGlu (C-term) +GluGluGlu (E) +GluGluGluGlu (C-term) +GluGluGluGlu (E) +Glutathione (C) +Gly->Ala (G) +Gly->Arg (G) +Gly->Asp (G) +Gly->Cys (G) +Gly->Glu (G) +Gly->Ser (G) +Gly->Trp (G) +Gly->Val (G) +Gly-loss+Amide (G) +Glycerophospho (S) +GlycerylPE (E) +Glycosyl (P) +GlyGly (C) +GlyGly (K) +GlyGly (S) +GlyGly (T) +GPIanchor (C-term) +Guanidinyl (K) +Heme (C) +Heme (H) +Hep (K) +Hep (N) +Hep (Q) +Hep (R) +Hep (S) +Hep (T) +Hex (C) +Hex (K) +Hex (N) +Hex (N-term) +Hex (R) +Hex (T) +Hex (W) +Hex (Y) +Hex(1)HexNAc(1)dHex(1) (N) +Hex(1)HexNAc(1)NeuAc(1) (N) +Hex(1)HexNAc(1)NeuAc(1) (S) +Hex(1)HexNAc(1)NeuAc(1) (T) +Hex(1)HexNAc(1)NeuAc(2) (N) +Hex(1)HexNAc(1)NeuAc(2) (S) +Hex(1)HexNAc(1)NeuAc(2) (T) +Hex(1)HexNAc(2) (N) +Hex(1)HexNAc(2)dHex(1) (N) +Hex(1)HexNAc(2)dHex(1)Pent(1) (N) +Hex(1)HexNAc(2)dHex(2) (N) +Hex(1)HexNAc(2)Pent(1) (N) +Hex(2) (K) +Hex(2) (R) +Hex(2)HexNAc(2) (N) +Hex(2)HexNAc(2)dHex(1) (N) +Hex(2)HexNAc(2)Pent(1) (N) +Hex(3) (N) +Hex(3)HexNAc(1)Pent(1) (N) +Hex(3)HexNAc(2) (N) +Hex(3)HexNAc(2)P(1) (N) +Hex(3)HexNAc(4) (N) +Hex(4)HexNAc(4) (N) +Hex(5)HexNAc(2) (N) +Hex(5)HexNAc(4) (N) +Hex1HexNAc1 (S) +Hex1HexNAc1 (T) +HexN (K) +HexN (N) +HexN (T) +HexN (W) +HexNAc (N) +HexNAc (S) +HexNAc (T) +HexNAc(1)dHex(1) (N) +HexNAc(1)dHex(2) (N) +HexNAc(2) (N) +HexNAc(2)dHex(1) (N) +HexNAc(2)dHex(2) (N) +His->Arg (H) +His->Asn (H) +His->Asp (H) +His->Gln (H) +His->Leu (H) +His->Pro (H) +His->Tyr (H) +HMVK (C) +HNE (C) +HNE (H) +HNE (K) +HNE+Delta:H(2) (C) +HNE+Delta:H(2) (H) +HNE+Delta:H(2) (K) +HNE-Delta:H(2)O (C) +HNE-Delta:H(2)O (H) +HNE-Delta:H(2)O (K) +HPG (R) +Hydroxycinnamyl (C) +Hydroxyfarnesyl (C) +Hydroxyheme (E) +Hydroxymethyl (N) +Hydroxytrimethyl (K) +Hypusine (K) +IBTP (C) +ICAT-C (C) +ICAT-C:13C(9) (C) +ICAT-D (C) +ICAT-D:2H(8) (C) +ICAT-G (C) +ICAT-G:2H(8) (C) +ICAT-H (C) +ICAT-H:13C(6) (C) +ICPL (K) +ICPL (N-term) +ICPL (N-term) +ICPL:13C(6) (K) +ICPL:13C(6) (N-term) +ICPL:13C(6) (N-term) +ICPL:13C(6)2H(4) (K) +ICPL:13C(6)2H(4) (N-term) +ICPL:13C(6)2H(4) (N-term) +ICPL:2H(4) (K) +ICPL:2H(4) (N-term) +ICPL:2H(4) (N-term) +IDEnT (C) +IED-Biotin (C) +IGBP (C) +IGBP:13C(2) (C) +Ile->Arg (I) +Ile->Asn (I) +Ile->Lys (I) +Ile->Met (I) +Ile->Phe (I) +Ile->Ser (I) +Ile->Thr (I) +Ile->Val (I) +IMID (K) +IMID:2H(4) (K) +Iminobiotin (K) +Iminobiotin (N-term) +Iodo (H) +Iodo (Y) +IodoU-AMP (F) +IodoU-AMP (W) +IodoU-AMP (Y) +Isopropylphospho (S) +Isopropylphospho (T) +Isopropylphospho (Y) +iTRAQ4plex (K) +iTRAQ4plex (N-term) +iTRAQ4plex (Y) +iTRAQ4plex114 (K) +iTRAQ4plex114 (N-term) +iTRAQ4plex114 (Y) +iTRAQ4plex115 (K) +iTRAQ4plex115 (N-term) +iTRAQ4plex115 (Y) +iTRAQ8plex (K) +iTRAQ8plex (N-term) +iTRAQ8plex (Y) +iTRAQ8plex:13C(6)15N(2) (K) +iTRAQ8plex:13C(6)15N(2) (N-term) +iTRAQ8plex:13C(6)15N(2) (Y) +Label:13C(1)2H(3) (M) +Label:13C(5) (P) +Label:13C(5)15N(1) (V) +Label:13C(6) (I) +Label:13C(6) (K) +Label:13C(6) (L) +Label:13C(6) (R) +Label:13C(6)+Acetyl (K) +Label:13C(6)+GlyGly (K) +Label:13C(6)15N(1) (I) +Label:13C(6)15N(1) (L) +Label:13C(6)15N(2) (K) +Label:13C(6)15N(2)+Acetyl (K) +Label:13C(6)15N(2)+GlyGly (K) +Label:13C(6)15N(4) (R) +Label:13C(8)15N(2) (R) +Label:13C(9) (F) +Label:13C(9) (Y) +Label:13C(9)+Phospho (Y) +Label:13C(9)15N(1) (F) +Label:18O(1) (C-term) +Label:18O(1) (S) +Label:18O(1) (T) +Label:18O(1) (Y) +Label:18O(2) (C-term) +Label:2H(3) (L) +Label:2H(4) (K) +Label:2H(4)+Acetyl (K) +Label:2H(4)+GlyGly (K) +Label:2H(9)13C(6)15N(2) (K) +lapachenole (C) +Leu->Arg (L) +Leu->Gln (L) +Leu->His (L) +Leu->Met (L) +Leu->Phe (L) +Leu->Pro (L) +Leu->Ser (L) +Leu->Trp (L) +Leu->Val (L) +LeuArgGlyGly (K) +LG-Hlactam-K (K) +LG-Hlactam-K (N-term) +LG-Hlactam-R (R) +LG-lactam-K (K) +LG-lactam-K (N-term) +LG-lactam-R (R) +Lipoyl (K) +Lys->Allysine (K) +Lys->AminoadipicAcid (K) +Lys->Arg (K) +Lys->Asn (K) +Lys->Gln (K) +Lys->Glu (K) +Lys->Ile (K) +Lys->Met (K) +Lys->Thr (K) +Lys-loss (K) +Lysbiotinhydrazide (K) +maleimide (C) +maleimide (K) +Maleimide-PEO2-Biotin (C) +Malonyl (C) +Malonyl (S) +Menadione (C) +Menadione (K) +Menadione-HQ (C) +Menadione-HQ (K) +Met->Arg (M) +Met->Hse (M) +Met->Hsl (M) +Met->Ile (M) +Met->Leu (M) +Met->Lys (M) +Met->Thr (M) +Met->Val (M) +Met-loss (M) +Met-loss+Acetyl (M) +Methyl (C) +Methyl (C-term) +Methyl (D) +Methyl (E) +Methyl (H) +Methyl (I) +Methyl (K) +Methyl (L) +Methyl (N) +Methyl (N-term) +Methyl (N-term) +Methyl (Q) +Methyl (R) +Methyl (S) +Methyl (T) +Methyl+Acetyl:2H(3) (K) +Methyl+Deamidated (N) +Methyl+Deamidated (Q) +Methyl:2H(2) (K) +Methyl:2H(3) (C-term) +Methyl:2H(3) (D) +Methyl:2H(3) (E) +Methyl:2H(3)13C(1) (R) +Methylamine (S) +Methylamine (T) +Methylphosphonate (S) +Methylphosphonate (T) +Methylphosphonate (Y) +Methylpyrroline (K) +Methylthio (C) +Methylthio (D) +Methylthio (N) +MG-H1 (R) +Microcin (C-term) +MicrocinC7 (C-term) +Molybdopterin (C) +MolybdopterinGD (C) +MolybdopterinGD (D) +MolybdopterinGD+Delta:S(-1)Se(1) (C) +Myristoleyl (G) +Myristoyl (C) +Myristoyl (G) +Myristoyl (K) +Myristoyl+Delta:H(-4) (G) +NA-LNO2 (C) +NA-LNO2 (H) +NA-OA-NO2 (C) +NA-OA-NO2 (H) +NBS (W) +NBS:13C(6) (W) +NDA (K) +NDA (N-term) +NEIAA (C) +NEIAA (Y) +NEIAA:2H(5) (C) +NEIAA:2H(5) (Y) +NEM:2H(5) (C) +Nethylmaleimide (C) +Nethylmaleimide+water (C) +Nethylmaleimide+water (K) +NHS-LC-Biotin (K) +NHS-LC-Biotin (N-term) +NIC (N-term) +NIPCAM (C) +Nitro (W) +Nitro (Y) +Nitrosyl (C) +Nmethylmaleimide (C) +Nmethylmaleimide (K) +Nmethylmaleimide+water (C) +NO_SMX_SEMD (C) +NO_SMX_SIMD (C) +NO_SMX_SMCT (C) +O-Diethylphosphate (S) +O-Diethylphosphate (T) +O-Diethylphosphate (Y) +O-Dimethylphosphate (S) +O-Dimethylphosphate (T) +O-Dimethylphosphate (Y) +O-Ethylphosphate (S) +O-Ethylphosphate (T) +O-Ethylphosphate (Y) +O-Isopropylmethylphosphonate (S) +O-Isopropylmethylphosphonate (T) +O-Isopropylmethylphosphonate (Y) +O-Methylphosphate (S) +O-Methylphosphate (T) +O-Methylphosphate (Y) +O-pinacolylmethylphosphonate (S) +O-pinacolylmethylphosphonate (T) +O-pinacolylmethylphosphonate (Y) +Octanoyl (S) +Octanoyl (T) +OxArgBiotin (R) +OxArgBiotinRed (R) +Oxidation (C) +Oxidation (D) +Oxidation (F) +Oxidation (G) +Oxidation (H) +Oxidation (K) +Oxidation (M) +Oxidation (N) +Oxidation (P) +Oxidation (R) +Oxidation (W) +Oxidation (Y) +OxLysBiotin (K) +OxLysBiotinRed (K) +OxProBiotin (P) +OxProBiotinRed (P) +Palmitoleyl (C) +Palmitoyl (C) +Palmitoyl (K) +Palmitoyl (N-term) +Palmitoyl (S) +Palmitoyl (T) +Pentylamine (Q) +PentylamineBiotin (Q) +PEO-Iodoacetyl-LC-Biotin (C) +PET (S) +PET (T) +PGA1-biotin (C) +Phe->Cys (F) +Phe->Ile (F) +Phe->Ser (F) +Phe->Tyr (F) +Phe->Val (F) +Phenylisocyanate (N-term) +Phenylisocyanate:2H(5) (N-term) +Phospho (C) +Phospho (D) +Phospho (H) +Phospho (R) +Phospho (S) +Phospho (T) +Phospho (Y) +Phosphoadenosine (H) +Phosphoadenosine (K) +Phosphoadenosine (T) +Phosphoadenosine (Y) +Phosphoguanosine (H) +Phosphoguanosine (K) +PhosphoHex (S) +PhosphoHexNAc (S) +Phosphopantetheine (S) +PhosphoribosyldephosphoCoA (S) +PhosphoUridine (H) +PhosphoUridine (Y) +Phycocyanobilin (C) +Phycoerythrobilin (C) +Phytochromobilin (C) +Piperidine (K) +Piperidine (N-term) +Pro->Ala (P) +Pro->Arg (P) +Pro->Gln (P) +Pro->His (P) +Pro->Leu (P) +Pro->pyro-Glu (P) +Pro->Pyrrolidinone (P) +Pro->Pyrrolidone (P) +Pro->Ser (P) +Pro->Thr (P) +probiotinhydrazide (P) +Propionamide (C) +Propionamide:2H(3) (C) +Propionyl (K) +Propionyl (N-term) +Propionyl:13C(3) (K) +Propionyl:13C(3) (N-term) +PropylNAGthiazoline (C) +PyMIC (N-term) +PyridoxalPhosphate (K) +Pyridylacetyl (K) +Pyridylacetyl (N-term) +Pyridylethyl (C) +Pyro-carbamidomethyl (C) +PyruvicAcidIminyl (C) +PyruvicAcidIminyl (K) +PyruvicAcidIminyl (V) +QAT (C) +QAT:2H(3) (C) +QEQTGG (K) +QQQTGG (K) +Quinone (W) +Quinone (Y) +Retinylidene (K) +Ser->Ala (S) +Ser->Arg (S) +Ser->Asn (S) +Ser->Cys (S) +Ser->Gly (S) +Ser->Ile (S) +Ser->LacticAcid (S) +Ser->Phe (S) +Ser->Pro (S) +Ser->Thr (S) +Ser->Trp (S) +Ser->Tyr (S) +SMA (K) +SMA (N-term) +SPITC (K) +SPITC (N-term) +SPITC:13C(6) (K) +SPITC:13C(6) (N-term) +Succinyl (K) +Succinyl (N-term) +Succinyl (N-term) +Succinyl:13C(4) (K) +Succinyl:13C(4) (N-term) +Succinyl:2H(4) (K) +Succinyl:2H(4) (N-term) +SulfanilicAcid (C-term) +SulfanilicAcid (D) +SulfanilicAcid (E) +SulfanilicAcid:13C(6) (C-term) +SulfanilicAcid:13C(6) (D) +SulfanilicAcid:13C(6) (E) +Sulfide (C) +Sulfo (C) +Sulfo (S) +Sulfo (T) +Sulfo (Y) +Sulfo-NHS-LC-LC-Biotin (K) +Sulfo-NHS-LC-LC-Biotin (N-term) +Thioacyl (K) +Thioacyl (N-term) +Thiophos-S-S-biotin (S) +Thiophos-S-S-biotin (T) +Thiophos-S-S-biotin (Y) +Thiophospho (S) +Thiophospho (T) +Thiophospho (Y) +Thr->Ala (T) +Thr->Arg (T) +Thr->Asn (T) +Thr->Ile (T) +Thr->Lys (T) +Thr->Met (T) +Thr->Pro (T) +Thr->Ser (T) +Thrbiotinhydrazide (T) +Thyroxine (Y) +TMAB (K) +TMAB (N-term) +TMAB:2H(9) (K) +TMAB:2H(9) (N-term) +TMPP-Ac (N-term) +TMT (K) +TMT (N-term) +TMT2plex (K) +TMT2plex (N-term) +TMT6plex (K) +TMT6plex (N-term) +TNBS (K) +TNBS (N-term) +trifluoro (L) +Triiodo (Y) +Triiodothyronine (Y) +Trimethyl (A) +Trimethyl (K) +Trimethyl (R) +Trioxidation (C) +Tripalmitate (C) +Trp->Arg (W) +Trp->Cys (W) +Trp->Gly (W) +Trp->Hydroxykynurenin (W) +Trp->Kynurenin (W) +Trp->Leu (W) +Trp->Oxolactone (W) +Trp->Ser (W) +Tyr->Asn (Y) +Tyr->Asp (Y) +Tyr->Cys (Y) +Tyr->Dha (Y) +Tyr->His (Y) +Tyr->Phe (Y) +Tyr->Ser (Y) +Val->Ala (V) +Val->Asp (V) +Val->Glu (V) +Val->Gly (V) +Val->Ile (V) +Val->Met (V) +Val->Phe (V) +Xlink:B10621 (C) +Xlink:DMP (K) +Xlink:DMP (N-term) +Xlink:DMP-s (K) +Xlink:DMP-s (N-term) +Xlink:SSD (K) +ZGB (K) +ZGB (N-term)
--- a/openms_wrapper.py Wed Dec 19 00:33:53 2012 -0500 +++ b/openms_wrapper.py Fri May 10 17:31:05 2013 -0400 @@ -4,6 +4,7 @@ from ConfigParser import SafeConfigParser from xml.etree import ElementTree import subprocess +from re import compile DEBUG = False @@ -11,7 +12,15 @@ def main(): (options, args) = _parse_args() for executable, config_path in zip(options.executables, options.configs): - _run_openms(executable, config_path) + command_handler = COMMAND_HANDLERS.get(executable, _run_openms) + command_handler(executable, config_path) + + +def _run_shell(executable, config_path): + command = open(config_path, "r").read().strip() + if DEBUG: + print "Running shell command %s" % command + _exec(command) def _run_openms(executable, config_path): @@ -24,18 +33,31 @@ print 'With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable) _exec("%s -ini openms.ini" % executable) +COMMAND_HANDLERS = { + "__SHELL__": _run_shell, +} + + +def _fail(message, return_code=1): + print message + sys.exit(return_code) + def _exec(command): proc = subprocess.Popen(args=command, shell=True) return_code = proc.wait() if return_code != 0: - sys.exit(return_code) + _fail("Error executing command [%s], return code is %d" % (command, return_code), return_code) def _set_options(tree, executable, options): executable_node = tree.find("./NODE[@name='%s']" % executable) + if executable_node is None: + _fail("Could not find options for executable %s" % executable) options_node = executable_node.find("./NODE[@name='1']") for key, raw_value in options.items("simple_options"): + if raw_value is None: + _fail("No value found key %s" % key) value = _parse_value(raw_value) _set_option(options_node, key.split("!"), value) _set_option(options_node, ["no_progress"], "true", required=False) @@ -44,26 +66,53 @@ def _set_option(node, key_parts, value, required=True): key = key_parts[0] if len(key_parts) == 1: - item = node.find("./ITEM[@name='%s']" % key) - if item is not None: - item.set("value", value) - elif required: - raise Exception("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node)) + if not _set_item_value(node, key, value) and \ + not _set_list_item_value(node, key, value) and \ + required: + _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node)) else: + if not node: + _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node)) sub_node = node.find("./NODE[@name='%s']" % key) + if not sub_node: + _fail("Failed to find node for key %s" % key) _set_option(sub_node, key_parts[1:], value, required) +def _set_item_value(node, key, value): + item = node.find("./ITEM[@name='%s']" % key) + if item is not None: + item.set("value", value) + return item is not None + + +def _set_list_item_value(node, key, values): + item = node.find("./ITEMLIST[@name='%s']" % key) + if item is not None: + for value in values.split(","): + ElementTree.SubElement(item, "LISTITEM", {"value": value}) + return item is not None + + def _parse_value(raw_value): value = raw_value - if raw_value in VALUE_FUNCTIONS: - value = VALUE_FUNCTIONS[raw_value](raw_value) + for pattern, function in VALUE_FUNCTIONS.iteritems(): + try: + match = pattern.match(value) + except TypeError: + print "Invalid value found config file %s" % value + sys.exit(1) + if match: + value = function(*match.groups()) + if value is None: + print "Failed to properly parse raw value %s" % raw_value + sys.exit(1) return value ## Special value parser for various OpenMS components -def _get_pepnovo_models_path(_): - pepnovo_path = _get_pepnovo_executable_path(None) +def _get_pepnovo_models_path(): + pepnovo_path = _which('PepNovo') pepnovo_dir = os.path.split(pepnovo_path)[0] guesses = [os.path.join(pepnovo_dir, 'Models'), os.path.join(pepnovo_dir, '..', 'Models'), @@ -76,13 +125,6 @@ return models_dir -def _get_pepnovo_executable_path(_): - return _which("PepNovo") - -VALUE_FUNCTIONS = {"@PEPNOVO_MODELS_PATH@": _get_pepnovo_models_path, - "@PEPNOVO_EXECUTABLE_PATH@": _get_pepnovo_executable_path} - - # http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python def _which(program): @@ -96,12 +138,18 @@ else: for path in os.environ["PATH"].split(os.pathsep): exe_file = os.path.join(path, program) + print path if is_exe(exe_file): return exe_file return None +VALUE_FUNCTIONS = {compile(r"\@WHICH\((.*)\)\@"): _which, + compile(r"\@PEPNOVO_MODELS_PATH\@"): _get_pepnovo_models_path, + } + + def _parse_args(): parser = OptionParser() parser.add_option("-e", "--executable", dest="executables", default=[], action="append") @@ -111,6 +159,7 @@ def _load_options(config_path): config_parser = SafeConfigParser() + config_parser.optionxform = str config_parser.read(config_path) return config_parser
--- a/peak_file_converter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/peak_file_converter.xml Fri May 10 17:31:05 2013 -0400 @@ -19,16 +19,16 @@ <inputs> <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/> <param type="select" name="out_format" label="Output Type"> - <option value="mzml">mzML</option> - <option value="mzxml">mzXML</option> - <option value="mgf">MGF</option> - <option value="ms2">MS2</option> + <option value="mzML">mzML</option> + <option value="mzXML">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> </param> </inputs> <outputs> <data format="mzml" name="out"> <change_format> - <when input="out_format" value="mzxml" format="mzxml" /> + <when input="out_format" value="mzXML" format="mzxml" /> <when input="out_format" value="mgf" format="mgf" /> <when input="out_format" value="ms2" format="ms2" /> </change_format>
--- a/peak_file_filter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/peak_file_filter.xml Fri May 10 17:31:05 2013 -0400 @@ -2,9 +2,11 @@ <description> Extract portions of peak lists. </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'FileFilter' --config $config </command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peak_list_preprocessor.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,211 @@ +<tool id="openms_peak_list_preprocessor" version="0.1" name="Peak List Preprocessor"> + <description> + Wizard to apply multiple OpenMS signal preprocessing tools for peak lists. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <configfiles> + <configfile name="setup_input">cp '$input' 'output.mzML'</configfile> + <configfile name="rename">mv 'output.mzML' 'input.mzML'</configfile> + <configfile name="copy_output">mv 'output.mzML' '$output'</configfile> + <configfile name="resampler_config">[simple_options] +#if $resample.do +in=input.mzML +out=output.mzML +sampling_rate=$resample.sampling_rate +#end if +</configfile> + <configfile name="noise_filter_config">[simple_options] +#set $noise_filter_type = str($noise.type) +in=input.mzML +out=output.mzML +#if $noise_filter_type == 'NoiseFilterGaussian' + +#end if +#if $noise_filter_type == 'NoiseFilterSGolay' + +#end if + </configfile> + <configfile name="baseline_config">[simple_options] +in=input.mzML +out=output.mzML +#if $baseline.do + +#end if + </configfile> + <configfile name="peak_picker_config">[simple_options] +#set $peak_picker_type = str($peak_picker.type) +in=input.mzML +out=output.mzML +#if $peak_picker_type == 'PeakPickerHiRes' +algorithm!signal_to_noise=$peak_picker.signal_to_noise +algorithm!ms1_only=$peak_picker.ms1_only +#end if +#if $peak_picker_type == 'PeakPickerWavelet' +algorithm!signal_to_noise=$peak_picker.signal_to_noise +#if $peak_picker.peak_width.estimate +algorithm!estimate_peak_width=true +#else +algorithm!estimate_peak_width=false +algorithm!peak_width=$peak_picker.peak_width.peak_width +#end if +#end if + </configfile> + <configfile name="mass_corrector_config">[simple_options] +in=input.mzML +out=output.mzML + </configfile> + <configfile name="spectra_filter_config">[simple_options] +in=input.mzML +out=output.mzML +#set $spectra_filter_type = str($spectra_filter.type) + </configfile> + </configfiles> + <command interpreter="python"> + openms_wrapper.py + --executable '__SHELL__' --config $setup_input + #if $resample.do + --executable '__SHELL__' --config $rename + --executable 'Resampler' --config $resampler_config + #end if + #set $noise_filter_type = str($noise.type) + #if $noise_filter_type != "none" + --executable '__SHELL__' --config $rename + --executable '$noise_filter_type' --config $noise_filter_config + #end if + #if $baseline.do + --executable '__SHELL__' --config $rename + --executable 'BaselineFilter' --config $baseline_config + #end if + #set $peak_picker_type = str($peak_picker.type) + #if $peak_picker_type != "none" + --executable '__SHELL__' --config $rename + --executable '$peak_picker_type' --config $peak_picker_config + #if $peak_picker_type == "PeakPickerHiRes" + #if $peak_picker.use_high_res_mass_corrector + --executable '__SHELL__' --config $rename + --executable 'HighResPrecursorMassCorrector' --config $mass_corrector_config + #end if + #end if + #end if + #set $spectra_filter_type = str($spectra_filter.type) + #if $spectra_filter_type != "none" + --executable '__SHELL__' --config $rename + --executable '$spectra_filter_type' --config $spectra_filter_config + #end if + --executable '__SHELL__' --config $copy_output + </command> + <inputs> + <!-- TODO: Maybe even have a conversion step here. --> + <param format="mzML" name="input" type="data" label="Input Peak List (mzML)"/> + <conditional name="resample"> + <param name="do" type="boolean" label="Resample" help="If you want to use the Savitzky Golay filter, or Baseline filter with non equally spaced profile data, e.g. TOF data, you have should generate equally spaced data by resampling."> + </param> + <when value="false"> + </when> + <when value="true"> + <expand macro="sampling_rate_param" /> + </when> + </conditional> + <conditional name="noise"> + <param name="type" type="select" label="Noise Filter" help=""> + <option value="none" select="true">None</option> + <option value="NoiseFilterGaussian">Gaussian</option> + <option value="NoiseFilterSGolay">Savitzky Golay</option> + </param> + <when value="none"> + </when> + <when value="NoiseFilterGaussian"> + </when> + <when value="NoiseFilterSGolay"> + </when> + </conditional> + <conditional name="baseline"> + <param name="do" type="boolean" label="Apply Baseline Filter" help="Executes the top-hat filter to remove the baseline of an MS experiment." /> + <when value="false"> + </when> + <when value="true"> + </when> + </conditional> + <conditional name="peak_picker"> + <param name="type" type="select" label="Peak Picker" help=""> + <option value="none" select="true">None</option> + <option value="PeakPickerHiRes">High Resolution</option> + <option value="PeakPickerWavelet">Wavelet</option> + </param> + <when value="none"> + </when> + <when value="PeakPickerHiRes"> + <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked. (0.0 disables SNT estimation!)" value="1.0" type="float" /> + <param name="ms1_only" type="boolean" label="MS1 Only" truevalue="true" falsevalue="false" /> + <param name="use_high_res_mass_corrector" label="Correct precursor m/z on centroided high resolution data." checked="false" type="boolean" /> + </when> + <when value="PeakPickerWavelet"> + <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked." value="1.0" type="float" /> + <conditional name="peak_width"> + <param name="estimate" label="Estimate Peak Width" type="boolean" checked="false" /> + <when value="true"> + </when> + <when value="false"> + <param name="peak_width" type="float" value="0.15" help="Approximate fwhm of the peaks." label="Peak Width" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="spectra_filter"> + <param name="type" type="select" label="Apply Spectra Filter" help=""> + <option value="none" select="true">None</option> + <option value="SpectraFilterNLargest">N Largest</option> + <option value="SpectraFilterNormalizer">Normalizer</option> + <option value="SpectraFilterScaler">Scaler</option> + <option value="SpectraFilterBernNorm">Bern et. al. normalization</option> + <option value="SpectraFilterMarkerMower">Marker Mower</option> + <option value="SpectraFilterParentPeakMower">Parent Peak Mower</option> + <option value="SpectraFilterSqrtMower">Square Root Mower</option> + <option value="SpectraFilterThresholdMower">Threshold Mower</option> + <option value="SpectraFilterWindowMower">Window Mower</option> + </param> + <when value="none"> + </when> + <when value="SpectraFilterNLargest"> + <!-- 1 param --> + </when> + <when value="SpectraFilterNormalizer"> + <!-- 1 param --> + </when> + <when value="SpectraFilterScaler"> + <!-- 3 params --> + </when> + <when value="SpectraFilterBernNorm"> + </when> + <when value="SpectraFilterMarkerMower"> + </when> + <when value="SpectraFilterParentPeakMower"> + <!-- Tons of params --> + </when> + <when value="SpectraFilterSqrtMower"> + </when> + <when value="SpectraFilterThresholdMower"> + <!-- 1 param --> + </when> + <when value="SpectraFilterWindowMower"> + <!-- 2 params --> + </when> + </conditional> + </inputs> + <outputs> + <data format="mzml" name="output" /> + </outputs> + <help> +**What it does** + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/peak_picker_hi_res.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/peak_picker_hi_res.xml Fri May 10 17:31:05 2013 -0400 @@ -1,9 +1,11 @@ <tool id="openms_peak_picker_hi_res" version="0.1" name="Peak Peaker (Hi Res)"> <description> </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command> openms_wrapper.py --executable 'PeakPickerHiRes' --config $config </command>
--- a/pepnovo_adapter.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/pepnovo_adapter.xml Fri May 10 17:31:05 2013 -0400 @@ -1,11 +1,13 @@ <tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)"> <description> - </description> - <requirements> - <requirement type="package">openms</requirement> + <macros> + <import>macros.xml</import> + </macros> + <expnad macro="stdio" /> + <expand macro="requires"> <requirement type="package">pepnovo</requirement> - </requirements> + </expand> <command interpreter="python"> openms_wrapper.py #if $input_block.do_clean @@ -22,17 +24,18 @@ #end if out=${out} model_directory=@PEPNOVO_MODELS_PATH@ -pepnovo_executable=@PEPNOVO_EXECUTABLE_PATH@ +pepnovo_executable=@WHICH(PepNovo)@ temp_data_directory=. model=${model} digest=${digest} -#if $corrections != "none" +num_solutions=${num_solutions} +#if str($corrections) != "none" correct_pm=true #end if -#if $corrections == "mass" +#if str($corrections) == "mass" use_spectrum_charge=true #end if -#if $corrections == "mz" +#if str($corrections) == "mz" use_spectrum_mz=true #end if $quality_filter @@ -42,6 +45,14 @@ #if $override_fragment.do_override fragment_tolerance=${override_fragment.fragment_tolerance} #end if +#set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods]) +#if $fixed_mods_str +fixed_modifications=$fixed_mods_str +#end if +#set $variable_mods_str=",".join([str($variable_mod.variable_mod) for $variable_mod in $variable_mods]) +#if $variable_mods_str +variable_modifications=$variable_mods_str +#end if </configfile> <configfile name="inputConfig">[simple_options] in=${input_block.input1} @@ -52,7 +63,7 @@ </configfiles> <inputs> <conditional name="input_block"> - <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suiteable for PepNovo." /> + <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suitable for PepNovo." /> <when value="true"> <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" /> </when> @@ -76,6 +87,22 @@ <option value="mz">Find optimal precursor m/z values.</option> <option value="charge">Find optimal charge values.</option> </param> + <repeat name="fixed_mods" title="Fixed Modification"> + <param name="fixed_mod" type="select" label="Fixed Modification"> + <options from_file="openms_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </repeat> + <repeat name="variable_mods" title="Variable Modification"> + <param name="variable_mod" type="select" label="Variable Modification"> + <options from_file="openms_mods.loc"> + <column name="name" index="0"/> + <column name="value" index="0" /> + </options> + </param> + </repeat> <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/> <conditional name="override_pm"> <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" /> @@ -97,6 +124,9 @@ <when value="false"> </when> </conditional> + <param name="num_solutions" type="integer" label="Number of Solutions" value="20"> + <validator type="in_range" message="1 <= Number of Solutions <= 2000" min="1" max="2000"/> + </param> </inputs> <outputs> <data format="idxml" name="out" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_indexer.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,70 @@ +<tool id="openms_peptide_indexer" version="0.1.0" name="Peptide Indexer"> + <description> + Refreshes the protein references for all peptide hits from a idXML file. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'PeptideIndexer' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +fasta=$database +out=$output +decoy_string=$decoy_string +#if $decoy_string_position == "prefix" +prefix=true +#end if +$extact_search +$write_protein_sequence +$keep_unreferenced_proteins +aaa_max=$aaa_max +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Identification Input" type="data" format="idxml" /> + <param name="database" label="Database" type="data" format="fasta" /> + <param name="decoy_string" type="text" value="_rev" label="Decoy string"/> + <param name="decoy_string_position" type="select" label="Decoy Position"> + <option value="suffix" selected="true">Suffix</option> + <option value="prefix">Prefix</option> + </param> + <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" /> + <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" /> + <param name="keep_unreferenced_proteins" label="Keep Unreferenced Proteins" truevalue="keep_unreferenced_proteins=true" falsevalue="" type="boolean" /> + <param name="aaa_max" type="integer" value="4" label="Maximum Number of Ambiguous Amino Acids" help=" Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" /> + </inputs> + <outputs> + <data format="idxml" name="output" /> + </outputs> + <help> +**What it does** + +Each peptide hit is annotated by a target_decoy string, indicating if the peptide sequence is found in a 'target', a 'decoy' or in both 'target+decoy' protein. This information is crucial for the FalseDiscoveryRate IDPosteriorErrorProbability tools. + +Note: +Make sure that your protein names in the database contain a correctly formatted decoy string. This can be ensured by using DecoyDatabase. If the decoy identifier is not recognized successfully all proteins will be assumed to stem from the target-part of the query. +E.g., "sw|P33354_REV|YEHR_ECOLI Uncharacterized lipop..." is invalid, since the tool has no knowledge of how SwissProt entries are build up. A correct identifier could be "rev_sw|P33354|YEHR_ECOLI Uncharacterized li ..." or "sw|P33354|YEHR_ECOLI_rev Uncharacterized li", depending on if you are using prefix annotation or not. +This tool will also give you some target/decoy statistics when its done. Look carefully! + +By default the tool will fail, if an unmatched peptide occurs, i.e. the database does not contain the corresponding protein. You can force the tool to return successfully in this case by using the flag 'allow_unmatched'. + +Some search engines (such as Mascot) will replace ambiguous AA's in the protein database with unambiguous AA' in the reported peptides, e.g., exchange 'X' with 'H'. This will cause this peptide not to be found by exactly matching its sequence. However, we can recover these cases by using tolerant search in these cases (done automatically). In all cases we require ambiguous AA's in peptide sequence to match exactly in the protein DB (i.e., 'X' in peptide only matches 'X'). + +Two search modes are available: + +exact: Peptide sequences require exact match in protein database. If no protein for this peptide can be found, tolerant matching is automatically used for this peptide. Thus, the results for these peptides are identical for both search modes. +tolerant: Allow ambiguous AA's in protein sequence, e.g., 'M' in peptide will match 'X' in protein. This mode might yield more protein hits for some peptides (even though they have exact matches as well). +The exact mode is much faster (about x10) and consumes less memory (about x2.5), but might fail to report a few proteins with ambiguous AAs for some peptides. Usually these proteins are putative, however. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- a/pepxml_protxml_merger.xml Wed Dec 19 00:33:53 2012 -0500 +++ b/pepxml_protxml_merger.xml Fri May 10 17:31:05 2013 -0400 @@ -1,9 +1,11 @@ <tool id="openms_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML"> <description> </description> - <requirements> - <requirement type="package">openms</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> <command interpreter="python"> openms_wrapper.py --executable 'IDMerger' --config $config </command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/protein_inference.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,42 @@ +<tool id="openms_protein_inference" version="0.1.0" name="Protein Inference"> + <description> + Computes a protein identification based on the number of identified peptides. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'PeptideIndexer' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$output +min_peptides_per_protein=${min_peptides_per_protein} +treat_charge_variants_separately=${treat_charge_variants_separately} +treat_modification_variants_separately=${treat_modification_variants_separately} +</configfile> + </configfiles> + <inputs> + <param name="input1" label="Identification Input" type="data" format="idxml" /> + <param name="min_peptides_per_protein" type="integer" value="2" label="Minimum Number of Peptides per Protein Identification" /> + <param name="treat_charge_variants_separately" label="Treat Charge Variants Separately" type="boolean" truevalue="true" falsevalue="false" checked="false" help="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences." /> + <param name="treat_modification_variants_separately" label="Treat Modification Variants Separately" type="boolean" truevalue="true" falsevalue="false" checked="false" help="If this flag is set, different modification variants of the same peptide sequence count as individual evidences." /> + </inputs> + <outputs> + <data format="idxml" name="output" /> + </outputs> + <help> +**What it does** + +This tool counts the peptide sequences that match a protein accession. From this count for all protein hits in the respective id run, only those proteins are accepted that have at least a given number of peptides sequences identified. The peptide identifications should be prefiltered with respect to false discovery rate and the score in general to remove bad identifications. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/protein_quantifier.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,62 @@ +<tool id="openms_protein_quantifier" version="0.1.0" name="Protein Quantifier"> + <description> + Compute peptide and protein abundances from annotated feature/consensus maps. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'ProteinQuantifier' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$map_input +#if $protein_prophet.use +protxml=$protxml +#end if +out=$protein_output +peptide_out=$peptide_output +top=$top +format!quoting=none +</configfile> + </configfiles> + <inputs> + <expand macro="map_input" /> + <conditional name="protein_prophet"> + <param name="use" label="Use ProteinProphet Results (converted to idXML)" help="For information about indistinguishable proteins." type="boolean" /> + <when value="false"> + </when> + <when value="true"> + <param name="protxml" label="Protein/Peptide Identifications Input" type="data" format="idxml" /> + </when> + </conditional> + <param name="top" label="Top" value="0" type="integer" /> + </inputs> + <outputs> + <data format="tabular" name="protein_output" /> + <data format="tabular" name="peptide_output" /> + </outputs> + <help> +**What it does** + +Quantification is based on the intensity values of the features in the input. Feature intensities are first accumulated to peptide abundances, according to the peptide identifications annotated to the features/feature groups. Then, abundances of the peptides of a protein are averaged to compute the protein abundance. + +The peptide-to-protein step uses the (e.g. 3) most abundant proteotypic peptides per protein to compute the protein abundances. This is a general version of the "top 3 approach" (but only for relative quantification) described in: +Silva et al.: Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition (Mol. Cell. Proteomics, 2006, PMID: 16219938). + +Only features/feature groups with unambiguous peptide annotation are used for peptide quantification, and generally only proteotypic peptides (i.e. those matching to exactly one protein) are used for protein quantification. As an exception to this rule, if ProteinProphet results for the whole sample set are provided with the protxml option, or are already included in a featureXML input, also groups of indistinguishable proteins will be quantified. The reported quantity then refers to the total for the whole group. + +Peptide/protein IDs from multiple identification runs can be handled, but will not be differentiated (i.e. protein accessions for a peptide will be accumulated over all identification runs). + +Peptides with the same sequence, but with different modifications are quantified separately on the peptide level, but treated as one peptide for the protein quantification (i.e. the contributions of differently-modified variants of the same peptide are accumulated). + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` +and ``Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308). doi:10.1021/pr300992u`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/silac_analyzer.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,74 @@ +<tool id="silac_analyzer" version="0.1.0" name="SILACAnalyzer"> + <description> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py + --executable 'SILACAnalyzer' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$out +sample!labels=[${labels}] +sample!missed_cleavages=${missed_cleavages} +sample!charge=${min_charge}:${max_charge} +sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide} +algorithm!rt_threshold=$rt_threshold +algorithm!rt_min=$rt_min +algorithm!intensity_cutoff=$intensity_cutoff +algorithm!intensity_correlation=$intensity_correlation +algorithm!model_deviation=$model_deviation +</configfile> + </configfiles> + <inputs> + <param name="input1" type="data" format="mzml" label="Input peak list" /> + <!-- TODO --> + <param name="labels" type="select" multiple="true" label="Labels"> + <option value="Arg6" >Arg6</option> + <option value="Arg10">Arg10</option> + <option value="Lys4" >Lys4</option> + <option value="Lys6" >Lys6</option> + <option value="Lys8" >Lys8</option> + <option value="dICPL4" >dICPL4</option> + <option value="dICPL6" >dICPL6</option> + <option value="dICPL10" >dICPL10</option> + <option value="Methyl4" >Methyl4</option> + <option value="Methyl8" >Methyl8</option> + <option value="Methyl12" >Methyl12</option> + <option value="Methyl16" >Methyl16</option> + <option value="Methyl24" >Methyl24</option> + <option value="Methyl32" >Methyl32</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" /> + <expand macro="raw_feature_finder_params" /> + <!-- + <param name="rt_threshold" type="float" value="50" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." /> + <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." /> + <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." /> + <param name="intensity_correlation" type="float" value="0.9" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." /> + <param name="model_deviation" type="float" value="6" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." /> + <param name="min_charge" type="integer" value="1" label="Minimum Charge" /> + <param name="max_charge" type="integer" value="5" label="Maximum Charge" /> + <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" /> + <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" /> + --> + </inputs> + <outputs> + <data format="consensusxml" name="out" /> + </outputs> + <help> +**What it does** + + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/text_exporter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,125 @@ +<tool id="openms_text_exporter" version="0.1.0" name="Text Exporter"> + <description> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py \ + --executable '__SHELL__' --config $link \ + --executable 'TextExporter' --config $config + </command> + <configfiles> + <configfile name="link">ln -s '${type.input}' 'input.${type.input.ext}'</configfile> + <configfile name="config">[simple_options] +in=input.${type.input.ext} +out=${out} +#set $input_type = str($type.input_type) +#if $input_type == "featurexml" +feature!minimal=${type.minimal} +#end if +no_ids=${no_ids} +</configfile> + </configfiles> + <inputs> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="featurexml">Features (FeatureXML)</option> + <option value="consensusxml">Consensus (ConsensusXML)</option> + <option value="idxml">Identifications (IdXML)</option> + <option value="mzml">Peak List (mzML)</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input Peak List"/> + </when> + <when value="featurexml"> + <param format="featurexml" name="input" type="data" label="Input Features"/> + <param name="minimal" type="boolean" label="Minimal Output" help="Set this flag to write only three attributes: RT, m/z, and intensity." truevalue="true" falsevalue="false" /> + </when> + <when value="consensusxml"> + <param format="consensusxml" name="input" type="data" label="Input Consensus"/> + </when> + <when value="idxml"> + <param format="idxml" name="input" type="data" label="Input Identifications"/> + </when> + </conditional> + <param name="no_ids" type="boolean" label="Suppress IDs" help="Supresses output of identification data." truevalue="true" falsevalue="false" /> + </inputs> + <outputs> + <data format="txt" name="out" /> + </outputs> + <help> +**What it does** + +The goal of this tool is to create output in a table format that is easily readable in Excel or OpenOffice. Lines in the output correspond to rows in the table. + +utput files begin with comment lines, starting with the special character "#". The last such line(s) will be a header with column names, but this may be preceded by more general comments. + +Because the OpenMS XML formats contain different kinds of data in a hierarchical structure, TextExporter produces somewhat unusual TSV/CSV files for many inputs: Different lines in the output may belong to different types of data, and the number of columns and the meanings of the individual fields depend on the type. In such cases, the first column always contains an indicator (in capital letters) for the data type of the current line. In addition, some lines have to be understood relative to a previous line, if there is a hierarchical relationship in the data. (See below for details and examples.) + +Missing values are represented by "-1" or "nan" in numeric fields and by blanks in character/text fields. + +Depending on the input and the parameters, the output contains the following columns: + +featureXML input: + +first column: RUN / PROTEIN / UNASSIGNEDPEPTIDE / FEATURE / PEPTIDE (indicator for the type of data in the current row) +a RUN line contains information about a protein identification run; further columns: run_id, score_type, score_direction, data_time, search_engine_version, parameters +a PROTEIN line contains data of a protein identified in the previously listed run; further columns: score, rank, accession, coverage, sequence +an UNASSIGNEDPEPTIDE line contains data of peptide hit that was not assigned to any feature; further columns: rt, mz, score, rank, sequence, charge, aa_before, aa_after, score_type, search_identifier, accessions +a FEATURE line contains data of a single feature; further columns: rt, mz, intensity, charge, width, quality, rt_quality, mz_quality, rt_start, rt_end +a PEPTIDE line contains data of a peptide hit annotated to the previous feature; further columns: same as for UNASSIGNEDPEPTIDE +With the no_ids flag, only FEATURE lines (without the FEATURE indicator) are written. + +With the feature:minimal flag, only the rt, mz, and intensity columns of FEATURE lines are written. + +consensusXML input: + +Output format produced for the out parameter: + +first column: MAP / RUN / PROTEIN / UNASSIGNEDPEPTIDE / CONSENSUS / PEPTIDE (indicator for the type of data in the current row) +a MAP line contains information about a sub-map; further columns: id, filename, label, size (potentially followed by further columns containing meta data, depending on the input) +a CONSENSUS line contains data of a single consensus feature; further columns: rt_cf, mz_cf, intensity_cf, charge_cf, width_cf, quality_cf, rt_X0, mz_X0, ..., rt_X1, mz_X1, ... +"..._cf" columns refer to the consensus feature itself, "..._Xi" columns refer to a sub-feature from the map with ID "Xi" (no quality column in this case); missing sub-features are indicated by "nan" values +see above for the formats of RUN, PROTEIN, UNASSIGNEDPEPTIDE, PEPTIDE lines +With the no_ids flag, only MAP and CONSENSUS lines are written. + +Output format produced for the consensus_centroids parameter: + +one line per consensus centroid +columns: rt, mz, intensity, charge, width, quality +Output format produced for the consensus_elements parameter: + +one line per sub-feature (element) of a consensus feature +first column: H / L (indicator for new/repeated element) +H indicates a new element, L indicates the replication of the first element of the current consensus feature (for plotting) +further columns: rt, mz, intensity, charge, width, rt_cf, mz_cf, intensity_cf, charge_cf, width_cf, quality_cf +"..._cf" columns refer to the consensus feature, the other columns refer to the sub-feature +Output format produced for the consensus_features parameter: + +one line per consensus feature (suitable for processing with e.g. R) +columns: same as for a CONSENSUS line above, followed by additional columns for identification data +additional columns: peptide_N0, n_diff_peptides_N0, protein_N0, n_diff_proteins_N0, peptide_N1, ... +"..._Ni" columns refer to the identification run with index "Ni", n_diff_... stands for "number of different ..."; different peptides/proteins in one column are separated by "/" +With the no_ids flag, the additional columns are not included. + +idXML input: + +first column: RUN / PROTEIN / PEPTIDE (indicator for the type of data in the current row) +see above for the formats of RUN, PROTEIN, PEPTIDE lines +additional column for PEPTIDE lines: predicted_rt +With the id:proteins_only flag, only RUN and PROTEIN lines are written. + +With the id:peptides_only flag, only PEPTIDE lines (without the PEPTIDE indicator) are written. + +With the id:first_dim_rt flag, the additional columns rt_first_dim and predicted_rt_first_dim are included for PEPTIDE lines. + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unimod.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,15140 @@ +<?xml version="1.0" encoding="utf-8"?> +<!--Copyright (C) 2002-2006 Unimod; this information may be copied, distributed and/or--> +<!--modified under certain conditions, but it comes WITHOUT ANY WARRANTY; see the--> +<!--accompanying Design Science License for more details--> +<umod:unimod xmlns:umod="http://www.unimod.org/xmlns/schema/unimod_2" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.unimod.org/xmlns/schema/unimod_2 http://www.unimod.org/xmlns/schema/unimod_2/unimod_2.xsd" + majorVersion="2" + minorVersion="0"> + <umod:elements> + <umod:elem title="H" full_name="Hydrogen" avge_mass="1.00794" mono_mass="1.007825035"/> + <umod:elem title="2H" full_name="Deuterium" avge_mass="2.014101779" + mono_mass="2.014101779"/> + <umod:elem title="Li" full_name="Lithium" avge_mass="6.941" mono_mass="7.016003"/> + <umod:elem title="C" full_name="Carbon" avge_mass="12.0107" mono_mass="12"/> + <umod:elem title="13C" full_name="Carbon13" avge_mass="13.00335483" + mono_mass="13.00335483"/> + <umod:elem title="N" full_name="Nitrogen" avge_mass="14.0067" mono_mass="14.003074"/> + <umod:elem title="15N" full_name="Nitrogen15" avge_mass="15.00010897" + mono_mass="15.00010897"/> + <umod:elem title="O" full_name="Oxygen" avge_mass="15.9994" mono_mass="15.99491463"/> + <umod:elem title="18O" full_name="Oxygen18" avge_mass="17.9991603" mono_mass="17.9991603"/> + <umod:elem title="F" full_name="Fluorine" avge_mass="18.9984032" mono_mass="18.99840322"/> + <umod:elem title="Na" full_name="Sodium" avge_mass="22.98977" mono_mass="22.9897677"/> + <umod:elem title="P" full_name="Phosphorous" avge_mass="30.973761" mono_mass="30.973762"/> + <umod:elem title="S" full_name="Sulfur" avge_mass="32.065" mono_mass="31.9720707"/> + <umod:elem title="Cl" full_name="Chlorine" avge_mass="35.453" mono_mass="34.96885272"/> + <umod:elem title="K" full_name="Potassium" avge_mass="39.0983" mono_mass="38.9637074"/> + <umod:elem title="Ca" full_name="Calcium" avge_mass="40.078" mono_mass="39.9625906"/> + <umod:elem title="Fe" full_name="Iron" avge_mass="55.845" mono_mass="55.9349393"/> + <umod:elem title="Ni" full_name="Nickel" avge_mass="58.6934" mono_mass="57.9353462"/> + <umod:elem title="Zn" full_name="Zinc" avge_mass="65.409" mono_mass="63.9291448"/> + <umod:elem title="Se" full_name="Selenium" avge_mass="78.96" mono_mass="79.9165196"/> + <umod:elem title="Br" full_name="Bromine" avge_mass="79.904" mono_mass="78.9183361"/> + <umod:elem title="Ag" full_name="Silver" avge_mass="107.8682" mono_mass="106.905092"/> + <umod:elem title="Hg" full_name="Mercury" avge_mass="200.59" mono_mass="201.970617"/> + <umod:elem title="Au" full_name="Gold" avge_mass="196.96655" mono_mass="196.966543"/> + <umod:elem title="I" full_name="Iodine" avge_mass="126.90447" mono_mass="126.904473"/> + <umod:elem title="Mo" full_name="Molybdenum" avge_mass="95.94" mono_mass="97.9054073"/> + <umod:elem title="Cu" full_name="Copper" avge_mass="63.546" mono_mass="62.9295989"/> + <umod:elem title="e" full_name="electron" avge_mass="0.000549" mono_mass="0.000549"/> + <umod:elem title="B" full_name="Boron" avge_mass="10.811" mono_mass="11.0093055"/> + <umod:elem title="As" full_name="Arsenic" avge_mass="74.9215942" mono_mass="74.9215942"/> + </umod:elements> + <umod:modifications> + <umod:mod title="Acetyl" full_name="Acetylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2008-02-15 05:20:02" + approved="1" + record_id="1"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="6"/> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="5"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="4"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Multiple" + spec_group="2"> + <umod:misc_notes>GIST acetyl light</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Multiple" + spec_group="1"> + <umod:misc_notes>PT and GIST acetyl light</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="7"> + <umod:misc_notes>O-acetyl</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="8"/> + <umod:delta mono_mass="42.010565" avge_mass="42.0367" composition="H(2) C(2) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>14730666</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15350136</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0055</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>IonSource acetylation tutorial</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.ionsource.com/Card/acetylation/acetylation.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Chemical Reagents for Protein Modification 3rd edition, pp 215-221, Roger L. Lundblad, CRC Press, New York, N.Y., 2005</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11999733</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0043</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0044</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0354</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0045</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0056</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0046</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0051</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0052</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0364</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0041</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0049</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0048</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0047</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0042</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0050</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0053</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0054</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>ACET</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PNAS 2006 103: 18574-18579</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1073/pnas.0608995103</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Amidated" full_name="Amidation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-14 08:10:18" + approved="1" + record_id="2"> + <umod:specificity hidden="0" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="0" site="C-term" position="Any C-term" classification="Artefact" + spec_group="2"/> + <umod:delta mono_mass="-0.984016" avge_mass="-0.9848" composition="H N O(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0100</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0099</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0098</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0097</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0096</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0095</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0094</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0093</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0092</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0091</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0090</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0089</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0081</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0082</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0083</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0084</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0085</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0086</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0087</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0088</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AMID</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Biotin" full_name="Biotinylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:27:08" + approved="1" + record_id="3"> + <umod:specificity hidden="0" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="226.077598" avge_mass="226.2954" + composition="H(14) C(10) N(2) O(2) S"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0117</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>BIOT</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Carbamidomethyl" full_name="Iodoacetamide derivative" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 10:18:27" + approved="1" + record_id="4"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Artefact" + spec_group="5"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Artefact" + spec_group="4"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Artefact" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Artefact" + spec_group="6"/> + <umod:delta mono_mass="57.021464" avge_mass="57.0513" composition="H(3) C(2) N O"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Carboxyamidomethylation</umod:alt_name> + <umod:xref> + <umod:text>Creasy, D. M., Cottrell, J. S., Proteomics 2 1426-34 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11510821</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Boja, E. S., Fales, H. M., Anal. Chem. 73 3576-82 (2001)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12422359</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Carbamyl" full_name="Carbamylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:09:40" + approved="0" + record_id="5"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Artefact" + spec_group="4"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Artefact" + spec_group="3"/> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Multiple" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Multiple" + spec_group="1"/> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="Artefact" + spec_group="5"/> + <umod:delta mono_mass="43.005814" avge_mass="43.0247" composition="H C N O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0343</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12203680</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0332</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>IonSource carbamylation tutorial</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.ionsource.com/Card/carbam/carbam.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>10978403</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Carbamylation is an irreversible process of non-enzymatic modification of proteins by the breakdown products of urea isocyanic acid reacts with the N-term of a proteine or side chains of lysine and arginine residues</umod:misc_notes> + </umod:mod> + <umod:mod title="Carboxymethyl" full_name="Iodoacetic acid derivative" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 10:21:50" + approved="1" + record_id="6"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Artefact" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="4"> + <umod:misc_notes>Hydroxylethanone</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="58.005479" avge_mass="58.0361" composition="H(2) C(2) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Carboxymethylation</umod:alt_name> + </umod:mod> + <umod:mod title="Deamidated" full_name="Deamidation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:11:50" + approved="0" + record_id="7"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="2"> + <umod:misc_notes>Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N" position="Anywhere" classification="Artefact" + spec_group="1"> + <umod:misc_notes>Convertion of glycosylated asparagine residues upon deglycosylation with PGNase F in H2O</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="Q" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:specificity hidden="1" site="F" position="Protein N-term" + classification="Post-translational" + spec_group="3"/> + <umod:delta mono_mass="0.984016" avge_mass="0.9848" composition="H(-1) N(-1) O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>phenyllactyl from N-term Phe</umod:alt_name> + <umod:alt_name>Citrullination</umod:alt_name> + <umod:xref> + <umod:text>IonSource tutorial</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.ionsource.com/Card/Deamidation/deamidation.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>CITR</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FLAC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0128</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0214</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>6838602</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15700232</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DEAM</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-G" full_name="Gygi ICAT(TM) d0" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 17:00:43" + approved="1" + record_id="8"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="486.251206" avge_mass="486.6253" + composition="H(38) C(22) N(4) O(6) S"> + <umod:element symbol="H" number="38"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>10504701</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Gygi S.P., et. al. Nat Biotechnol. 1999 Oct;17(10):994-9</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-G:2H(8)" full_name="Gygi ICAT(TM) d8" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 17:01:35" + approved="1" + record_id="9"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="494.301420" avge_mass="494.6746" + composition="H(30) 2H(8) C(22) N(4) O(6) S"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="2H" number="8"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>10504701</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Gygi S.P., et. al. Nat Biotechnol. 1999 Oct;17(10):994-9</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Met->Hse" full_name="Homoserine" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-13 15:40:08" + approved="1" + record_id="10"> + <umod:specificity hidden="0" site="M" position="Any C-term" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-29.992806" avge_mass="-30.0922" composition="H(-2) C(-1) O S(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:misc_notes>Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH.</umod:misc_notes> + </umod:mod> + <umod:mod title="Met->Hsl" full_name="Homoserine lactone" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:10:15" + approved="0" + record_id="11"> + <umod:specificity hidden="0" site="M" position="Any C-term" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-48.003371" avge_mass="-48.1075" composition="H(-4) C(-1) S(-1)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>Donald Voet, Judith G. Voet (1995): Biochemistry; p 115</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH.</umod:misc_notes> + </umod:mod> + <umod:mod title="ICAT-D:2H(8)" full_name="Applied Biosystems original ICAT(TM) d8" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 16:56:23" + approved="1" + record_id="12"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="450.275205" avge_mass="450.6221" + composition="H(26) 2H(8) C(20) N(4) O(5) S"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="2H" number="8"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:Ignore mono_mass="227.085423" avge_mass="227.3033" + composition="H(15) C(10) N(2) O(2) S "> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="288.16838" avge_mass="288.4223" + composition="H(18) 2H(4) C(13) N(3) O(2) S "> + <umod:element symbol="H" number="18"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="13"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="332.194594" avge_mass="332.4749" + composition="H(22) 2H(4) C(15) N(3) O(3) S "> + <umod:element symbol="H" number="22"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="411.288115" avge_mass="411.6092" + composition="H(27) 2H(8) C(18) N(4) O(4) S "> + <umod:element symbol="H" number="27"/> + <umod:element symbol="2H" number="8"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="485.270751" avge_mass="485.7109" + composition="H(29) 2H(8) C(20) N(4) O(5) S(2) "> + <umod:element symbol="H" number="29"/> + <umod:element symbol="2H" number="8"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="2"/> + </umod:Ignore> + <umod:Ignore mono_mass="509.270751" avge_mass="509.7323" + composition="H(29) 2H(8) C(22) N(4) O(5) S(2) "> + <umod:element symbol="H" number="29"/> + <umod:element symbol="2H" number="8"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="2"/> + </umod:Ignore> + <umod:xref> + <umod:text>Structure</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/images/icat_reagent.gif</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Molecular & Cellular Proteomics 2:428-442, 2003</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.mcponline.org/cgi/content/full/2/7/428</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-D" full_name="Applied Biosystems original ICAT(TM) d0" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 16:53:48" + approved="1" + record_id="13"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="442.224991" avge_mass="442.5728" + composition="H(34) C(20) N(4) O(5) S"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:Ignore mono_mass="227.085423" avge_mass="227.3033" + composition="H(15) C(10) N(2) O(2) S "> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="284.143273" avge_mass="284.3977" + composition="H(22) C(13) N(3) O(2) S "> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="13"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="328.169488" avge_mass="328.4502" + composition="H(26) C(15) N(3) O(3) S "> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="403.237901" avge_mass="403.5599" + composition="H(35) C(18) N(4) O(4) S "> + <umod:element symbol="H" number="35"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:Ignore> + <umod:Ignore mono_mass="477.220537" avge_mass="477.6616" + composition="H(37) C(20) N(4) O(5) S(2) "> + <umod:element symbol="H" number="37"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="2"/> + </umod:Ignore> + <umod:Ignore mono_mass="501.220537" avge_mass="501.683" + composition="H(37) C(22) N(4) O(5) S(2) "> + <umod:element symbol="H" number="37"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="2"/> + </umod:Ignore> + <umod:xref> + <umod:text>Structure</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/images/icat_reagent.gif</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Molecular & Cellular Proteomics 2:428-442, 2003</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.mcponline.org/cgi/content/full/2/7/428</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="NIPCAM" full_name="N-isopropylcarboxamidomethyl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 12:39:14" + approved="1" + record_id="17"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="99.068414" avge_mass="99.1311" composition="H(9) C(5) N O"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Dimethylacrylamide, DMA</umod:alt_name> + <umod:xref> + <umod:text>Krutzsch and Inman, Analytical Biochemistry, 209, 109-116, (1993)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Galvani et.al. (2000) Electrophoresis vol 22 p2046-p2074</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8465942</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11465505</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PEO-Iodoacetyl-LC-Biotin" + full_name="Biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:40:00" + approved="0" + record_id="20"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="414.193691" avge_mass="414.5196" + composition="H(30) C(18) N(4) O(5) S"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Pierce EZ-Link PEO-Iodoacetyl Biotin</umod:alt_name> + <umod:xref> + <umod:text>12038753</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>J. Biol. Chem., Vol. 278, Issue 7, 4500-4509, February 14, 2003</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.jbc.org/cgi/content/full/278/7/4500#F1</umod:url> + </umod:xref> + <umod:xref> + <umod:text>15253424</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phospho" full_name="Phosphorylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 12:11:24" + approved="1" + record_id="21"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="6"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="5"> + <umod:misc_notes>Rare</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="3"> + <umod:misc_notes>Rare</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="Y" position="Anywhere" classification="Post-translational" + spec_group="2"> + <umod:misc_notes>Usually don't see beta elimination of phosphate</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>Rare</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="T" position="Anywhere" classification="Post-translational" + spec_group="1"> + <umod:NeutralLoss mono_mass="97.976896" avge_mass="97.9952" flag="false" + composition="H(3) O(4) P"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="P" number="1"/> + </umod:NeutralLoss> + <umod:NeutralLoss mono_mass="0.000000" avge_mass="0.0000" flag="false" composition="0"/> + </umod:specificity> + <umod:specificity hidden="0" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"> + <umod:NeutralLoss mono_mass="0.000000" avge_mass="0.0000" flag="false" composition="0"/> + <umod:NeutralLoss mono_mass="97.976896" avge_mass="97.9952" flag="false" + composition="H(3) O(4) P"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="P" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:delta mono_mass="79.966331" avge_mass="79.9799" composition="H O(3) P"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>IonSource</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.ionsource.com/Card/phos/phos.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>AA0037</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0033</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0038</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0039</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0222</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PHOS</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0034</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0036</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0035</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Protein which is posttranslationally modified by the attachment of at least one phosphate group usually on serine, threonine or tyrosine residues, but also on aspartic acid or histidine residues.</umod:misc_notes> + </umod:mod> + <umod:mod title="Dehydrated" full_name="Dehydration" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:05:47" + approved="0" + record_id="23"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Chemical derivative" + spec_group="6"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="5"> + <umod:misc_notes>beta-elimination</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>beta-elimination</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="3"> + <umod:misc_notes>beta-elimination</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="Q" position="Protein C-term" + classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="0" site="C" position="Any N-term" classification="Artefact" + spec_group="7"> + <umod:misc_notes>Pyro-carboxymethyl as a delta from Carboxymethyl-Cys</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-18.010565" avge_mass="-18.0153" composition="H(-2) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:alt_name>didehydroalanine</umod:alt_name> + <umod:alt_name>C-terminal imide</umod:alt_name> + <umod:alt_name>Prompt loss of phosphate from phosphorylated residue</umod:alt_name> + <umod:alt_name>D-Succinimide</umod:alt_name> + <umod:xref> + <umod:text>DHAS</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0303</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0302</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0181</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0182</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DHB</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Propionamide" full_name="Acrylamide adduct" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 10:35:51" + approved="1" + record_id="24"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="71.037114" avge_mass="71.0779" composition="H(5) C(3) N O"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pyridylacetyl" full_name="pyridylacetyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 12:47:43" + approved="1" + record_id="25"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="119.037114" avge_mass="119.1207" composition="H(5) C(7) N O"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>9276974</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Pyro-carbamidomethyl" + full_name="S-carbamoylmethylcysteine cyclization (N-terminus)" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:05:25" + approved="0" + record_id="26"> + <umod:specificity hidden="0" site="C" position="Any N-term" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="39.994915" avge_mass="40.0208" composition="C(2) O"> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Carboxymethyl-Cys cyclization (N-terminus)</umod:alt_name> + <umod:alt_name>Carbamidomethyl-Cys cyclization (N-terminus)</umod:alt_name> + <umod:xref> + <umod:text>12643538</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>J. Proteome Res. 1, 181-187 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Cyclisation of N-term Carbamidomethyl-Cys or Carboxymethyl-Cys. The delta is relative to Cys. For a delta relative to alkylated Cys, see Ammonia-loss and Dehydrated.</umod:misc_notes> + </umod:mod> + <umod:mod title="Glu->pyro-Glu" full_name="Pyro-glu from E" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2008-06-05 13:54:56" + approved="1" + record_id="27"> + <umod:specificity hidden="0" site="E" position="Any N-term" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="-18.010565" avge_mass="-18.0153" composition="H(-2) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0031</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Miller et.al. Arch. Biochem. Biophy. (1993) 301, 41-52.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8442665</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PYRE</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Gln->pyro-Glu" full_name="Pyro-glu from Q" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-13 17:06:57" + approved="1" + record_id="28"> + <umod:specificity hidden="0" site="Q" position="Any N-term" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="-17.026549" avge_mass="-17.0305" composition="H(-3) N(-1)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="N" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0031</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PYRR</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="SMA" full_name="N-Succinimidyl-3-morpholine acetate" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:41:18" + approved="1" + record_id="29"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="127.063329" avge_mass="127.1412" composition="H(9) C(6) N O(2)"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>10446193</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Sherman, N. E., Yates, N. A., Shabanowitz, J., Hunt, D. F., Jeffery, W. A., Bartlet-Jones, M., and Pappin, D. J. C. (1995) Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, May 21-26, 1995, Atlanta, GA</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cation:Na" full_name="Sodium adduct" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-14 19:43:17" + approved="1" + record_id="30"> + <umod:specificity hidden="0" site="D" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="0" site="C-term" position="Any C-term" classification="Artefact" + spec_group="1"/> + <umod:specificity hidden="0" site="E" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:delta mono_mass="21.981943" avge_mass="21.9818" composition="H(-1) Na"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="Na" number="1"/> + </umod:delta> + <umod:misc_notes>Proton replaced by sodium cation</umod:misc_notes> + </umod:mod> + <umod:mod title="Pyridylethyl" full_name="S-pyridylethylation" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 12:43:38" + approved="1" + record_id="31"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="105.057849" avge_mass="105.1372" composition="H(7) C(7) N"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>11760118</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl" full_name="Methylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-14 10:32:35" + approved="1" + record_id="34"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="14"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="13"/> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="10"/> + <umod:specificity hidden="0" site="E" position="Anywhere" classification="Post-translational" + spec_group="12"/> + <umod:specificity hidden="0" site="D" position="Anywhere" classification="Post-translational" + spec_group="12"/> + <umod:specificity hidden="0" site="C-term" position="Any C-term" classification="Multiple" + spec_group="11"/> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="Post-translational" + spec_group="9"/> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="Post-translational" + spec_group="8"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="7"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="5"/> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Post-translational" + spec_group="6"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Post-translational" + spec_group="4"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="14.015650" avge_mass="14.0266" composition="H(2) C"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + </umod:delta> + <umod:alt_name>methyl ester</umod:alt_name> + <umod:xref> + <umod:text>METH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0318</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0338</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0064</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0061</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0063</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0065</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0069</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0336</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0305</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0272</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0076</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0071</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0070</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0073</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0234</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0273</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0317</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0337</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0299</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0072</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11875433</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0105</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Oxidation" full_name="Oxidation or Hydroxylation" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2008-02-15 05:37:07" + approved="0" + record_id="35"> + <umod:specificity hidden="0" site="W" position="Anywhere" classification="Artefact" + spec_group="10"/> + <umod:specificity hidden="0" site="H" position="Anywhere" classification="Artefact" + spec_group="10"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="9"> + <umod:misc_notes>Cysteine sulfenic acid</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="M" position="Anywhere" classification="Artefact" + spec_group="8"> + <umod:NeutralLoss mono_mass="0.000000" avge_mass="0.0000" flag="false" composition="0"/> + <umod:NeutralLoss mono_mass="63.998285" avge_mass="64.1069" flag="false" composition="H(4) C O S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="7"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="6"/> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Artefact" + spec_group="5"/> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>Proline oxidation to glutamic semialdehyde</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="G" position="Any C-term" classification="Pre-translational" + spec_group="11"> + <umod:misc_notes>Hydroxyglycine derivative in amidation pathway</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="15.994915" avge_mass="15.9994" composition="O"> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>HYDR</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0322</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11212008</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11120890</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DOPA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CSEA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14661084</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0026</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15569593</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0205</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0215</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Lagerwerf FM, van de Weert M, Heerma W, Haverkamp J, Rapid Commun Mass Spectrom. 1996;10(15):1905-10</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0029</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0030</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9004526</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0028</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11461766</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0027</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0235</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0146</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14661085</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12781462</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>2057999</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dimethyl" full_name="di-Methylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-18 14:35:31" + approved="1" + record_id="36"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Post-translational" + spec_group="4"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="P" position="Protein N-term" + classification="Post-translational" + spec_group="5"/> + <umod:delta mono_mass="28.031300" avge_mass="28.0532" composition="H(4) C(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>DIMETH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0311</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0068</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14570711</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0067</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12964758</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0075</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0066</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Trimethyl" full_name="tri-Methylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-18 14:31:46" + approved="1" + record_id="37"> + <umod:specificity hidden="1" site="A" position="Protein N-term" + classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="42.046950" avge_mass="42.0797" composition="H(6) C(3)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>12590383</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0074</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0062</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Role of arginine and its methylated derivatives in cancer biology and treatment</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.cancerci.com/content/1/1/3</umod:url> + </umod:xref> + <umod:xref> + <umod:text>J. Hirota et. al., Rapid Commun. Mass Spectrom., 17 371-6 (2003)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>TRIMETH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>RESID gives the delta as 43 Da?</umod:misc_notes> + </umod:mod> + <umod:mod title="Methylthio" full_name="Beta-methylthiolation" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:17:13" + approved="0" + record_id="39"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Multiple" + spec_group="3"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="45.987721" avge_mass="46.0916" composition="H(2) C S"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Methyl methanethiosulfonate</umod:alt_name> + <umod:alt_name>MMTS</umod:alt_name> + <umod:xref> + <umod:text>J. A. Kowalak and K. A. Walsh, Protein Science (1996) 5: 1625-1632</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0232</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>TRC data sheet</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.trc-canada.com/white_papers.lasso</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Applied Biosystems iTRAQ(TM) Reagents Chemistry Reference Guide Part Number 4351918 Rev. A</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>AA0320</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8844851</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0101</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>BMTH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Sulfo" full_name="O-Sulfonation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 11:16:55" + approved="1" + record_id="40"> + <umod:specificity hidden="0" site="Y" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="0" site="T" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="0" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>Sulfitolysis</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="79.956815" avge_mass="80.0632" composition="O(3) S"> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0362</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0361</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>SULF</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0171</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Medzihradszky et al., Mol. Cell. Proteomics 2004, 3, 429-440</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14752058</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0172</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hex" full_name="Hexose" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 14:11:32" + approved="1" + record_id="41"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Other glycosylation" + spec_group="8"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Other glycosylation" + spec_group="7"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other glycosylation" + spec_group="6"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Other glycosylation" + spec_group="4"/> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Other glycosylation" + spec_group="5"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Other glycosylation" + spec_group="3"> + <umod:misc_notes>glycation</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other glycosylation" + spec_group="1"> + <umod:misc_notes>glycation</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="162.052824" avge_mass="162.1406" composition="Hex"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:alt_name>Fructose</umod:alt_name> + <umod:alt_name>Glucose</umod:alt_name> + <umod:alt_name>Galactose</umod:alt_name> + <umod:alt_name>Mannose</umod:alt_name> + <umod:xref> + <umod:text>GLUC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15279557</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0152</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0157</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0327</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0217</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CMAN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Lipoyl" full_name="Lipoyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:06:53" + approved="1" + record_id="42"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="188.032956" avge_mass="188.3103" composition="H(12) C(8) O S(2)"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>PDOC00168</umod:text> + <umod:source>Prosite</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0118</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>LIPY</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3522581</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>This group is normally a substituent on N6 of a lysine residue of an enzyme or other protein</umod:misc_notes> + </umod:mod> + <umod:mod title="HexNAc" full_name="N-Acetylhexosamine" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:10:27" + approved="1" + record_id="43"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Other glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="203.079373" avge_mass="203.1925" composition="HexNAc"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>GLCN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0151</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0154</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3086323</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0155</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>The amine derivative of a hexose formed by replacing a hydroxyl group with an amino group.(+acetyl group)</umod:misc_notes> + </umod:mod> + <umod:mod title="Farnesyl" full_name="Farnesylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:11:38" + approved="1" + record_id="44"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="204.187801" avge_mass="204.3511" composition="H(24) C(15)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="15"/> + </umod:delta> + <umod:xref> + <umod:text>15609361</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0102</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FARN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Myristoyl" full_name="Myristoylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:13:17" + approved="1" + record_id="45"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="G" position="Any N-term" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="210.198366" avge_mass="210.3556" composition="H(26) C(14) O"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>PDOC00008</umod:text> + <umod:source>Prosite</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0059</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0307</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0078</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>MYRI</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PyridoxalPhosphate" full_name="Pyridoxal phosphate" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:35:42" + approved="1" + record_id="46"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="229.014009" avge_mass="229.1266" composition="H(8) C(8) N O(5) P"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Biochemistry; D.Voet and J.G.Voet WILEY(p728)</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0119</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PLP</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>The co-enzyme derivative of vitamin B6. Forms Schiff\'s bases of substrate amino acids during catalysis of transamination, decarboxylation and racemisation reactions.</umod:misc_notes> + </umod:mod> + <umod:mod title="Palmitoyl" full_name="Palmitoylation" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:38:43" + approved="1" + record_id="47"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="4"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="5"/> + <umod:delta mono_mass="238.229666" avge_mass="238.4088" composition="H(30) C(16) O"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0080</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0079</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0106</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0077</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PALM</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0339</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0060</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Palmitoylation is a post-translational modification that consists in the addition of a 16 carbons fatty acid, palmitate, to a cysteine residue through the creation of a thioester link.</umod:misc_notes> + </umod:mod> + <umod:mod title="GeranylGeranyl" full_name="Geranyl-geranyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 15:47:48" + approved="1" + record_id="48"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="272.250401" avge_mass="272.4681" composition="H(32) C(20)"> + <umod:element symbol="H" number="32"/> + <umod:element symbol="C" number="20"/> + </umod:delta> + <umod:xref> + <umod:text>AA0104</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15609361</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>GERA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phosphopantetheine" full_name="Phosphopantetheine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 16:00:24" + approved="1" + record_id="49"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="340.085794" avge_mass="340.3330" + composition="H(21) C(11) N(2) O(6) P S"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0150</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PPAN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Protein which contains at least one phosphopantetheine as the prosthetic group. In acyl carrier proteins (ACP) for example, it serves as a \'swinging arm\' for the attachment of activated fatty acid and amino-acid groups.</umod:misc_notes> + </umod:mod> + <umod:mod title="FAD" full_name="Flavin adenine dinucleotide" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-16 17:16:18" + approved="1" + record_id="50"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="783.141486" avge_mass="783.5339" + composition="H(31) C(27) N(9) O(15) P(2)"> + <umod:element symbol="H" number="31"/> + <umod:element symbol="C" number="27"/> + <umod:element symbol="N" number="9"/> + <umod:element symbol="O" number="15"/> + <umod:element symbol="P" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0143</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Structure</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.aw-bc.com/mathews/EF/FAD.GIF</umod:url> + </umod:xref> + <umod:xref> + <umod:text>AA0144</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0145</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0221</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FAD</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Tripalmitate" full_name="N-acyl diglyceride cysteine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-18 11:47:54" + approved="1" + record_id="51"> + <umod:specificity hidden="1" site="C" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="788.725777" avge_mass="789.3049" composition="H(96) C(51) O(5)"> + <umod:element symbol="H" number="96"/> + <umod:element symbol="C" number="51"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>10356335</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Guanidinyl" full_name="Guanidination" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-10-15 19:58:44" + approved="1" + record_id="52"> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="42.021798" avge_mass="42.0400" composition="H(2) C N(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="2"/> + </umod:delta> + <umod:alt_name>homoarginine</umod:alt_name> + <umod:xref> + <umod:text>11078590</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>ASMS 2001 abstract</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.indiana.edu/~reillyjp/ASMS2001posters/beardsley_poster.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>11821862</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11085420</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Anal. Biochem. 287, p110-117, 2000</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Specific for sidechain of lysine. Does not modify the N-termini except for glycine at a slower rate than the side chain of lysine.</umod:misc_notes> + </umod:mod> + <umod:mod title="HNE" full_name="4-hydroxynonenal (HNE)" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-08-19 19:17:11" + date_time_modified="2006-11-14 11:38:12" + approved="1" + record_id="53"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="156.115030" avge_mass="156.2221" composition="H(16) C(9) O(2)"> + <umod:element symbol="H" number="16"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>11327326</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Poli G, Schaur RJ., IUBMB Life 2000 Oct-Nov;50(4-5):315-21</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>A lipid-type modification. HNE forms a Michael addition product on Cysteine, Histidine and Lysines. Unusually, it doesn\'t replace a hydrogen on the amino acid side chain.</umod:misc_notes> + </umod:mod> + <umod:mod title="Glucuronyl" full_name="N-glucuronylation" username_of_poster="jcottrell" + group_of_poster="users" + date_time_posted="2002-10-01 21:36:48" + date_time_modified="2006-10-16 17:26:21" + approved="1" + record_id="54"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:delta mono_mass="176.032088" avge_mass="176.1241" composition="H(8) C(6) O(6)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:alt_name>glucuronosyl</umod:alt_name> + <umod:xref> + <umod:text>AA0291</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0058</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Lin, T.S. Kolattukudy, P.E., Eur. J. Biochem. 106, 341-351, 1980</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>7398618</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>The addition of a sugar unit to a protein amino acid, e.g. the addition of glycan chains to proteins. Addition of glucuronic acid. Observed for N-term G</umod:misc_notes> + </umod:mod> + <umod:mod title="Glutathione" full_name="glutathione disulfide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2002-10-03 09:10:19" + date_time_modified="2006-10-16 15:51:52" + approved="1" + record_id="55"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="305.068156" avge_mass="305.3076" + composition="H(15) C(10) N(3) O(6) S"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>3083866</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8344916</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0229</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>GLUT</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Acetyl:2H(3)" + full_name="Acetate labeling reagent (N-term & K) (heavy form, +3amu)" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 16:41:56" + date_time_modified="2006-10-16 10:02:50" + approved="1" + record_id="56"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="45.029395" avge_mass="45.0552" composition="H(-1) 2H(3) C(2) O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>N-trideuteriumacetoxy</umod:alt_name> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11999733</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Propionyl" + full_name="Propionate labeling reagent light form (N-term & K)" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 16:52:38" + date_time_modified="2006-10-16 10:17:00" + approved="1" + record_id="58"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="56.026215" avge_mass="56.0633" composition="H(4) C(3) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11999733</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Propionyl:13C(3)" + full_name="Propionate labeling reagent heavy form (+3amu), N-term & K" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 16:55:47" + date_time_modified="2006-10-16 10:27:21" + approved="1" + record_id="59"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="59.036279" avge_mass="59.0412" composition="H(4) 13C(3) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="13C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. 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Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GIST-Quat:2H(6)" + full_name="Quaternary amine labeling reagent heavy form (+6amu), N-term & K" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 17:12:27" + date_time_modified="2006-10-16 13:40:56" + approved="1" + record_id="62"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"> + <umod:NeutralLoss mono_mass="65.111160" avge_mass="65.1472" flag="false" + composition="H(3) 2H(6) C(3) N"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:NeutralLoss mono_mass="65.111160" avge_mass="65.1472" flag="false" + composition="H(3) 2H(6) C(3) N"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:delta mono_mass="133.137375" avge_mass="133.2212" composition="H(7) 2H(6) C(7) N O"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. 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Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Succinyl" + full_name="Succinic anhydride labeling reagent light form (N-term & K)" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 17:17:07" + date_time_modified="2006-10-16 12:40:39" + approved="1" + record_id="64"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="100.016044" avge_mass="100.0728" composition="H(4) C(4) O(3)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0130</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Succinyl:2H(4)" + full_name="Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term & K" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 17:19:51" + date_time_modified="2006-10-16 12:42:10" + approved="1" + record_id="65"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="104.041151" avge_mass="104.0974" composition="2H(4) C(4) O(3)"> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Succinyl:13C(4)" + full_name="Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), N-term & K" + username_of_poster="penner" + group_of_poster="users" + date_time_posted="2002-10-16 17:23:58" + date_time_modified="2006-10-16 12:41:49" + approved="1" + record_id="66"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="104.029463" avge_mass="104.0434" composition="H(4) 13C(4) O(3)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="13C" number="4"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11857757</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12175151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="probiotinhydrazide" + full_name="oxidized proline biotinylated with biotin hydrazide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:56:20" + date_time_modified="2006-11-14 12:12:19" + approved="0" + record_id="357"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="258.115047" avge_mass="258.3405" + composition="H(18) C(10) N(4) O(2) S"> + <umod:element symbol="H" number="18"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15174056</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Pro->pyro-Glu" full_name="proline oxidation to pyroglutamic acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:58:42" + date_time_modified="2006-10-14 10:03:34" + approved="1" + record_id="359"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="13.979265" avge_mass="13.9835" composition="H(-2) O"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>10717661</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="His->Asn" full_name="histidine oxidation to aspargine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:43:27" + date_time_modified="2008-01-24 15:40:23" + approved="1" + record_id="348"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"> + <umod:misc_notes>Could also be classed as chemical derivative</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-23.015984" avge_mass="-23.0366" composition="H(-1) C(-2) N(-1) O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="His->Asp" full_name="histidine oxidation to aspartic acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:44:32" + date_time_modified="2008-01-24 15:40:44" + approved="1" + record_id="349"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"> + <umod:misc_notes>Could also be classed as chemical derivative</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-22.031969" avge_mass="-22.0519" + composition="H(-2) C(-2) N(-2) O(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Trp->Hydroxykynurenin" + full_name="tryptophan oxidation to hydroxykynurenin" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:47:20" + date_time_modified="2006-11-14 17:40:45" + approved="1" + record_id="350"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="19.989829" avge_mass="19.9881" composition="C(-1) O(2)"> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Degradation of the amino acids Isoleucine, Leucine and Tryptophan</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.lbqp.unb.br/bioq/htm/aulas2D/deg_aa_ile_leu_trp.htm?reload_coolmenus</umod:url> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(4)C(3)" full_name="Propionaldehyde +40" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-08-12 20:04:01" + date_time_modified="2006-10-15 18:30:52" + approved="1" + record_id="256"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="40.031300" avge_mass="40.0639" composition="H(4) C(3)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + </umod:delta> + </umod:mod> + <umod:mod title="Delta:H(4)C(2)" full_name="Acetaldehyde +28" username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-08-12 20:02:38" + date_time_modified="2006-10-15 17:55:18" + approved="1" + record_id="255"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="28.031300" avge_mass="28.0532" composition="H(4) C(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:misc_notes>Reduction of Schiff base formed between K amino group and acetaldehyde</umod:misc_notes> + </umod:mod> + <umod:mod title="Cys->Dha" full_name="Dehydroalanine (from Cysteine)" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-02 17:31:11" + date_time_modified="2006-10-13 15:27:46" + approved="1" + record_id="368"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-33.987721" avge_mass="-34.0809" composition="H(-2) S(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>11212008</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Arg->GluSA" full_name="Arginine oxidation to glutamic semialdehyde" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:38:24" + date_time_modified="2006-11-16 15:25:28" + approved="1" + record_id="344"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-43.053433" avge_mass="-43.0711" composition="H(-5) C(-1) N(-3) O"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Arginine oxidation to gamma-glutamyl semialdehyde</umod:alt_name> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Jesus Requena, Chien-Chung Chao, Rodney L. Levine, and Earl R. Stadtman, Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins, PNAS 98 69-74 (2001)</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.pnas.org/cgi/content/full/98/1/69</umod:url> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>1680314</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Trioxidation" full_name="cysteine oxidation to cysteic acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:39:38" + date_time_modified="2006-10-16 10:12:44" + approved="1" + record_id="345"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="47.984744" avge_mass="47.9982" composition="O(3)"> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>14678012</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Iminobiotin" full_name="Iminobiotinylation" + username_of_poster="toppolzer" + group_of_poster="users" + date_time_posted="2002-11-25 16:01:48" + date_time_modified="2006-10-16 15:26:37" + approved="1" + record_id="89"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="225.093583" avge_mass="225.3106" composition="H(15) C(10) N(3) O S"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>9750125</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ESP" full_name="ESP-Tag light d0" username_of_poster="toppolzer" + group_of_poster="users" + date_time_posted="2002-11-25 16:12:50" + date_time_modified="2006-10-16 15:58:19" + approved="1" + record_id="90"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="338.177647" avge_mass="338.4682" + composition="H(26) C(16) N(4) O(2) S"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Poster abstract P-48</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.wzw.tum.de/proteomik/forum2003/Posters-Abstracts.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="ESP:2H(10)" full_name="ESP-Tag heavy d10" username_of_poster="toppolzer" + group_of_poster="users" + date_time_posted="2002-11-25 16:18:58" + date_time_modified="2006-10-16 16:03:06" + approved="1" + record_id="91"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="348.240414" avge_mass="348.5299" + composition="H(16) 2H(10) C(16) N(4) O(2) S"> + <umod:element symbol="H" number="16"/> + <umod:element symbol="2H" number="10"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Poster abstract P-48</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.wzw.tum.de/proteomik/forum2003/Posters-Abstracts.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="NHS-LC-Biotin" full_name="NHS-LC-Biotin" username_of_poster="toppolzer" + group_of_poster="users" + date_time_posted="2002-12-04 09:55:19" + date_time_modified="2006-11-14 11:14:57" + approved="0" + record_id="92"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="339.161662" avge_mass="339.4530" + composition="H(25) C(16) N(3) O(3) S"> + <umod:element symbol="H" number="25"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Introduction to Protein Labeling</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:url> + </umod:xref> + <umod:xref> + <umod:text>EZ-Link Sulfo-NHS-Biotin Reagents</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=8D38BA83-EFDC-421A-853F-E96EBA380612</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="EDT-maleimide-PEO-biotin" full_name="EDT-maleimide-PEO-biotin" + username_of_poster="take" + group_of_poster="users" + date_time_posted="2002-12-27 09:08:56" + date_time_modified="2006-11-14 11:15:06" + approved="0" + record_id="93"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="601.206246" avge_mass="601.8021" + composition="H(39) C(25) N(5) O(6) S(3)"> + <umod:element symbol="H" number="39"/> + <umod:element symbol="C" number="25"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>EZ-Link Maleimide PEOn-Biotin (n = 2 and 11)</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=01031005</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="IMID" full_name="IMID d0" username_of_poster="Liao" + group_of_poster="users" + date_time_posted="2003-01-09 04:14:06" + date_time_modified="2006-10-16 10:33:45" + approved="1" + record_id="94"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="68.037448" avge_mass="68.0773" composition="H(4) C(3) N(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="2"/> + </umod:delta> + <umod:alt_name>2-methoxy-4,5-dihydro-1H-imidazole derivative</umod:alt_name> + <umod:alt_name>Lys imidazole</umod:alt_name> + <umod:xref> + <umod:text>11746907</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Rapid Communications in Mass Spectrometry, Volume 15, Issue 24 , Pages 2387 - 2392</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1002/rcm.517</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Agilent Lys Tag 4H Reagent Kit</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chem.agilent.com/cag/lystag.asp</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Poster: Kelly Zhang, Gordon Nicol, Nina Zolotarjova, Cory Szafranski, Jerome Bailey, Liang-Sheng Yang, and Barry Boyes</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chem.agilent.com/cag/other/IMTHUPO2003.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="IMID:2H(4)" full_name="IMID d4" username_of_poster="Liao" + group_of_poster="users" + date_time_posted="2003-01-09 04:15:25" + date_time_modified="2006-10-16 11:06:13" + approved="1" + record_id="95"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="72.062555" avge_mass="72.1019" composition="2H(4) C(3) N(2)"> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="2"/> + </umod:delta> + <umod:alt_name>2-methoxy-4,5-dihydro-1H-imidazole derivative</umod:alt_name> + <umod:xref> + <umod:text>Rapid Communications in Mass Spectrometry, Volume 15, Issue 24 , Pages 2387 - 2392</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1002/rcm.517</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Agilent Lys Tag 4H Reagent Kit</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chem.agilent.com/cag/lystag.asp</umod:url> + </umod:xref> + <umod:xref> + <umod:text>11746907</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Poster: Kelly Zhang, Gordon Nicol, Nina Zolotarjova, Cory Szafranski, Jerome Bailey, Liang-Sheng Yang, and Barry Boyes</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chem.agilent.com/cag/other/IMTHUPO2003.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Lysbiotinhydrazide" + full_name="oxidized Lysine biotinylated with biotin hydrazide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:51:13" + date_time_modified="2006-11-14 12:12:01" + approved="0" + record_id="353"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="241.088497" avge_mass="241.3100" + composition="H(15) C(10) N(3) O(2) S"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Propionamide:2H(3)" full_name="Acrylamide d3" username_of_poster="Liao" + group_of_poster="users" + date_time_posted="2003-01-14 08:10:30" + date_time_modified="2006-10-16 11:07:07" + approved="1" + record_id="97"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="74.055944" avge_mass="74.0964" composition="H(2) 2H(3) C(3) N O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Nitro" full_name="Oxidation to nitro" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:52:38" + date_time_modified="2006-10-16 10:02:15" + approved="1" + record_id="354"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="44.985078" avge_mass="44.9976" composition="H(-1) N O(2)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>8839040</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-C" full_name="Applied Biosystems cleavable ICAT(TM) light" + username_of_poster="tpjd2" + group_of_poster="users" + date_time_posted="2003-01-27 10:27:11" + date_time_modified="2006-10-16 15:32:17" + approved="1" + record_id="105"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="227.126991" avge_mass="227.2603" composition="H(17) C(10) N(3) O(3)"> + <umod:element symbol="H" number="17"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>ICAT page from the Royal Society of Chemistry</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/icat.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Applied Biosystems product page</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600902</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Cleavable ICAT Reagent Kit for Protein Labeling</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04333373.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(2)C(2)" full_name="Acetaldehyde +26" username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-08-12 20:01:03" + date_time_modified="2006-10-14 19:44:29" + approved="1" + record_id="254"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="26.015650" avge_mass="26.0373" composition="H(2) C(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>7744761</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Lys modification is formation of Schiff base.</umod:misc_notes> + </umod:mod> + <umod:mod title="Trp->Kynurenin" full_name="tryptophan oxidation to kynurenin" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:48:33" + date_time_modified="2006-10-14 09:39:53" + approved="1" + record_id="351"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="3.994915" avge_mass="3.9887" composition="C(-1) O"> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Lys->Allysine" full_name="Lysine oxidation to aminoadipic semialdehyde" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:49:59" + date_time_modified="2006-10-13 18:27:28" + approved="1" + record_id="352"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-1.031634" avge_mass="-1.0311" composition="H(-3) N(-1) O"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0121</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>ALLYS</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11120890</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-C:13C(9)" full_name="Applied Biosystems cleavable ICAT(TM) heavy" + username_of_poster="tpjd2" + group_of_poster="users" + date_time_posted="2003-01-27 10:32:53" + date_time_modified="2006-10-16 15:34:14" + approved="1" + record_id="106"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="236.157185" avge_mass="236.1942" + composition="H(17) C 13C(9) N(3) O(3)"> + <umod:element symbol="H" number="17"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="13C" number="9"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Cleavable ICAT Reagent Kit for Protein Labeling</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04333373.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Applied Biosystems product page</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600902</umod:url> + </umod:xref> + <umod:xref> + <umod:text>ICAT page from the Royal Society of Chemistry</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/icat.htm</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="FormylMet" full_name="Addition of N-formyl met" + username_of_poster="jphilip" + group_of_poster="users" + date_time_posted="2003-01-27 18:24:14" + date_time_modified="2006-10-16 14:08:15" + approved="1" + record_id="107"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Pre-translational" + spec_group="1"> + <umod:misc_notes>only with Listeria monocytogenes (gram-positive bacteria)</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="159.035399" avge_mass="159.2062" composition="H(9) C(6) N O(2) S"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0021</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>10825024</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8758896</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Nethylmaleimide" full_name="N-ethylmaleimide on cysteines" + username_of_poster="Pflieger" + group_of_poster="users" + date_time_posted="2003-01-30 09:52:51" + date_time_modified="2006-10-16 13:36:10" + approved="1" + record_id="108"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="125.047679" avge_mass="125.1253" composition="H(7) C(6) N O(2)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>CysNEM</umod:alt_name> + <umod:xref> + <umod:text>reaction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemistry.ucsc.edu/~fink/231/Image118.gif</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12777388</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11813307</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="OxLysBiotinRed" + full_name="Oxidized lysine biotinylated with biotin-LC-hydrazide, reduced" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 00:53:43" + date_time_modified="2006-11-14 12:10:49" + approved="0" + record_id="112"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="354.172562" avge_mass="354.4676" + composition="H(26) C(16) N(4) O(3) S"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="IBTP" full_name="Thio Ether Formation - BTP Adduct" + username_of_poster="MRCDunn" + group_of_poster="users" + date_time_posted="2003-03-13 09:36:40" + date_time_modified="2006-10-16 15:52:42" + approved="1" + record_id="119"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="316.138088" avge_mass="316.3759" composition="H(21) C(22) P"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>J. Biol. Chem 2002 vol277 pp17048-17056</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11861642</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="OxLysBiotin" + full_name="Oxidized lysine biotinylated with biotin-LC-hydrazide" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 01:25:11" + date_time_modified="2006-11-14 12:10:53" + approved="0" + record_id="113"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="352.156911" avge_mass="352.4518" + composition="H(24) C(16) N(4) O(3) S"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="OxProBiotinRed" + full_name="Oxidized proline biotinylated with biotin-LC-hydrazide, reduced" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 01:34:28" + date_time_modified="2006-11-14 12:11:11" + approved="0" + record_id="114"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="371.199111" avge_mass="371.4982" + composition="H(29) C(16) N(5) O(3) S"> + <umod:element symbol="H" number="29"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="OxProBiotin" + full_name="Oxidized Proline biotinylated with biotin-LC-hydrazide" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 01:35:44" + date_time_modified="2006-11-14 12:11:17" + approved="0" + record_id="115"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="369.183461" avge_mass="369.4823" + composition="H(27) C(16) N(5) O(3) S"> + <umod:element symbol="H" number="27"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="OxArgBiotin" + full_name="Oxidized arginine biotinylated with biotin-LC-hydrazide" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 01:41:19" + date_time_modified="2006-11-14 12:11:31" + approved="0" + record_id="116"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="310.135113" avge_mass="310.4118" + composition="H(22) C(15) N(2) O(3) S"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Reference http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>http://web.indstate.edu/thcme/mwking/nitrogen-metabolism.html#urea</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="OxArgBiotinRed" + full_name="Oxidized arginine biotinylated with biotin-LC-hydrazide, reduced" + username_of_poster="S_Lee" + group_of_poster="users" + date_time_posted="2003-02-21 01:43:00" + date_time_modified="2006-11-14 12:11:35" + approved="0" + record_id="117"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="312.150763" avge_mass="312.4277" + composition="H(24) C(15) N(2) O(3) S"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>http://web.indstate.edu/thcme/mwking/nitrogen-metabolism.html#urea</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="EDT-iodoacetyl-PEO-biotin" full_name="EDT-iodo-PEO-biotin" + username_of_poster="take" + group_of_poster="users" + date_time_posted="2003-02-24 07:18:42" + date_time_modified="2006-10-16 17:01:15" + approved="1" + record_id="118"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="490.174218" avge_mass="490.7034" + composition="H(34) C(20) N(4) O(4) S(3)"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="3"/> + </umod:delta> + </umod:mod> + <umod:mod title="GlyGly" full_name="ubiquitinylation residue" + username_of_poster="gielbert" + group_of_poster="users" + date_time_posted="2003-04-30 13:32:37" + date_time_modified="2008-04-21 18:24:57" + approved="1" + record_id="121"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Other" spec_group="3"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="4"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="114.042927" avge_mass="114.1026" composition="H(6) C(4) N(2) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>glycineglycine</umod:alt_name> + <umod:xref> + <umod:text>Grou et al., J Biol Chem. 2008 Mar 22; Epub</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.jbc.org/cgi/content/abstract/M800402200v1</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Wang et al., J Cell Biol. 2007 May 21;177(4):613-24</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/pubmed/17502423</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12872131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>The Ubiquitin System for Protein Modification and Degradation</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.nottingham.ac.uk/biochemcourses/students/ub/ubindex.html</umod:url> + </umod:xref> + <umod:misc_notes>The two glycine residues left on ubiquitinylated lysine after tryptic digestion</umod:misc_notes> + </umod:mod> + <umod:mod title="Formyl" full_name="Formylation" username_of_poster="pnacman" + group_of_poster="users" + date_time_posted="2003-05-01 13:28:36" + date_time_modified="2006-11-14 12:01:57" + approved="1" + record_id="122"> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="5"> + <umod:misc_notes>A protein in which either the N-terminal N-formylmethionine has not been processed by the methionyl-tRNA formyltransferase or which is posttranslationally modified by the attachment of at least one formyl group.</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Artefact" + spec_group="4"> + <umod:misc_notes>Can occur under CNBr cleavage conditions (70% HCOOH)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Artefact" + spec_group="1"> + <umod:misc_notes>Can occur under CNBr cleavage conditions (70% HCOOH)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Artefact" + spec_group="2"> + <umod:misc_notes>Can occur under CNBr cleavage conditions (70% HCOOH)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Artefact" + spec_group="3"> + <umod:misc_notes>Can occur under CNBr cleavage conditions (70% HCOOH)</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="27.994915" avge_mass="28.0101" composition="C O"> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0211</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15799070</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0021</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FORM</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0384</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0057</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0384</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-H" full_name="N-iodoacetyl, p-chlorobenzyl-12C6-glucamine" + username_of_poster="allis" + group_of_poster="users" + date_time_posted="2003-05-07 19:54:20" + date_time_modified="2006-10-16 16:02:00" + approved="1" + record_id="123"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="345.097915" avge_mass="345.7754" composition="H(20) C(15) N O(6) Cl"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="Cl" number="1"/> + </umod:delta> + <umod:alt_name>Harbury glyco-ICAT C12</umod:alt_name> + <umod:xref> + <umod:text>Silverman, Harbury, J. Biol. Chem. 2002, 277, 34, pp. 30968-30975</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12185208</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="ICAT-H:13C(6)" full_name="N-iodoacetyl, p-chlorobenzyl-13C6-glucamine" + username_of_poster="allis" + group_of_poster="users" + date_time_posted="2003-05-07 19:56:12" + date_time_modified="2006-10-16 16:04:02" + approved="1" + record_id="124"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="351.118044" avge_mass="351.7313" + composition="H(20) C(9) 13C(6) N O(6) Cl"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="Cl" number="1"/> + </umod:delta> + <umod:alt_name>Harbury glyco-ICAT C13</umod:alt_name> + <umod:xref> + <umod:text>Silverman, Harbury, J. Biol. Chem. 2002, 277, 34, pp. 30968-30975</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12185208</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cation:K" full_name="Replacement of proton by potassium" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-15 18:29:43" + date_time_modified="2006-10-18 11:17:39" + approved="1" + record_id="530"> + <umod:specificity hidden="1" site="C-term" position="Any C-term" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="37.955882" avge_mass="38.0904" composition="H(-1) K"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="K" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thioacyl" full_name="thioacylation of primary amines (N-term and Lys)" + username_of_poster="rabah" + group_of_poster="users" + date_time_posted="2003-06-05 13:38:19" + date_time_modified="2006-10-16 12:37:13" + approved="1" + record_id="126"> + <umod:specificity hidden="1" site="N-term" position="Anywhere" classification="Other" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="87.998285" avge_mass="88.1283" composition="H(4) C(3) O S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>3,3-Dithio-bis-(sulfosuccinimidyl)propionate</umod:alt_name> + <umod:xref> + <umod:text>Lomant, A.J. and Fairbanks, G., J.Mol. Biol. 104, 243-261 (1976)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Lee,W.T. and Conrad, D.H. 1985, J. Immunol. 134:518</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11710128</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3155470</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>957432</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Fluoro" full_name="fluorophenylalanine replacement of phenylalanine" + username_of_poster="jschulte" + group_of_poster="users" + date_time_posted="2003-06-19 19:54:25" + date_time_modified="2007-07-08 18:42:53" + approved="1" + record_id="127"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Non-standard residue" + spec_group="2"/> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Non-standard residue" + spec_group="1"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Non-standard residue" + spec_group="3"/> + <umod:delta mono_mass="17.990578" avge_mass="17.9905" composition="H(-1) F"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="F" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>1093385</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Fluorescein" + full_name="5-Iodoacetamidofluorescein (Molecular Probe, Eugene, OR)" + username_of_poster="Philip" + group_of_poster="users" + date_time_posted="2003-06-25 02:58:18" + date_time_modified="2006-10-16 16:42:41" + approved="1" + record_id="128"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="388.082112" avge_mass="388.3497" composition="H(14) C(22) N O(6)"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:xref> + <umod:text>5-iodoacetamidofluorescein, [63368-54-7]</umod:text> + <umod:source>CAS Registry</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3578767</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Gorman, J. J., Eur. J. Biochem 1987, 168-9</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Gorman, J. J., Anal Biochem 1984, 160, 376</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3311742</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Iodo" full_name="Iodination" username_of_poster="brettsp" + group_of_poster="users" + date_time_posted="2003-07-10 15:43:17" + date_time_modified="2006-10-16 13:38:03" + approved="1" + record_id="129"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="125.896648" avge_mass="125.8965" composition="H(-1) I"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="I" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>2026710</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15627961</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diiodo" full_name="di-Iodination" username_of_poster="brettsp" + group_of_poster="users" + date_time_posted="2003-07-10 15:49:42" + date_time_modified="2006-10-16 15:45:24" + approved="1" + record_id="130"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="251.793296" avge_mass="251.7931" composition="H(-2) I(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="I" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>15627961</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Triiodo" full_name="tri-Iodination" username_of_poster="brettsp" + group_of_poster="users" + date_time_posted="2003-07-10 15:51:32" + date_time_modified="2006-10-16 16:36:49" + approved="1" + record_id="131"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="377.689944" avge_mass="377.6896" composition="H(-3) I(3)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="I" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>2026710</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15627961</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Myristoleyl" full_name="(cis-delta 5)-tetradecaenoyl" + username_of_poster="tomneubert" + group_of_poster="users" + date_time_posted="2003-07-18 21:30:51" + date_time_modified="2006-10-16 15:11:18" + approved="1" + record_id="134"> + <umod:specificity hidden="1" site="G" position="Protein N-term" classification="Co-translational" + spec_group="1"/> + <umod:delta mono_mass="208.182715" avge_mass="208.3398" composition="H(24) C(14) O"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>myristoyl with one double bond</umod:alt_name> + <umod:alt_name>C14:1 acylation</umod:alt_name> + <umod:xref> + <umod:text>Neubert TA, Johnson RS, Hurley JB, Walsh KA (1992). The rod transducin alpha subunit amino terminus is heterogeneously fatty acylated. J Biol Chem. 267(26):18274-7.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>1326520</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Found on vision signal transduction proteins</umod:misc_notes> + </umod:mod> + <umod:mod title="Pro->Pyrrolidinone" full_name="Proline oxidation to pyrrolidinone" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 23:00:19" + date_time_modified="2006-10-13 15:37:42" + approved="1" + record_id="360"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-30.010565" avge_mass="-30.0260" composition="H(-2) C(-1) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Myristoyl+Delta:H(-4)" + full_name="(cis,cis-delta 5, delta 8)-tetradecadienoyl" + username_of_poster="tomneubert" + group_of_poster="users" + date_time_posted="2003-07-18 21:36:44" + date_time_modified="2006-10-16 15:10:51" + approved="1" + record_id="135"> + <umod:specificity hidden="1" site="G" position="Protein N-term" classification="Co-translational" + spec_group="1"/> + <umod:delta mono_mass="206.167065" avge_mass="206.3239" composition="H(22) C(14) O"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>myristoyl with 2 double bonds</umod:alt_name> + <umod:alt_name>C14:2 fatty acylation</umod:alt_name> + <umod:xref> + <umod:text>Neubert TA, Johnson RS, Hurley JB, Walsh KA (1992). The rod transducin alpha subunit amino terminus is heterogeneously fatty acylated. J Biol Chem. 267(26):18274-7.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>1326520</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Found on vision signal transduction proteins</umod:misc_notes> + </umod:mod> + <umod:mod title="Benzoyl" full_name="labeling reagent light form (N-term & K)" + username_of_poster="samirjulka" + group_of_poster="users" + date_time_posted="2003-07-31 22:24:05" + date_time_modified="2006-10-16 12:41:22" + approved="1" + record_id="136"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="104.026215" avge_mass="104.1061" composition="H(4) C(7) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Julka,S.Regnier,F.E Anal Chem. 2004 Oct 1;76(19):5799-806.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15456300</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hex(5)HexNAc(2)" full_name="N-linked glycan core" + username_of_poster="tpjd2" + group_of_poster="users" + date_time_posted="2003-08-06 11:31:37" + date_time_modified="2006-10-16 17:22:04" + approved="1" + record_id="137"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1216.422863" avge_mass="1217.0880" composition="Hex(5) HexNAc(2)"> + <umod:element symbol="H" number="76"/> + <umod:element symbol="C" number="46"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="35"/> + </umod:delta> + <umod:alt_name>Man5</umod:alt_name> + <umod:misc_notes>Core structure of high-mannose N-linked oligosaccharides</umod:misc_notes> + </umod:mod> + <umod:mod title="Dansyl" full_name="5-dimethylaminonaphthalene-1-sulfonyl" + username_of_poster="allis" + group_of_poster="users" + date_time_posted="2003-08-19 02:51:24" + date_time_modified="2006-10-16 15:36:09" + approved="1" + record_id="139"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="233.051049" avge_mass="233.2862" composition="H(11) C(12) N O(2) S"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>dansyl chloride [605-65-2]</umod:text> + <umod:source>CAS Registry</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="a-type-ion" full_name="ISD a-series (C-Term)" + username_of_poster="suckau" + group_of_poster="users" + date_time_posted="2003-09-02 16:17:09" + date_time_modified="2006-10-14 07:46:22" + approved="1" + record_id="140"> + <umod:specificity hidden="1" site="C-term" position="Any C-term" classification="Other" + spec_group="1"> + <umod:misc_notes>Virtual Modification for MS/MS of a-type ions</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-29.002740" avge_mass="-29.0180" composition="H(-1) C(-1) O(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:alt_name>Decarboxylation of C-terminus as reaction inside the mass spectrometer</umod:alt_name> + <umod:xref> + <umod:text>14588022</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>D. Suckau, A. Resemann, Anal. Chem., 75(21):5817-24 (2003)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>MS/MS experiments of mass spectrometric a-ions (MS^3) can be used for protein identification by library searching. T3-sequencing is such a technique (see reference). Search engines must recognize this \'virtual modification\' for this purpose.</umod:misc_notes> + </umod:mod> + <umod:mod title="Amidine" + full_name="amidination of lysines or N-terminal amines with methyl acetimidate" + username_of_poster="pnacman" + group_of_poster="users" + date_time_posted="2003-09-25 11:04:41" + date_time_modified="2006-10-15 18:32:25" + approved="1" + record_id="141"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="41.026549" avge_mass="41.0519" composition="H(3) C(2) N"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>ASMS 2004 abstract</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.indiana.edu/~reillyjp/ASMS2004/janecki_Ext-Abs%20Amidination.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12643539</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>6273432</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="HexNAc(1)dHex(1)" full_name="HexNAc1dHex1" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:28:45" + date_time_modified="2006-10-16 16:03:39" + approved="1" + record_id="142"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="349.137281" avge_mass="349.3337" composition="dHex HexNAc"> + <umod:element symbol="H" number="23"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="9"/> + </umod:delta> + </umod:mod> + <umod:mod title="HexNAc(2)" full_name="HexNAc2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:37:55" + date_time_modified="2006-10-16 16:43:09" + approved="1" + record_id="143"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="406.158745" avge_mass="406.3850" composition="HexNAc(2)"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="10"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(3)" full_name="Hex3" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:39:30" + date_time_modified="2006-10-16 16:59:36" + approved="1" + record_id="144"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="486.158471" avge_mass="486.4218" composition="Hex(3)"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="O" number="15"/> + </umod:delta> + </umod:mod> + <umod:mod title="HexNAc(1)dHex(2)" full_name="HexNAc1dHex2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:40:57" + date_time_modified="2006-10-16 17:01:52" + approved="1" + record_id="145"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="495.195190" avge_mass="495.4749" composition="dHex(2) HexNAc"> + <umod:element symbol="H" number="33"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="13"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(1)dHex(1)" full_name="Hex1HexNAc1dHex1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:42:27" + date_time_modified="2006-10-16 17:02:06" + approved="1" + record_id="146"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="511.190105" avge_mass="511.4743" composition="dHex Hex HexNAc"> + <umod:element symbol="H" number="33"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="14"/> + </umod:delta> + </umod:mod> + <umod:mod title="HexNAc(2)dHex(1)" full_name="HexNAc2dHex1" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:44:18" + date_time_modified="2006-10-16 17:04:11" + approved="1" + record_id="147"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="552.216654" avge_mass="552.5262" composition="dHex HexNAc(2)"> + <umod:element symbol="H" number="36"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="14"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(2)" full_name="Hex1HexNAc2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:48:18" + date_time_modified="2006-10-16 17:04:35" + approved="1" + record_id="148"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="568.211569" avge_mass="568.5256" composition="Hex HexNAc(2)"> + <umod:element symbol="H" number="36"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="15"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(1)NeuAc(1)" full_name="Hex1HexNAc1NeuAc1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:51:19" + date_time_modified="2007-10-20 19:29:29" + approved="1" + record_id="149"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="O-linked glycosylation" + spec_group="2"/> + <umod:delta mono_mass="656.227613" avge_mass="656.5877" composition="Hex HexNAc NeuAc"> + <umod:element symbol="H" number="40"/> + <umod:element symbol="C" number="25"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="18"/> + </umod:delta> + <umod:xref> + <umod:text>Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="HexNAc(2)dHex(2)" full_name="HexNAc2dHex2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:52:36" + date_time_modified="2006-10-16 17:11:45" + approved="1" + record_id="150"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="698.274563" avge_mass="698.6674" composition="dHex(2) HexNAc(2)"> + <umod:element symbol="H" number="46"/> + <umod:element symbol="C" number="28"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="18"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(2)Pent(1)" full_name="Hex1HexNAc2Pent1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:53:29" + date_time_modified="2006-10-16 17:12:02" + approved="1" + record_id="151"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="700.253828" avge_mass="700.6403" composition="Pent Hex HexNAc(2)"> + <umod:element symbol="H" number="44"/> + <umod:element symbol="C" number="27"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="19"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(2)dHex(1)" full_name="Hex1HexNAc2dHex1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:54:18" + date_time_modified="2006-10-16 17:12:59" + approved="1" + record_id="152"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="714.269478" avge_mass="714.6668" composition="dHex Hex HexNAc(2)"> + <umod:element symbol="H" number="46"/> + <umod:element symbol="C" number="28"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="19"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(2)HexNAc(2)" full_name="Hex2HexNAc2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:55:08" + date_time_modified="2006-10-16 17:13:17" + approved="1" + record_id="153"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="730.264392" avge_mass="730.6662" composition="Hex(2) HexNAc(2)"> + <umod:element symbol="H" number="46"/> + <umod:element symbol="C" number="28"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="20"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(3)HexNAc(1)Pent(1)" full_name="Hex3HexNAc1Pent1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:56:02" + date_time_modified="2006-10-16 17:18:03" + approved="1" + record_id="154"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="821.280102" avge_mass="821.7289" composition="Pent Hex(3) HexNAc"> + <umod:element symbol="H" number="51"/> + <umod:element symbol="C" number="31"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="24"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(2)dHex(1)Pent(1)" full_name="Hex1HexNAc2dHex1Pent1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:57:01" + date_time_modified="2006-10-16 17:18:41" + approved="1" + record_id="155"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="846.311736" avge_mass="846.7815" + composition="Pent dHex Hex HexNAc(2)"> + <umod:element symbol="H" number="54"/> + <umod:element symbol="C" number="33"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="23"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(2)dHex(2)" full_name="Hex1HexNAc2dHex2" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:57:52" + date_time_modified="2006-10-16 17:18:56" + approved="1" + record_id="156"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="860.327386" avge_mass="860.8080" composition="dHex(2) Hex HexNAc(2)"> + <umod:element symbol="H" number="56"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="23"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(2)HexNAc(2)Pent(1)" full_name="Hex2HexNAc2Pent1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:58:38" + date_time_modified="2006-10-16 17:19:11" + approved="1" + record_id="157"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="862.306651" avge_mass="862.7809" composition="Pent Hex(2) HexNAc(2)"> + <umod:element symbol="H" number="54"/> + <umod:element symbol="C" number="33"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="24"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(2)HexNAc(2)dHex(1)" full_name="Hex2HexNAc2dHex1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:59:18" + date_time_modified="2006-10-16 17:19:27" + approved="1" + record_id="158"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="876.322301" avge_mass="876.8074" composition="dHex Hex(2) HexNAc(2)"> + <umod:element symbol="H" number="56"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="24"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(3)HexNAc(2)" full_name="Hex3HexNAc2" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 12:59:59" + date_time_modified="2006-10-16 17:19:58" + approved="1" + record_id="159"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="892.317216" avge_mass="892.8068" composition="Hex(3) HexNAc(2)"> + <umod:element symbol="H" number="56"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="25"/> + </umod:delta> + <umod:alt_name>chitobiose core</umod:alt_name> + </umod:mod> + <umod:mod title="Hex(1)HexNAc(1)NeuAc(2)" full_name="Hex1HexNAc1NeuAc2" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 13:01:06" + date_time_modified="2007-10-20 19:30:21" + approved="1" + record_id="160"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="O-linked glycosylation" + spec_group="2"/> + <umod:delta mono_mass="947.323029" avge_mass="947.8423" composition="Hex HexNAc NeuAc(2)"> + <umod:element symbol="H" number="57"/> + <umod:element symbol="C" number="36"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="26"/> + </umod:delta> + <umod:xref> + <umod:text>Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hex(3)HexNAc(2)P(1)" full_name="Hex3HexNAc2P1" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2003-09-29 13:02:02" + date_time_modified="2006-10-16 17:20:48" + approved="1" + record_id="161"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="923.290978" avge_mass="923.7806" composition="P Hex(3) HexNAc(2)"> + <umod:element symbol="H" number="56"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="25"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Delta:S(-1)Se(1)" full_name="Selenium replaces sulphur" + username_of_poster="pnacman" + group_of_poster="users" + date_time_posted="2003-10-14 11:24:28" + date_time_modified="2006-10-16 10:11:58" + approved="1" + record_id="162"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="Non-standard residue" + spec_group="1"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Non-standard residue" + spec_group="2"> + <umod:misc_notes>Selenocysteine conventionally represented by 1 letter code U</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="47.944449" avge_mass="46.8950" composition="S(-1) Se"> + <umod:element symbol="S" number="-1"/> + <umod:element symbol="Se" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12148805</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0022</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="NBS:13C(6)" full_name="Shimadzu NBS-13C" username_of_poster="kuyama" + group_of_poster="users" + date_time_posted="2004-01-07 07:22:34" + date_time_modified="2007-08-31 10:35:22" + approved="0" + record_id="171"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="159.008578" avge_mass="159.1144" composition="H(3) 13C(6) N O(2) S"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>NBS reagent heavy</umod:alt_name> + <umod:xref> + <umod:text>Rapid Communications in Mass Spectrometry, 17, 1642-1650 (2003)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12845591</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl:2H(3)13C(1)" full_name="monomethylated arginine" + username_of_poster="sams" + group_of_poster="users" + date_time_posted="2005-06-30 18:19:34" + date_time_modified="2006-10-14 19:40:53" + approved="1" + record_id="329"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="18.037835" avge_mass="18.0377" composition="H(-1) 2H(3) 13C"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="13C" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Identifying and quantifying in vivo methylation sites by heavy methyl SILAC, Shao-En Ong et al., Nature methods 1(2) 2004, 1-8</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dimethyl:2H(6)13C(2)" full_name="dimethylated arginine" + username_of_poster="sams" + group_of_poster="users" + date_time_posted="2005-06-30 18:21:32" + date_time_modified="2006-10-15 18:26:53" + approved="1" + record_id="330"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="36.075670" avge_mass="36.0754" composition="H(-2) 2H(6) 13C(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="13C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Identifying and quantifying in vivo methylation sites by heavy methyl SILAC, Shao-En Ong et al., Nature Methods 1(2) 1-8</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="NBS" full_name="Shimadzu NBS-12C" username_of_poster="kuyama" + group_of_poster="users" + date_time_posted="2004-01-07 07:25:07" + date_time_modified="2007-08-31 10:34:53" + approved="0" + record_id="172"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="152.988449" avge_mass="153.1585" composition="H(3) C(6) N O(2) S"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>2-nitrobenzenesulfenyl</umod:alt_name> + <umod:xref> + <umod:text>12845591</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Rapid Communications in Mass Spectrometry, 17, 1642-1650 (2003)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(1)O(-1)18O(1)" full_name="glycosylated asparagine 18O labeling" + username_of_poster="lobvi" + group_of_poster="users" + date_time_posted="2003-12-11 18:24:58" + date_time_modified="2006-10-14 09:36:39" + approved="1" + record_id="170"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="3.012071" avge_mass="3.0077" composition="H O(-1) 18O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="18O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>1443554</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Anal. Biochem. 1992, 205:151-158</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in 18O labelled water.</umod:misc_notes> + </umod:mod> + <umod:mod title="QAT" full_name="APTA-d0" username_of_poster="s_julka" + group_of_poster="users" + date_time_posted="2004-04-08 17:12:14" + date_time_modified="2006-10-16 15:01:07" + approved="1" + record_id="195"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="170.141913" avge_mass="170.2520" composition="H(18) C(9) N(2) O"> + <umod:element symbol="H" number="18"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>(3-acrylamidopropyl)trimethylammonium</umod:alt_name> + <umod:xref> + <umod:text>15283597</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="BHT" + full_name="Michael addition of BHT quinone methide to Cysteine and Lysine" + username_of_poster="gonzo" + group_of_poster="users" + date_time_posted="2004-02-05 22:02:53" + date_time_modified="2006-10-16 15:19:41" + approved="1" + record_id="176"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="2"> + <umod:misc_notes>Secondary adduct - much less common as C</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"> + <umod:misc_notes>Secondary adduct - much less common as C</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="3"> + <umod:misc_notes>Primary adduct formed</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="218.167065" avge_mass="218.3346" composition="H(22) C(15) O"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Butylated Hydroxytoluene</umod:alt_name> + <umod:xref> + <umod:text>9448752</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>BHT metabolism has been studied in rats and mice in relation to tumor promotion.</umod:misc_notes> + </umod:mod> + <umod:mod title="Delta:H(4)C(2)O(-1)S(1)" full_name="S-Ethylcystine from Serine" + username_of_poster="UCDMSF" + group_of_poster="users" + date_time_posted="2005-06-20 20:09:02" + date_time_modified="2006-10-16 10:00:57" + approved="1" + record_id="327"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="44.008456" avge_mass="44.1188" composition="H(4) C(2) O(-1) S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>2005 ASMS poster Presentation TP 527</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Phosphoserine to S-ethylcystine\r\nvia Beta elimination/Michael addition of ethylthiol</umod:misc_notes> + </umod:mod> + <umod:mod title="DAET" full_name="phosphorylation to amine thiol" + username_of_poster="chemgirl18" + group_of_poster="users" + date_time_posted="2004-02-11 20:34:16" + date_time_modified="2006-10-16 12:34:48" + approved="1" + record_id="178"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="87.050655" avge_mass="87.1866" composition="H(9) C(4) N O(-1) S"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>b-elimination thiol derivatization</umod:alt_name> + <umod:xref> + <umod:text>12216740</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>DAET = 2-(dimethylamino)ethanethiol; The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site.</umod:misc_notes> + </umod:mod> + <umod:mod title="Pro->Pyrrolidone" full_name="Pyrrolidone from Proline" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-02 17:39:05" + date_time_modified="2006-11-14 11:12:17" + approved="0" + record_id="369"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="-27.994915" avge_mass="-28.0101" composition="C(-1) O(-1)"> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(9)" full_name="13C(9) Silac label" username_of_poster="hs" + group_of_poster="users" + date_time_posted="2004-02-16 21:19:47" + date_time_modified="2007-08-22 18:31:52" + approved="1" + record_id="184"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:delta mono_mass="9.030193" avge_mass="8.9339" composition="C(-9) 13C(9)"> + <umod:element symbol="C" number="-9"/> + <umod:element symbol="13C" number="9"/> + </umod:delta> + <umod:alt_name>heavy tyrosine</umod:alt_name> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(9)+Phospho" full_name="C13 label (Phosphotyrosine)" + username_of_poster="hs" + group_of_poster="users" + date_time_posted="2004-02-22 04:42:33" + date_time_modified="2006-10-16 12:37:51" + approved="1" + record_id="185"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="88.996524" avge_mass="88.9138" composition="H C(-9) 13C(9) O(3) P"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="-9"/> + <umod:element symbol="13C" number="9"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:alt_name>heavy phosphotyrosine</umod:alt_name> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)" full_name="13C(6) Silac label" username_of_poster="hs" + group_of_poster="users" + date_time_posted="2004-02-28 19:54:10" + date_time_modified="2007-08-22 18:29:56" + approved="1" + record_id="188"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="Isotopic label" + spec_group="5"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="6.020129" avge_mass="5.9559" composition="C(-6) 13C(6)"> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="13C" number="6"/> + </umod:delta> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="HPG" full_name="Hydroxyphenylglyoxal arginine" + username_of_poster="gcarven" + group_of_poster="users" + date_time_posted="2004-02-26 20:19:25" + date_time_modified="2006-10-17 11:46:39" + approved="1" + record_id="186"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="132.021129" avge_mass="132.1162" composition="H(4) C(8) O(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>HPG arginine</umod:alt_name> + <umod:xref> + <umod:text>11698400</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11914093</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="2HPG" full_name="2 Hydroxyphenylglyoxal arginine" + username_of_poster="gcarven" + group_of_poster="users" + date_time_posted="2004-02-26 22:05:25" + date_time_modified="2006-10-17 11:46:56" + approved="1" + record_id="187"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="282.052824" avge_mass="282.2476" composition="H(10) C(16) O(5)"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:alt_name>2 HPG arginine</umod:alt_name> + <umod:xref> + <umod:text>11698400</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>OH-PGO and PGO react with arginine at a stoichiometry of 2:1</umod:misc_notes> + </umod:mod> + <umod:mod title="QAT:2H(3)" full_name="APTA d3" username_of_poster="s_julka" + group_of_poster="users" + date_time_posted="2004-04-08 17:15:04" + date_time_modified="2006-10-16 15:01:35" + approved="1" + record_id="196"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="174.168569" avge_mass="174.2784" + composition="H(16) 2H(3) C(9) N(2) O"> + <umod:element symbol="H" number="16"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>(3-acrylamidopropyl)trimethylammonium</umod:alt_name> + <umod:xref> + <umod:text>15283597</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:18O(2)" full_name="O18 label at both C-terminal oxygens" + username_of_poster="Hensbergen" + group_of_poster="users" + date_time_posted="2004-03-30 14:20:29" + date_time_modified="2006-11-14 12:01:04" + approved="1" + record_id="193"> + <umod:specificity hidden="0" site="C-term" position="Any C-term" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="4.008491" avge_mass="3.9995" composition="O(-2) 18O(2)"> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="18O" number="2"/> + </umod:delta> + <umod:alt_name>Double O18 (C-term)</umod:alt_name> + <umod:xref> + <umod:text>11467524</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="AccQTag" full_name="6-aminoquinolyl-N-hydroxysuccinimidyl carbamate" + username_of_poster="davidcreasy" + group_of_poster="users" + date_time_posted="2004-04-08 12:01:19" + date_time_modified="2006-10-16 14:59:12" + approved="1" + record_id="194"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="170.048013" avge_mass="170.1674" composition="H(6) C(10) N(2) O"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Waters Application Note 930494</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www2.waters.com/watprod.nsf/newdocs/930494</umod:url> + </umod:xref> + <umod:xref> + <umod:text>14997490</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Hochleitner, E. O. et al, Proteomics 2004, 4, 669-676,</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dimethyl:2H(4)" full_name="DiMethyl-CHD2" username_of_poster="PhilipHsu" + group_of_poster="users" + date_time_posted="2004-04-20 07:07:29" + date_time_modified="2006-10-15 18:24:07" + approved="1" + record_id="199"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Isotopic label" + spec_group="3"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="32.056407" avge_mass="32.0778" composition="2H(4) C(2)"> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:alt_name>reductive amination</umod:alt_name> + <umod:xref> + <umod:text>Anal Chem 2003. 75, 6843</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14670044</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Jue-Liang Hsu, Sheng-Yu Huang, and Shu-Hui Chen. Stable-Isotope based Multiplex Labeling Coupled with LC-MS/MS, HUPO 3rd ANNUAL WORLD CONGRESS, Bejing (China) 2004</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="EQAT" full_name="EAPTA d0" username_of_poster="s_julka" + group_of_poster="users" + date_time_posted="2004-04-08 17:21:08" + date_time_modified="2006-10-16 15:05:02" + approved="1" + record_id="197"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="184.157563" avge_mass="184.2786" composition="H(20) C(10) N(2) O"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="EQAT:2H(5)" full_name="EAPTA d5" username_of_poster="s_julka" + group_of_poster="users" + date_time_posted="2004-04-08 17:25:24" + date_time_modified="2006-10-16 15:07:31" + approved="1" + record_id="198"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="189.188947" avge_mass="189.3094" + composition="H(15) 2H(5) C(10) N(2) O"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="2H" number="5"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ethanedithiol" full_name="EDT" username_of_poster="take" + group_of_poster="users" + date_time_posted="2004-04-20 08:27:30" + date_time_modified="2006-10-16 11:07:38" + approved="1" + record_id="200"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="75.980527" avge_mass="76.1838" composition="H(4) C(2) O(-1) S(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>11507762</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="NEIAA:2H(5)" full_name="N-ethyl iodoacetamide-d5" + username_of_poster="Botting" + group_of_poster="users" + date_time_posted="2004-05-18 11:11:52" + date_time_modified="2006-10-16 12:38:09" + approved="1" + record_id="212"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="90.084148" avge_mass="90.1353" composition="H(2) 2H(5) C(4) N O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="5"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12766232</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(6)C(6)O(1)" full_name="Acrolein addition +94" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-05-06 18:54:17" + date_time_modified="2006-10-16 12:38:28" + approved="1" + record_id="205"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="94.041865" avge_mass="94.1112" composition="H(6) C(6) O"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Acrolein94, FDP</umod:alt_name> + </umod:mod> + <umod:mod title="Delta:H(4)C(3)O(1)" full_name="Acrolein addition +56" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-05-06 18:55:58" + date_time_modified="2006-10-16 10:16:29" + approved="1" + record_id="206"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="56.026215" avge_mass="56.0633" composition="H(4) C(3) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Acrolein56</umod:alt_name> + <umod:xref> + <umod:text>10825247</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15541752</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(2)C(3)" full_name="Acrolein addition +38" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-05-06 18:57:08" + date_time_modified="2006-10-15 18:30:31" + approved="1" + record_id="207"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="38.015650" avge_mass="38.0480" composition="H(2) C(3)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + </umod:delta> + <umod:alt_name>Acrolein38</umod:alt_name> + </umod:mod> + <umod:mod title="Delta:H(4)C(6)" full_name="Acrolein addition +76" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-05-06 18:59:23" + date_time_modified="2006-10-16 11:08:13" + approved="1" + record_id="208"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="76.031300" avge_mass="76.0960" composition="H(4) C(6)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="6"/> + </umod:delta> + <umod:alt_name>Acrolein76</umod:alt_name> + </umod:mod> + <umod:mod title="Delta:H(8)C(6)O(2)" full_name="Acrolein addition +112" + username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-05-06 19:00:25" + date_time_modified="2006-10-16 12:46:03" + approved="1" + record_id="209"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="112.052430" avge_mass="112.1265" composition="H(8) C(6) O(2)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Acrolein112</umod:alt_name> + </umod:mod> + <umod:mod title="ADP-Ribosyl" full_name="ADP Ribose addition" + username_of_poster="ionjockey" + group_of_poster="users" + date_time_posted="2004-05-27 20:53:37" + date_time_modified="2006-10-16 17:03:46" + approved="1" + record_id="213"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Other glycosylation" + spec_group="5"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other glycosylation" + spec_group="4"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Other glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Other glycosylation" + spec_group="1"/> + <umod:delta mono_mass="541.061110" avge_mass="541.3005" + composition="H(21) C(15) N(5) O(13) P(2)"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="13"/> + <umod:element symbol="P" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0237</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0169</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Structure</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://betelgeuse.u-strasbg.fr/DocPARP/DocPARG/images/Structure-pADPR.jpg</umod:url> + </umod:xref> + <umod:xref> + <umod:text>AA0168</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0231</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15842200</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0295</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>ADP</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="NEIAA" full_name="N-ethyl iodoacetamide-d0" username_of_poster="Botting" + group_of_poster="users" + date_time_posted="2004-05-18 11:10:37" + date_time_modified="2006-10-16 12:15:11" + approved="1" + record_id="211"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="85.052764" avge_mass="85.1045" composition="H(7) C(4) N O"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12766232</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="iTRAQ4plex" + full_name="Representative mass and accurate mass for 116 & 117" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2004-06-08 14:04:07" + date_time_modified="2006-11-14 11:06:16" + approved="0" + record_id="214"> + <umod:specificity hidden="0" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="144.102063" avge_mass="144.1544" + composition="H(12) C(4) 13C(3) N 15N O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="13C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="15N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>AKA iTRAQ4plex116/7</umod:alt_name> + <umod:alt_name>Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry</umod:alt_name> + <umod:xref> + <umod:text>Applied Biosystems Chemistry Reference Guide</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf</umod:url> + </umod:xref> + <umod:misc_notes>Different channels have the same nominal mass but slightly different exact masses. Use this value for all channels for quantitation purposes</umod:misc_notes> + </umod:mod> + <umod:mod title="Crotonaldehyde" full_name="Crotonaldehyde" username_of_poster="fatcat" + group_of_poster="users" + date_time_posted="2004-08-12 19:56:03" + date_time_modified="2006-10-16 10:35:31" + approved="1" + record_id="253"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="70.041865" avge_mass="70.0898" composition="H(6) C(4) O"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>11283024</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Bromo" full_name="bromination" username_of_poster="gerribe" + group_of_poster="users" + date_time_posted="2005-09-06 08:31:51" + date_time_modified="2006-10-16 11:10:31" + approved="1" + record_id="340"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="77.910511" avge_mass="78.8961" composition="H(-1) Br"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="Br" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>BROM</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0179</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0180</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0173</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0176</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0175</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0174</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9033387</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Amino" full_name="Tyrosine oxidation to 2-aminotyrosine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 21:18:23" + date_time_modified="2006-10-14 10:39:53" + approved="1" + record_id="342"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="15.010899" avge_mass="15.0146" composition="H N"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Argbiotinhydrazide" + full_name="oxidized Arginine biotinylated with biotin hydrazide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 22:36:58" + date_time_modified="2006-11-14 12:10:30" + approved="0" + record_id="343"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="199.066699" avge_mass="199.2700" composition="H(13) C(9) N O(2) S"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15828771</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:18O(1)" full_name="O18 Labeling" username_of_poster="chemgirl18" + group_of_poster="users" + date_time_posted="2004-08-27 21:57:17" + date_time_modified="2006-10-13 18:53:41" + approved="1" + record_id="258"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>alkaline phosphatase to dephosphorylate</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>alkaline phosphatase to dephosphorylate</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>alkaline phosphatase to dephosphorylate</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="C-term" position="Any C-term" classification="Isotopic label" + spec_group="4"> + <umod:misc_notes>digesting in labelled water</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="2.004246" avge_mass="1.9998" composition="O(-1) 18O"> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="18O" number="1"/> + </umod:delta> + <umod:alt_name>H2 18O Alkaline Phosphatase</umod:alt_name> + <umod:xref> + <umod:text>11467524</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)15N(2)" full_name="13C(6) 15N(2) Silac label" + username_of_poster="hs01" + group_of_poster="users" + date_time_posted="2004-08-30 16:23:02" + date_time_modified="2006-10-19 10:30:33" + approved="1" + record_id="259"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="8.014199" avge_mass="7.9427" composition="C(-6) 13C(6) N(-2) 15N(2)"> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="15N" number="2"/> + </umod:delta> + <umod:alt_name>heavy lysine</umod:alt_name> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Thiophospho" full_name="Thiophosphorylation" + username_of_poster="mrbladergroen" + group_of_poster="users" + date_time_posted="2004-09-01 13:20:58" + date_time_modified="2006-10-16 12:38:48" + approved="1" + record_id="260"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Other" spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="95.943487" avge_mass="96.0455" composition="H O(2) P S"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12110917</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="SPITC" full_name="4-sulfophenyl isothiocyanate" + username_of_poster="hatlevig" + group_of_poster="users" + date_time_posted="2004-09-14 20:01:29" + date_time_modified="2006-10-16 15:26:00" + approved="1" + record_id="261"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:delta mono_mass="214.971084" avge_mass="215.2495" composition="H(5) C(7) N O(3) S(2)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:alt_name>N-terminal / lysine sulfonation</umod:alt_name> + <umod:xref> + <umod:text>Wang et al. 2004. Rapid Commun Mass Spectrom. 18(1):96-102</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Chen et. al. Rapid Commun Mass Spectrom. 2004;18(2):191-8.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Shimadzu application note</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.shimadzu-biotech.net/literature/application_note/202_1.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>14745769</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14689565</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>16526082</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="IGBP" full_name="Light IDBEST tag for quantitation" + username_of_poster="zqiao" + group_of_poster="users" + date_time_posted="2004-07-26 23:02:04" + date_time_modified="2006-10-19 11:13:26" + approved="1" + record_id="243"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="296.016039" avge_mass="297.1478" + composition="H(13) C(12) N(2) O(2) Br"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="Br" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Under construction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.targetdiscovery.com/index.php?topic=prod.idbe</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Target discovery , Inc. IDBEST IGBP user manual</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cytopiloyne" full_name="nucleophilic addtion to cytopiloyne" + username_of_poster="ymchiang" + group_of_poster="users" + date_time_posted="2004-11-10 03:13:23" + date_time_modified="2006-10-16 16:35:54" + approved="1" + record_id="270"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="7"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="6"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="5"/> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="4"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="362.136553" avge_mass="362.3738" composition="H(22) C(19) O(7)"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="O" number="7"/> + </umod:delta> + <umod:xref> + <umod:text>15549660</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulate T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell.</umod:misc_notes> + </umod:mod> + <umod:mod title="Cytopiloyne+water" full_name="nucleophilic addition to cytopiloyne+H2O" + username_of_poster="ymchiang" + group_of_poster="users" + date_time_posted="2004-11-11 05:23:17" + date_time_modified="2006-10-16 16:37:10" + approved="1" + record_id="271"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="7"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="6"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="5"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="4"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="380.147118" avge_mass="380.3891" composition="H(24) C(19) O(8)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="O" number="8"/> + </umod:delta> + <umod:xref> + <umod:text>15549660</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulated T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell.</umod:misc_notes> + </umod:mod> + <umod:mod title="Label:13C(6)15N(4)" full_name="13C(6) 15N(4) Silac label" + username_of_poster="AFCS" + group_of_poster="users" + date_time_posted="2004-10-20 17:49:33" + date_time_modified="2006-10-19 10:30:51" + approved="1" + record_id="267"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="10.008269" avge_mass="9.9296" + composition="C(-6) 13C(6) N(-4) 15N(4)"> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="-4"/> + <umod:element symbol="15N" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(9)15N(1)" full_name="13C(9) 15N(1) Silac label" + username_of_poster="Deepa" + group_of_poster="users" + date_time_posted="2004-11-05 18:51:13" + date_time_modified="2006-10-19 10:31:10" + approved="1" + record_id="269"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in AQUA experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="10.027228" avge_mass="9.9273" composition="C(-9) 13C(9) N(-1) 15N"> + <umod:element symbol="C" number="-9"/> + <umod:element symbol="13C" number="9"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="15N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12771378</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:2H(3)" full_name="Trideuteration" username_of_poster="mmolloy" + group_of_poster="users" + date_time_posted="2004-09-29 08:52:01" + date_time_modified="2006-10-14 09:38:54" + approved="1" + record_id="262"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>for SILAC expt</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="3.018830" avge_mass="3.0185" composition="H(-3) 2H(3)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="2H" number="3"/> + </umod:delta> + <umod:alt_name>Trideuteration</umod:alt_name> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(5)15N(1)" full_name="13C(5) 15N(1) Silac label" + username_of_poster="Deepa" + group_of_poster="users" + date_time_posted="2004-11-05 18:49:37" + date_time_modified="2006-10-19 10:30:08" + approved="1" + record_id="268"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in AQUA experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="6.013809" avge_mass="5.9567" composition="C(-5) 13C(5) N(-1) 15N"> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="13C" number="5"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="15N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12771378</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PET" full_name="phosphorylation to pyridyl thiol" + username_of_poster="vbad" + group_of_poster="users" + date_time_posted="2004-10-07 08:55:33" + date_time_modified="2006-10-16 12:48:51" + approved="1" + record_id="264"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="121.035005" avge_mass="121.2028" composition="H(7) C(7) N O(-1) S"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>b-elimination PET derivatisation</umod:alt_name> + <umod:xref> + <umod:text>Manfredo Quadroni in: ''Proteome Research: Mass Spectrometry (ed. P.James)'' pp 187-206</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>PET = 2-[4-pyridyl]ethanethiol. This modification is a chemical derivative, based on a alkaline catalysed beta-elimination of phosphoserines and phosphothreonines and subsequent 1,4-addition of 2-[4-pyridine]ethanethiol. These modified serines and threonines produce in MS/MS a characteristic fragment which can be used for precursor-ion-scan experiments.</umod:misc_notes> + </umod:mod> + <umod:mod title="CAF" full_name="sulfonation of N-terminus" username_of_poster="chens002" + group_of_poster="users" + date_time_posted="2004-11-16 14:25:33" + date_time_modified="2007-01-03 19:34:35" + approved="1" + record_id="272"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="135.983029" avge_mass="136.1265" composition="H(4) C(3) O(4) S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Ettan CAF MALDI</umod:alt_name> + <umod:xref> + <umod:text>Anal.Chem 75(7):156A-165A</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15732931</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>16046801</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>N-terminal sulfonation of diglycine to detect ubiquitination sites</umod:misc_notes> + </umod:mod> + <umod:mod title="Xlink:SSD" + full_name="covalent modification of lysine by cross-linking reagent" + username_of_poster="tom" + group_of_poster="users" + date_time_posted="2004-11-16 20:20:17" + date_time_modified="2006-10-17 11:43:47" + approved="1" + record_id="273"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="253.095023" avge_mass="253.2512" composition="H(15) C(12) N O(5)"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>Partis MD et al. 1983 J Prot Chem 2 263-277</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Nitrosyl" full_name="S-nitrosylation" username_of_poster="dengh" + group_of_poster="users" + date_time_posted="2004-12-11 00:23:12" + date_time_modified="2006-10-15 18:00:14" + approved="1" + record_id="275"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="28.990164" avge_mass="28.9982" composition="H(-1) N O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0230</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>10442087</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>NTRY</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15688001</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues.</umod:misc_notes> + </umod:mod> + <umod:mod title="AEBS" full_name="Aminoethylbenzenesulfonylation" + username_of_poster="plattm" + group_of_poster="users" + date_time_posted="2004-12-14 04:38:25" + date_time_modified="2006-10-16 15:04:42" + approved="1" + record_id="276"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Artefact" + spec_group="5"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Artefact" + spec_group="4"> + <umod:misc_notes>Primary site of modification</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" classification="Artefact" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="183.035399" avge_mass="183.2276" composition="H(9) C(8) N O(2) S"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Biochim Biophys Acta. 1996 Feb 16; 1299(3):353-7</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>8597590</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Potential protein modification when using AEBSF (Pefabloc) as a serine protease inhibitor.</umod:misc_notes> + </umod:mod> + <umod:mod title="Ethanolyl" full_name="Ethanolation of Cys" username_of_poster="knierman" + group_of_poster="users" + date_time_posted="2005-01-11 04:26:47" + date_time_modified="2006-10-16 10:01:41" + approved="1" + record_id="278"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>from reaction of SH group with iodoethanol</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="44.026215" avge_mass="44.0526" composition="H(4) C(2) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Anal Biochem. 2004 Oct 1;333(1):174-81</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15351294</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>A simplified procedure for the reduction and alkylation of cysteine residues in proteins prior to proteolytic digestion and mass spectral analysis. Hale JE, Butler JP, Gelfanova V, You JS, Knierman MD.</umod:misc_notes> + </umod:mod> + <umod:mod title="HMVK" + full_name="Michael addition of hydroxymethylvinyl ketone to cysteine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-03 15:59:33" + date_time_modified="2006-10-16 12:15:35" + approved="1" + record_id="371"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="86.036779" avge_mass="86.0892" composition="H(6) C(4) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>hydroxymethylvinyl ketone</umod:alt_name> + <umod:xref> + <umod:text>11743741</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Ethyl" full_name="Ethylation" username_of_poster="Qishanl" + group_of_poster="users" + date_time_posted="2005-01-27 23:18:07" + date_time_modified="2006-10-15 17:59:14" + approved="1" + record_id="280"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Multiple" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Multiple" + spec_group="1"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Artefact" + spec_group="3"/> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="4"/> + <umod:delta mono_mass="28.031300" avge_mass="28.0532" composition="H(4) C(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>9629898</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="CoenzymeA" full_name="Cysteine modified Coenzyme A" + username_of_poster="tremis" + group_of_poster="users" + date_time_posted="2005-02-01 17:10:00" + date_time_modified="2006-10-16 17:15:18" + approved="1" + record_id="281"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="765.099560" avge_mass="765.5182" + composition="H(34) C(21) N(7) O(16) P(3) S"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="21"/> + <umod:element symbol="N" number="7"/> + <umod:element symbol="O" number="16"/> + <umod:element symbol="P" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Structure</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://commons.wikimedia.org/wiki/Image:Coenzyme_a.png</umod:url> + </umod:xref> + <umod:xref> + <umod:text>AA0306</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl+Deamidated" full_name="Deamidation followed by a methylation" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-14 10:39:08" + date_time_modified="2007-02-04 12:25:42" + approved="1" + record_id="528"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:delta mono_mass="14.999666" avge_mass="15.0113" composition="H C N(-1) O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Glutamate methyl ester</umod:alt_name> + <umod:xref> + <umod:text>P02942</umod:text> + <umod:source>Swiss-Prot</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DEAME</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Anal Chem. 2007 Jan 15;79(2):673-81.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:H(5)C(2)" full_name="Dimethylation of proline residue" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-15 18:02:34" + date_time_modified="2006-10-15 18:03:16" + approved="1" + record_id="529"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="29.039125" avge_mass="29.0611" composition="H(5) C(2)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>DIMETP</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl:2H(2)" full_name="Deuterium Methylation of Lysine" + username_of_poster="Glebivanov" + group_of_poster="users" + date_time_posted="2005-02-13 01:26:38" + date_time_modified="2006-10-14 19:35:54" + approved="1" + record_id="284"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="16.028204" avge_mass="16.0389" composition="2H(2) C"> + <umod:element symbol="2H" number="2"/> + <umod:element symbol="C" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Nature. 2004 Nov 18;432(7015):353-60. Epub 2004 Nov 03</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15525938</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="SulfanilicAcid" full_name="Light Sulfanilic Acid (SA) C12" + username_of_poster="apanchaud" + group_of_poster="users" + date_time_posted="2005-02-17 15:48:07" + date_time_modified="2006-10-16 14:05:34" + approved="1" + record_id="285"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Isotopic label" + spec_group="3"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Any C-term" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="155.004099" avge_mass="155.1744" composition="H(5) C(6) N O(2) S"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>C-Terminal/Glutamate/Aspartate sulfonation</umod:alt_name> + <umod:xref> + <umod:text>ASMS 2005: Panchaud et al. (Poster ThP 509) ''Combining protein identification and quantitation: C-terminal isotope-coded tagging''</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="SulfanilicAcid:13C(6)" full_name="Heavy Sulfanilic Acid (SA) C13" + username_of_poster="apanchaud" + group_of_poster="users" + date_time_posted="2005-02-17 15:55:52" + date_time_modified="2006-10-16 14:08:42" + approved="1" + record_id="286"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Any C-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="161.024228" avge_mass="161.1303" composition="H(5) 13C(6) N O(2) S"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>C-Terminal/Glutamate/Aspartate sulfonation</umod:alt_name> + <umod:xref> + <umod:text>ASMS 2005: Panchaud et al. (Poster ThP 509) ''Combining protein identification and quantitation: C-terminal isotope-coded tagging''</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9254591</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Biotin-PEO-Amine" full_name="Biotin polyethyleneoxide amine" + username_of_poster="TBricker1" + group_of_poster="users" + date_time_posted="2005-03-02 16:49:17" + date_time_modified="2006-11-14 11:15:23" + approved="0" + record_id="289"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>EDC-coupled modification of D, E and C-terminus</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>EDC-coupled modification of D, E and C-terminus</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Chemical derivative" + spec_group="3"> + <umod:misc_notes>EDC-coupled modification of D, E and C-terminus</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="356.188212" avge_mass="356.4835" + composition="H(28) C(16) N(4) O(3) S"> + <umod:element symbol="H" number="28"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Introduction to Protein Labeling</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:url> + </umod:xref> + <umod:misc_notes>EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5\' phosphate groups</umod:misc_notes> + </umod:mod> + <umod:mod title="Trp->Oxolactone" full_name="Tryptophan oxidation to oxolactone" + username_of_poster="oxolactone" + group_of_poster="users" + date_time_posted="2005-02-25 23:30:20" + date_time_modified="2006-10-14 10:06:01" + approved="1" + record_id="288"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="13.979265" avge_mass="13.9835" composition="H(-2) O"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>7949339</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>The cleavage of a peptide bond between Try-Xxx with oxidation of tryptophan to the oxolactone occurs in the presence of BNPS-skatole. This is a useful method for the chemical cleavage of proteins specifically at tryptophan residues.</umod:misc_notes> + </umod:mod> + <umod:mod title="Biotin-HPDP" full_name="Pierce EZ-Link Biotin-HPDP" + username_of_poster="tgreco" + group_of_poster="users" + date_time_posted="2005-03-03 22:56:52" + date_time_modified="2006-11-14 11:14:29" + approved="0" + record_id="290"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="428.191582" avge_mass="428.6124" + composition="H(32) C(19) N(4) O(3) S(2)"> + <umod:element symbol="H" number="32"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>EZ-Link Biotin-HPDP (N-(6-(Biotinamido)hexyl)-3'-(2'-pyridyldithio)-propionamide</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=01031002</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:Hg(1)" full_name="Mercury Mercaptan" username_of_poster="tgreco" + group_of_poster="users" + date_time_posted="2005-03-03 23:53:00" + date_time_modified="2006-10-16 15:09:18" + approved="1" + record_id="291"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="201.970617" avge_mass="200.5900" composition="Hg"> + <umod:element symbol="Hg" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>10695144</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="IodoU-AMP" full_name="Cross-link of (Iodo)-uracil MP with W,F,Y" + username_of_poster="davidERICanderson" + group_of_poster="users" + date_time_posted="2005-03-04 22:57:55" + date_time_modified="2006-10-16 15:53:06" + approved="1" + record_id="292"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"> + <umod:misc_notes>Used in base/residue interactions (in principle?)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>Used in base/residue interactions (observed)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>Used in base/residue interactions (in principle?)</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="322.020217" avge_mass="322.1654" + composition="H(11) C(9) N(2) O(9) P"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="9"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:alt_name>UV induced cross-link product of Iodo-U-amp with WFY</umod:alt_name> + <umod:xref> + <umod:text>6540775</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11112526</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11567090</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>One note about this chemistry is that for W you have to take care of O2 big time (and extract the I-uracil monophosphate with organics to get rid of residual iodide).</umod:misc_notes> + </umod:mod> + <umod:mod title="CAMthiopropanoyl" full_name="3-(carbamidomethylthio)propanoyl" + username_of_poster="vanschra" + group_of_poster="users" + date_time_posted="2005-03-09 15:22:46" + date_time_modified="2006-10-16 13:58:55" + approved="1" + record_id="293"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="145.019749" avge_mass="145.1796" composition="H(7) C(5) N O(2) S"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>3-thiopropanoyl moiety from reduced DSP crosslinker or NHS-SS-biotin, modified with Iodoacetamide</umod:alt_name> + <umod:xref> + <umod:text>Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP (2004) Mol Cell Proteomics 3: 56-65</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Swaim CL, Smith JB, Smith DL (2004) J Am Soc Mass Spectrom 15:736-749</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15121203</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="IED-Biotin" full_name="biotinoyl-iodoacetyl-ethylenediamine" + username_of_poster="alexey" + group_of_poster="users" + date_time_posted="2005-03-10 16:28:09" + date_time_modified="2006-10-16 15:53:29" + approved="1" + record_id="294"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="326.141261" avge_mass="326.4145" + composition="H(22) C(14) N(4) O(3) S"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>10906242</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="dHex" full_name="Fucose" username_of_poster="rsack" + group_of_poster="users" + date_time_posted="2005-03-22 16:57:00" + date_time_modified="2006-10-16 14:02:33" + approved="1" + record_id="295"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="O-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="146.057909" avge_mass="146.1412" composition="dHex"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:alt_name>deoxyhexose</umod:alt_name> + <umod:xref> + <umod:text>15189151</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Mormann, M., Macek, B., Gonzalez de Peredo, A., Hofsteenge, J., Peter-Katalinic, J. (2004). ''Structural studies on protein O-fucosylation by electron capture dissoziation.'' International Journal of Mass Spectrometry 234:11-21</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11344537</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl:2H(3)" full_name="deuterated methyl ester" + username_of_poster="ndacoyas" + group_of_poster="users" + date_time_posted="2005-03-24 16:31:28" + date_time_modified="2006-10-14 19:36:59" + approved="1" + record_id="298"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Isotopic label" + spec_group="3"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="17.034480" avge_mass="17.0451" composition="H(-1) 2H(3) C"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="1"/> + </umod:delta> + <umod:misc_notes>esterification of carboxylic acids using D3-Methanolic HCl</umod:misc_notes> + </umod:mod> + <umod:mod title="Carboxy" full_name="Carboxylation" username_of_poster="Carol" + group_of_poster="users" + date_time_posted="2005-03-29 22:55:44" + date_time_modified="2006-11-14 11:08:50" + approved="0" + record_id="299"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>Gamma-carboxylation</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="3"> + <umod:misc_notes>Gamma-carboxylation</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="M" position="Protein N-term" + classification="Post-translational" + spec_group="5"/> + <umod:delta mono_mass="43.989829" avge_mass="44.0095" composition="C O(2)"> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0114</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>GGLU</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0363</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0032</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3802193</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0304</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Bromobimane" full_name="Monobromobimane derivative" + username_of_poster="catsriku" + group_of_poster="users" + date_time_posted="2005-04-04 23:03:13" + date_time_modified="2006-10-16 15:07:49" + approved="1" + record_id="301"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="190.074228" avge_mass="190.1986" composition="H(10) C(10) N(2) O(2)"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>mBromobimane</umod:alt_name> + <umod:xref> + <umod:text>7856876</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Menadione" full_name="Menadione quinone derivative" + username_of_poster="catsriku" + group_of_poster="users" + date_time_posted="2005-04-04 23:21:29" + date_time_modified="2007-07-12 07:36:32" + approved="0" + record_id="302"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="170.036779" avge_mass="170.1641" composition="H(6) C(11) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Vitamin k3 (Q)</umod:alt_name> + <umod:xref> + <umod:text>15939799</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="DeStreak" full_name="Cysteine mercaptoethanol" + username_of_poster="harald" + group_of_poster="users" + date_time_posted="2005-04-11 14:06:08" + date_time_modified="2006-10-16 11:07:55" + approved="1" + record_id="303"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="75.998285" avge_mass="76.1176" composition="H(4) C(2) O S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>12442261</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="dHex(1)Hex(3)HexNAc(4)" + full_name="Fucosylated biantennary (-2 galactose)" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 18:20:12" + date_time_modified="2006-10-16 17:22:46" + approved="1" + record_id="305"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1444.533870" avge_mass="1445.3331" + composition="dHex Hex(3) HexNAc(4)"> + <umod:element symbol="H" number="92"/> + <umod:element symbol="C" number="56"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="39"/> + </umod:delta> + </umod:mod> + <umod:mod title="dHex(1)Hex(4)HexNAc(4)" + full_name="Fucosylated biantennary (-1 galactose)" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:22:11" + date_time_modified="2006-10-16 17:23:48" + approved="1" + record_id="307"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1606.586693" avge_mass="1607.4737" + composition="dHex Hex(4) HexNAc(4)"> + <umod:element symbol="H" number="102"/> + <umod:element symbol="C" number="62"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="44"/> + </umod:delta> + </umod:mod> + <umod:mod title="dHex(1)Hex(5)HexNAc(4)" full_name="Fucosylated biantennary" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:25:17" + date_time_modified="2006-10-16 17:24:49" + approved="1" + record_id="308"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1768.639517" avge_mass="1769.6143" + composition="dHex Hex(5) HexNAc(4)"> + <umod:element symbol="H" number="112"/> + <umod:element symbol="C" number="68"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="49"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(3)HexNAc(4)" full_name="Biantennary (-2 galactose)" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:27:51" + date_time_modified="2006-10-16 17:22:29" + approved="1" + record_id="309"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1298.475961" avge_mass="1299.1919" composition="Hex(3) HexNAc(4)"> + <umod:element symbol="H" number="82"/> + <umod:element symbol="C" number="50"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="35"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(4)HexNAc(4)" full_name="Biantennary (-1 galactose)" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:33:37" + date_time_modified="2006-10-16 17:23:05" + approved="1" + record_id="310"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1460.528784" avge_mass="1461.3325" composition="Hex(4) HexNAc(4)"> + <umod:element symbol="H" number="92"/> + <umod:element symbol="C" number="56"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="40"/> + </umod:delta> + </umod:mod> + <umod:mod title="Hex(5)HexNAc(4)" full_name="Biantennary" username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:35:54" + date_time_modified="2006-10-16 17:24:34" + approved="1" + record_id="311"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="1622.581608" avge_mass="1623.4731" composition="Hex(5) HexNAc(4)"> + <umod:element symbol="H" number="102"/> + <umod:element symbol="C" number="62"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="45"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cysteinyl" full_name="Cysteinylation" username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 19:59:43" + date_time_modified="2006-12-17 11:28:36" + approved="1" + record_id="312"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Multiple" + spec_group="1"/> + <umod:delta mono_mass="119.004099" avge_mass="119.1423" composition="H(5) C(3) N O(2) S"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0025</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Lys-loss" full_name="Loss of C-terminal K from Heavy Chain of MAb" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 20:05:38" + date_time_modified="2006-10-13 15:00:47" + approved="1" + record_id="313"> + <umod:specificity hidden="1" site="K" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-128.094963" avge_mass="-128.1723" + composition="H(-12) C(-6) N(-2) O(-1)"> + <umod:element symbol="H" number="-12"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>16078144</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Nmethylmaleimide" full_name="Nmethylmaleimide" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-04-25 20:12:24" + date_time_modified="2006-10-16 17:26:09" + approved="1" + record_id="314"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="111.032028" avge_mass="111.0987" composition="H(5) C(5) N O(2)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + </umod:mod> + <umod:mod title="CyDye-Cy3" full_name="Cy3 CyDye DIGE Fluor saturation dye" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2006-03-27 11:17:51" + date_time_modified="2006-10-17 14:18:38" + approved="0" + record_id="494"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="672.298156" avge_mass="672.8335" + composition="H(44) C(37) N(4) O(6) S"> + <umod:element symbol="H" number="44"/> + <umod:element symbol="C" number="37"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Amersham (GE Healthcare) instruction leaflet 25800983PL Rev-B, 2003</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12872219</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="DimethylpyrroleAdduct" full_name="2,5-dimethypyrrole" + username_of_poster="Qishanl" + group_of_poster="users" + date_time_posted="2005-05-07 03:11:23" + date_time_modified="2006-10-16 11:14:22" + approved="1" + record_id="316"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="78.046950" avge_mass="78.1118" composition="H(6) C(6)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="6"/> + </umod:delta> + </umod:mod> + <umod:mod title="Delta:H(2)C(5)" full_name="MDA adduct +62" username_of_poster="rkupfer" + group_of_poster="users" + date_time_posted="2005-05-12 22:00:21" + date_time_modified="2006-10-16 10:29:55" + approved="1" + record_id="318"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="62.015650" avge_mass="62.0694" composition="H(2) C(5)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="5"/> + </umod:delta> + <umod:alt_name>MDA62</umod:alt_name> + <umod:misc_notes>usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues</umod:misc_notes> + </umod:mod> + <umod:mod title="Delta:H(2)C(3)O(1)" full_name="MDA adduct +54" + username_of_poster="rkupfer" + group_of_poster="users" + date_time_posted="2005-05-12 22:12:10" + date_time_modified="2006-10-16 10:15:34" + approved="1" + record_id="319"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>Malondialdehyde (MDA) adduct</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>5-hydro-5-methylimidazol-4-one, Methylglyoxal adduct</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="54.010565" avge_mass="54.0474" composition="H(2) C(3) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>MDA54</umod:alt_name> + <umod:xref> + <umod:text>Uchida K, Sakai K, Itakura K, Osawa T, Toyokuni S. 1977. Protein modification by lipid peroxidation products: formation of malondialdehyde-derived N(epsilon)-(2-propenol)lysine in proteins. Arch Biochem Biophys. 346(1):45-52</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Nethylmaleimide+water" full_name="Nethylmaleimidehydrolysis" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2005-05-16 22:18:42" + date_time_modified="2006-10-17 11:40:14" + approved="1" + record_id="320"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="143.058243" avge_mass="143.1406" composition="H(9) C(6) N O(3)"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Chemistry of Protein Conjugation and Crosslinking by Shan S. Wong, 1991, pg.32</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methyl+Acetyl:2H(3)" + full_name="Mono-methylated lysine labelled with Acetyl_heavy" + username_of_poster="buchanan" + group_of_poster="" + date_time_posted="2007-08-06 09:35:40" + date_time_modified="2007-09-07 16:56:17" + approved="0" + record_id="768"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="59.045045" avge_mass="59.0817" composition="H 2H(3) C(3) O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Xlink:B10621" full_name="bis-N-I-sulfonerahodamine" + username_of_poster="dengh" + group_of_poster="users" + date_time_posted="2005-05-17 22:56:12" + date_time_modified="2006-10-16 17:12:41" + approved="1" + record_id="323"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="713.093079" avge_mass="713.5626" + composition="H(30) C(31) N(4) O(6) S I"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="C" number="31"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + <umod:element symbol="I" number="1"/> + </umod:delta> + <umod:misc_notes>Invitrogen X-link reagent</umod:misc_notes> + </umod:mod> + <umod:mod title="DTBP" full_name="dimethyl 3,3\'-dithiobispropionimidate" + username_of_poster="takesin" + group_of_poster="users" + date_time_posted="2005-05-18 08:43:26" + date_time_modified="2006-11-14 11:16:21" + approved="0" + record_id="324"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="5"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="4"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="87.014270" avge_mass="87.1435" composition="H(5) C(3) N S"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Pierce data sheet</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/files/0668ss5.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>770170</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>imidoester cross-linker</umod:misc_notes> + </umod:mod> + <umod:mod title="FP-Biotin" + full_name="10-ethoxyphosphinyl-N-(biotinamidopentyl)decanamide" + username_of_poster="lmschopfer" + group_of_poster="users" + date_time_posted="2005-05-19 22:01:37" + date_time_modified="2007-01-10 16:18:52" + approved="0" + record_id="325"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="572.316129" avge_mass="572.7405" + composition="H(49) C(27) N(4) O(5) P S"> + <umod:element symbol="H" number="49"/> + <umod:element symbol="C" number="27"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>O-ethyl-N-(biotinamidopentyl)decanamido phosphonate</umod:alt_name> + <umod:xref> + <umod:text>10611275</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Liu, Patricelli and Cravatt; Activity-based protein profiling: The serine hydrolases. Proc Natl Acad Sci USA 96, 14694-14699 (1999)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Schopfer, Champion, Tamblyn, Thompson and Lockridge; Characteristic mass spectral fragments of the organophosphorus agent FP-biotin and FP-biotinylated peptides from trypsin and bovine albumin (Tyr410). Anal Biochem 345, 122-132 (2005)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>FP-biotin was designed to label the active site serine of serine esterases/proteases.</umod:misc_notes> + </umod:mod> + <umod:mod title="Thiophos-S-S-biotin" full_name="thiophosphate labeled with biotin-HPDP" + username_of_poster="lparker" + group_of_poster="users" + date_time_posted="2005-07-21 16:37:10" + date_time_modified="2006-10-16 17:02:42" + approved="1" + record_id="332"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"> + <umod:NeutralLoss mono_mass="525.142894" avge_mass="525.6658" flag="false" + composition="H(34) C(19) N(4) O(5) P S(3)"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="3"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:NeutralLoss mono_mass="525.142894" avge_mass="525.6658" flag="false" + composition="H(34) C(19) N(4) O(5) P S(3)"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="3"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:NeutralLoss mono_mass="525.142894" avge_mass="525.6658" flag="false" + composition="H(34) C(19) N(4) O(5) P S(3)"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="3"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:delta mono_mass="525.142894" avge_mass="525.6658" + composition="H(34) C(19) N(4) O(5) P S(3)"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="3"/> + </umod:delta> + <umod:alt_name>Thiophos-biotin disulfide</umod:alt_name> + </umod:mod> + <umod:mod title="Can-FP-biotin" full_name="6-N-biotinylaminohexyl isopropyl phosphate" + username_of_poster="lmschopfer" + group_of_poster="users" + date_time_posted="2005-07-21 20:54:00" + date_time_modified="2007-01-10 16:25:18" + approved="0" + record_id="333"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="447.195679" avge_mass="447.5291" + composition="H(34) C(19) N(3) O(5) P S"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>O-isopropyl-N-biotinylaminohexyl phosphonate</umod:alt_name> + <umod:xref> + <umod:text>Higson, Ferguson and Nikolaev; Synthesis of 6-N-biotinylaminohexyl isopropyl phosphorofluoridate: A potent tool for the inhibition/isolation of serine esterases and proteases. Synthesis 3, 407-409 (1999)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Commercially available from Toronto Research Chemicals Inc, as of 2005. Designed to label the active site serine of serine esterases/proteases.</umod:misc_notes> + </umod:mod> + <umod:mod title="HNE+Delta:H(2)" full_name="reduced 4-Hydroxynonenal" + username_of_poster="rkupfer" + group_of_poster="users" + date_time_posted="2005-08-10 20:52:36" + date_time_modified="2006-10-16 14:07:39" + approved="1" + record_id="335"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="158.130680" avge_mass="158.2380" composition="H(18) C(9) O(2)"> + <umod:element symbol="H" number="18"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Crabb JW et al, Protein Sci. 2002;11: 831</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Michael addition adduct of 4-hydroxynonenal with histidine, cystein and lysine residues stabilized by reduction with NaBH4</umod:misc_notes> + </umod:mod> + <umod:mod title="Thrbiotinhydrazide" + full_name="oxidized Threonine biotinylated with biotin hydrazide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-09-10 23:01:28" + date_time_modified="2006-11-14 12:12:13" + approved="0" + record_id="361"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="240.104482" avge_mass="240.3252" composition="H(16) C(10) N(4) O S"> + <umod:element symbol="H" number="16"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methylamine" full_name="Michael addition with methylamine" + username_of_poster="zhulx" + group_of_poster="users" + date_time_posted="2005-08-12 21:55:51" + date_time_modified="2006-10-14 10:02:51" + approved="1" + record_id="337"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="13.031634" avge_mass="13.0418" composition="H(3) C N O(-1)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>Rapid Commun. Mass Spectrom. 2002; 16: 999-1001</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diisopropylphosphate" full_name="O-Diisopropylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="users" + date_time_posted="2005-09-14 18:05:04" + date_time_modified="2007-01-15 15:23:33" + approved="0" + record_id="362"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="164.060231" avge_mass="164.1394" composition="H(13) C(6) O(3) P"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Main; Mode of action of anticholinesterases. Pharmac Ther 6, 579-628 (1979)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>A selective label for the active site serine of the serine esterase/protease family. It has also been shown to label tyrosine in serum albumin.</umod:misc_notes> + </umod:mod> + <umod:mod title="Isopropylphospho" full_name="O-Isopropylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="users" + date_time_posted="2005-09-14 18:08:20" + date_time_modified="2007-01-15 15:25:45" + approved="0" + record_id="363"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="122.013281" avge_mass="122.0596" composition="H(7) C(3) O(3) P"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Created by auto-catalytic dealkylation of the O-Diisopropylphosphate adduct.</umod:misc_notes> + </umod:mod> + <umod:mod title="ICPL:13C(6)" + full_name="Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form" + username_of_poster="suckau" + group_of_poster="users" + date_time_posted="2005-09-19 12:45:52" + date_time_modified="2008-09-03 15:27:07" + approved="0" + record_id="364"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Use when labelling post-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>Use when labelling pre-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="111.041593" avge_mass="111.0500" composition="H(3) 13C(6) N O"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Bruker Daltonics order reference</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.</umod:misc_notes> + </umod:mod> + <umod:mod title="ICPL" + full_name="Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form" + username_of_poster="suckau" + group_of_poster="users" + date_time_posted="2005-09-19 13:00:14" + date_time_modified="2008-09-03 15:26:36" + approved="0" + record_id="365"> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>Use when labelling pre-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Use when labelling post-digest</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="105.021464" avge_mass="105.0941" composition="H(3) C(6) N O"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Bruker Daltonics order reference</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.</umod:misc_notes> + </umod:mod> + <umod:mod title="Deamidated:18O(1)" full_name="Deamidation in presence of O18" + username_of_poster="gerribe" + group_of_poster="users" + date_time_posted="2005-09-22 15:30:16" + date_time_modified="2006-10-14 09:35:33" + approved="1" + record_id="366"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="2.988261" avge_mass="2.9845" composition="H(-1) N(-1) 18O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="18O" number="1"/> + </umod:delta> + <umod:misc_notes>Observed</umod:misc_notes> + </umod:mod> + <umod:mod title="Arg->Orn" full_name="Ornithine from Arginine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-05 17:55:25" + date_time_modified="2006-10-13 15:26:33" + approved="1" + record_id="372"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="-42.021798" avge_mass="-42.0400" composition="H(-2) C(-1) N(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-2"/> + </umod:delta> + <umod:xref> + <umod:text>15489230</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cation:Cu[I]" full_name="Replacement of proton by copper" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-16 10:29:12" + date_time_modified="2006-11-14 10:38:36" + approved="1" + record_id="531"> + <umod:specificity hidden="1" site="C-term" position="Any C-term" classification="Artefact" + spec_group="2"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="61.921774" avge_mass="62.5381" composition="H(-1) Cu"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="Cu" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Dehydro" full_name="Half of a disulfide bridge" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-06 20:57:01" + date_time_modified="2006-10-13 18:28:17" + approved="1" + record_id="374"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Multiple" + spec_group="1"/> + <umod:delta mono_mass="-1.007825" avge_mass="-1.0079" composition="H(-1)"> + <umod:element symbol="H" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0025</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diphthamide" full_name="Diphthamide" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-06 23:21:29" + date_time_modified="2006-10-16 13:43:13" + approved="1" + record_id="375"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="143.118438" avge_mass="143.2068" composition="H(15) C(7) N(2) O"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0040</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DIPH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hydroxyfarnesyl" full_name="hydroxyfarnesyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-07 20:36:20" + date_time_modified="2006-10-16 15:20:11" + approved="1" + record_id="376"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="220.182715" avge_mass="220.3505" composition="H(24) C(15) O"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0103</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FAR0</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diacylglycerol" full_name="diacylglycerol" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-07 20:41:21" + date_time_modified="2006-10-16 17:05:40" + approved="1" + record_id="377"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="576.511761" avge_mass="576.9334" composition="H(68) C(37) O(4)"> + <umod:element symbol="H" number="68"/> + <umod:element symbol="C" number="37"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>AA0107</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DIAC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Carboxyethyl" full_name="carboxyethyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-07 22:18:20" + date_time_modified="2006-10-16 10:36:16" + approved="1" + record_id="378"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="72.021129" avge_mass="72.0627" composition="H(4) C(3) O(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0115</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CETH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hypusine" full_name="hypusine" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-07 22:20:53" + date_time_modified="2006-10-16 12:35:24" + approved="1" + record_id="379"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="87.068414" avge_mass="87.1204" composition="H(9) C(4) N O"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0116</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>HYPU</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Retinylidene" full_name="retinal" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-07 22:27:27" + date_time_modified="2006-10-16 15:47:14" + approved="1" + record_id="380"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="266.203451" avge_mass="266.4204" composition="H(26) C(20)"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="20"/> + </umod:delta> + <umod:xref> + <umod:text>AA0120</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Lys->AminoadipicAcid" full_name="alpha-amino adipic acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 17:41:37" + date_time_modified="2006-10-14 10:33:11" + approved="1" + record_id="381"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="14.963280" avge_mass="14.9683" composition="H(-3) N(-1) O(2)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0122</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cys->PyruvicAcid" full_name="pyruvic acid from N-term cys" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 17:48:42" + date_time_modified="2006-10-13 16:42:55" + approved="1" + record_id="382"> + <umod:specificity hidden="1" site="C" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-33.003705" avge_mass="-33.0961" composition="H(-3) N(-1) O S(-1)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0127</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PYRUC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Ammonia-loss" full_name="Loss of ammonia" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:00:01" + date_time_modified="2007-07-15 20:11:01" + approved="0" + record_id="385"> + <umod:specificity hidden="0" site="C" position="Any N-term" classification="Artefact" + spec_group="3"> + <umod:misc_notes>Pyro-carbamidomethyl as a delta from Carbamidomethyl-Cys</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Protein N-term" + classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="T" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Chemical derivative" + spec_group="4"> + <umod:misc_notes>N-Succinimide</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-17.026549" avge_mass="-17.0305" composition="H(-3) N(-1)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="N" number="-1"/> + </umod:delta> + <umod:alt_name>oxobutanoic acid from N term Thr</umod:alt_name> + <umod:alt_name>pyruvic acid from N-term ser</umod:alt_name> + <umod:xref> + <umod:text>AA0127</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PYRUS</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0129</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>OXOB</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phycocyanobilin" full_name="phycocyanobilin" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:06:19" + date_time_modified="2006-10-16 17:07:44" + approved="1" + record_id="387"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="586.279135" avge_mass="586.6780" composition="H(38) C(33) N(4) O(6)"> + <umod:element symbol="H" number="38"/> + <umod:element symbol="C" number="33"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:alt_name>phycobiliviolin</umod:alt_name> + <umod:xref> + <umod:text>AA0258</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0131</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>phycocyanobilin and phycobiliviolin have different structures but the same empirical formula</umod:misc_notes> + </umod:mod> + <umod:mod title="Phycoerythrobilin" full_name="phycoerythrobilin" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:08:38" + date_time_modified="2006-10-16 17:08:02" + approved="1" + record_id="388"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="588.294785" avge_mass="588.6939" composition="H(40) C(33) N(4) O(6)"> + <umod:element symbol="H" number="40"/> + <umod:element symbol="C" number="33"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:xref> + <umod:text>AA0132</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phytochromobilin" full_name="phytochromobilin" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:23:58" + date_time_modified="2006-10-16 17:07:22" + approved="1" + record_id="389"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="584.263485" avge_mass="584.6621" composition="H(36) C(33) N(4) O(6)"> + <umod:element symbol="H" number="36"/> + <umod:element symbol="C" number="33"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:xref> + <umod:text>AA0133</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Heme" full_name="heme" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:27:20" + date_time_modified="2006-10-16 17:10:28" + approved="1" + record_id="390"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="616.177295" avge_mass="616.4873" + composition="H(32) C(34) N(4) O(4) Fe"> + <umod:element symbol="H" number="32"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="Fe" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0329</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0135</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0276</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Molybdopterin" full_name="molybdopterin" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:46:19" + date_time_modified="2006-10-16 17:02:25" + approved="1" + record_id="391"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="521.884073" avge_mass="520.2668" + composition="H(11) C(10) N(5) O(8) P S(2) Mo"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="8"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="S" number="2"/> + <umod:element symbol="Mo" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0142</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Quinone" full_name="quinone" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 18:56:28" + date_time_modified="2006-10-15 18:03:47" + approved="1" + record_id="392"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="29.974179" avge_mass="29.9829" composition="H(-2) O(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0147</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0148</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>TOPA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Glucosylgalactosyl" full_name="glucosylgalactosyl hydroxylysine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 19:19:13" + date_time_modified="2007-12-04 08:55:56" + approved="1" + record_id="393"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="O-linked glycosylation" + spec_group="1"> + <umod:NeutralLoss mono_mass="324.105647" avge_mass="324.2812" flag="false" composition="Hex(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="O" number="10"/> + </umod:NeutralLoss> + <umod:NeutralLoss mono_mass="162.052823" avge_mass="162.1406" flag="false" composition="Hex"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="5"/> + </umod:NeutralLoss> + <umod:PepNeutralLoss mono_mass="324.105647" avge_mass="324.2812" required="false" + composition="Hex(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="O" number="10"/> + </umod:PepNeutralLoss> + <umod:PepNeutralLoss mono_mass="162.052823" avge_mass="162.1406" required="false" composition="Hex"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="5"/> + </umod:PepNeutralLoss> + </umod:specificity> + <umod:delta mono_mass="340.100562" avge_mass="340.2806" composition="O Hex(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="O" number="11"/> + </umod:delta> + <umod:xref> + <umod:text>AA0153</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GPIanchor" full_name="glycosylphosphatidylinositol" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 19:31:10" + date_time_modified="2006-11-14 11:13:52" + approved="0" + record_id="394"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="123.008530" avge_mass="123.0477" composition="H(6) C(2) N O(3) P"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0158</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0159</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0160</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0161</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0162</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0163</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0164</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0165</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0166</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PhosphoribosyldephosphoCoA" + full_name="phosphoribosyl dephospho-coenzyme A" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 19:42:56" + date_time_modified="2006-10-16 17:19:42" + approved="1" + record_id="395"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="881.146904" avge_mass="881.6335" + composition="H(42) C(26) N(7) O(19) P(3) S"> + <umod:element symbol="H" number="42"/> + <umod:element symbol="C" number="26"/> + <umod:element symbol="N" number="7"/> + <umod:element symbol="O" number="19"/> + <umod:element symbol="P" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0167</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GlycerylPE" full_name="glycerylphosphorylethanolamine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 19:50:17" + date_time_modified="2006-10-16 15:08:39" + approved="1" + record_id="396"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="197.045310" avge_mass="197.1262" composition="H(12) C(5) N O(5) P"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0170</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Triiodothyronine" full_name="triiodo" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:08:28" + date_time_modified="2006-10-16 16:59:19" + approved="1" + record_id="397"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="469.716159" avge_mass="469.7850" composition="H C(6) O I(3)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="I" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>AA0177</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>THRN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Thyroxine" full_name="tetraiodo" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:10:14" + date_time_modified="2006-10-16 17:08:51" + approved="1" + record_id="398"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="595.612807" avge_mass="595.6815" composition="C(6) O I(4)"> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="I" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>AA0178</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>THRX</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Tyr->Dha" full_name="Dehydroalanine (from Tyrosine)" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:17:48" + date_time_modified="2006-10-13 15:02:50" + approved="1" + record_id="400"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-94.041865" avge_mass="-94.1112" composition="H(-6) C(-6) O(-1)"> + <umod:element symbol="H" number="-6"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0181</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Didehydro" full_name="2-amino-3-oxo-butanoic_acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:23:58" + date_time_modified="2008-07-30 12:01:47" + approved="1" + record_id="401"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="2"> + <umod:misc_notes>oxoalanine formylglycine</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Any C-term" classification="Artefact" + spec_group="4"> + <umod:misc_notes>Lactone formation from C-terminal hydroxylysine</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-2.015650" avge_mass="-2.0159" composition="H(-2)"> + <umod:element symbol="H" number="-2"/> + </umod:delta> + <umod:alt_name>oxoalanine</umod:alt_name> + <umod:xref> + <umod:text>AA0183</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0185</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0365</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>OXOAS</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DHY</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15705169</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cys->Oxoalanine" full_name="oxoalanine" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:29:10" + date_time_modified="2006-10-17 18:25:23" + approved="1" + record_id="402"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-17.992806" avge_mass="-18.0815" composition="H(-2) O S(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:alt_name>formylglycine</umod:alt_name> + <umod:xref> + <umod:text>AA0185</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>OXOAC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Dierks T, Miech C, Hummerjohann J, Schmidt B, Kertesz MA, von Figura K. Posttranslational formation of formylglycine in prokaryotic sulfatases by modification of either cysteine or serine. J. Biol. Chem. 1998; 273: 25 560</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Ser->LacticAcid" full_name="lactic acid from N-term Ser" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 20:34:16" + date_time_modified="2006-10-13 17:18:52" + approved="1" + record_id="403"> + <umod:specificity hidden="1" site="S" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-15.010899" avge_mass="-15.0146" composition="H(-1) N(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="N" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0186</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GluGlu" full_name="diglutamyl" username_of_poster="vcavett" + group_of_poster="users" + date_time_posted="2005-10-18 15:17:59" + date_time_modified="2006-10-17 13:49:07" + approved="0" + record_id="451"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="258.085186" avge_mass="258.2280" composition="H(14) C(10) N(2) O(6)"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + <umod:xref> + <umod:text>J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12356754</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phosphoadenosine" full_name="AMP binding site" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 21:34:01" + date_time_modified="2006-10-16 15:53:49" + approved="1" + record_id="405"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="4"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="329.052520" avge_mass="329.2059" + composition="H(12) C(10) N(5) O(6) P"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0371</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0227</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0203</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0267</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Glu" full_name="monoglutamyl" username_of_poster="vcavett" + group_of_poster="users" + date_time_posted="2005-10-18 15:07:18" + date_time_modified="2006-10-17 13:48:54" + approved="0" + record_id="450"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="129.042593" avge_mass="129.1140" composition="H(7) C(5) N O(3)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>12356754</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hydroxycinnamyl" full_name="hydroxycinnamyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 21:40:43" + date_time_modified="2006-10-16 14:02:07" + approved="1" + record_id="407"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="146.036779" avge_mass="146.1427" composition="H(6) C(9) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0207</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Glycosyl" full_name="glycosyl-L-hydroxyproline" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 21:57:16" + date_time_modified="2006-10-16 14:03:02" + approved="1" + record_id="408"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="O-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="148.037173" avge_mass="148.1140" composition="H(8) C(5) O(5)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>AA0212</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="FMNH" full_name="flavin mononucleotide" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 22:09:45" + date_time_modified="2006-10-16 16:57:46" + approved="1" + record_id="409"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="454.088965" avge_mass="454.3279" + composition="H(19) C(17) N(4) O(9) P"> + <umod:element symbol="H" number="19"/> + <umod:element symbol="C" number="17"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="9"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0353</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0220</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0352</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FMNH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Archaeol" full_name="S-diphytanylglycerol diether" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-11 22:15:37" + date_time_modified="2006-10-16 17:10:59" + approved="1" + record_id="410"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="634.662782" avge_mass="635.1417" composition="H(86) C(43) O(2)"> + <umod:element symbol="H" number="86"/> + <umod:element symbol="C" number="43"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0223</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>ARCH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Phenylisocyanate" full_name="phenyl isocyanate" + username_of_poster="TING" + group_of_poster="users" + date_time_posted="2005-10-14 21:13:16" + date_time_modified="2006-10-16 12:48:08" + approved="1" + record_id="411"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="119.037114" avge_mass="119.1207" composition="H(5) C(7) N O"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phenylisocyanate:2H(5)" full_name="d5-phenyl isocyanate" + username_of_poster="TING" + group_of_poster="users" + date_time_posted="2005-10-14 21:16:11" + date_time_modified="2006-10-16 13:35:26" + approved="1" + record_id="412"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="124.068498" avge_mass="124.1515" composition="2H(5) C(7) N O"> + <umod:element symbol="2H" number="5"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phosphoguanosine" full_name="phospho-guanosine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 15:50:03" + date_time_modified="2006-10-16 16:01:42" + approved="1" + record_id="413"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="345.047435" avge_mass="345.2053" + composition="H(12) C(10) N(5) O(7) P"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="7"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0325</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0228</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hydroxymethyl" full_name="hydroxymethyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 16:12:56" + date_time_modified="2006-10-15 18:04:18" + approved="1" + record_id="414"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="30.010565" avge_mass="30.0260" composition="H(2) C O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0236</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="MolybdopterinGD+Delta:S(-1)Se(1)" + full_name="L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 16:27:56" + date_time_modified="2006-10-17 11:44:58" + approved="1" + record_id="415"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="1620.930224" avge_mass="1618.9096" + composition="H(47) C(40) N(20) O(26) P(4) S(3) Se Mo"> + <umod:element symbol="H" number="47"/> + <umod:element symbol="C" number="40"/> + <umod:element symbol="N" number="20"/> + <umod:element symbol="O" number="26"/> + <umod:element symbol="P" number="4"/> + <umod:element symbol="S" number="3"/> + <umod:element symbol="Se" number="1"/> + <umod:element symbol="Mo" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0248</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dipyrrolylmethanemethyl" full_name="dipyrrolylmethanemethyl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 16:33:24" + date_time_modified="2006-11-14 10:37:01" + approved="1" + record_id="416"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="418.137616" avge_mass="418.3973" composition="H(22) C(20) N(2) O(8)"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="8"/> + </umod:delta> + <umod:xref> + <umod:text>AA0252</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PhosphoUridine" full_name="uridine phosphodiester" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 16:38:18" + date_time_modified="2006-10-16 15:52:11" + approved="1" + record_id="417"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="306.025302" avge_mass="306.1660" + composition="H(11) C(9) N(2) O(8) P"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="8"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0256</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Glycerophospho" full_name="glycerophospho" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:02:51" + date_time_modified="2006-10-16 14:03:40" + approved="1" + record_id="419"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="154.003110" avge_mass="154.0584" composition="H(7) C(3) O(5) P"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0264</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Carboxy->Thiocarboxy" full_name="thiocarboxylic acid" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:08:53" + date_time_modified="2006-10-14 10:59:20" + approved="1" + record_id="420"> + <umod:specificity hidden="1" site="G" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="15.977156" avge_mass="16.0656" composition="O(-1) S"> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>THIOG</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0265</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Sulfide" full_name="persulfide" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:22:45" + date_time_modified="2006-10-15 18:05:03" + approved="1" + record_id="421"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="31.972071" avge_mass="32.0650" composition="S"> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>CYSP</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0269</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PyruvicAcidIminyl" full_name="N-pyruvic acid 2-iminyl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:30:48" + date_time_modified="2006-10-16 10:35:08" + approved="1" + record_id="422"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="V" position="Protein N-term" + classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Protein N-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="70.005479" avge_mass="70.0468" composition="H(2) C(3) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0287</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0274</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0275</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Delta:Se(1)" full_name="selenyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:49:48" + date_time_modified="2006-10-16 11:14:44" + approved="1" + record_id="423"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="79.916520" avge_mass="78.9600" composition="Se"> + <umod:element symbol="Se" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0277</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="MolybdopterinGD" + full_name="molybdenum bis(molybdopterin guanine dinucleotide)" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:53:48" + date_time_modified="2006-10-17 11:44:28" + approved="1" + record_id="424"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="1572.985775" avge_mass="1572.0146" + composition="H(47) C(40) N(20) O(26) P(4) S(4) Mo"> + <umod:element symbol="H" number="47"/> + <umod:element symbol="C" number="40"/> + <umod:element symbol="N" number="20"/> + <umod:element symbol="O" number="26"/> + <umod:element symbol="P" number="4"/> + <umod:element symbol="S" number="4"/> + <umod:element symbol="Mo" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0281</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0375</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dioxidation" full_name="dihydroxy" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 17:59:33" + date_time_modified="2006-10-15 18:19:52" + approved="1" + record_id="425"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Post-translational" + spec_group="7"> + <umod:misc_notes>trihydroxyphenylalanine</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Chemical derivative" + spec_group="6"> + <umod:misc_notes>tryptophan oxidation to formylkynurenin</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="Chemical derivative" + spec_group="5"> + <umod:misc_notes>phenylalanine oxidation to dihydroxyphenylalanine</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="M" position="Anywhere" classification="Post-translational" + spec_group="4"> + <umod:misc_notes>Sulphone</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="3"/> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="8"> + <umod:misc_notes>sulfinic acid</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="31.989829" avge_mass="31.9988" composition="O(2)"> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>12686488</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0262</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CSIA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>MSONE</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DIHYDR</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>9252331</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0251</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0370</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0282</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0369</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0263</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Hyun Ae Woo, et. al., Science Vol. 300. no. 5619, pp. 653 - 656</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Octanoyl" full_name="octanoyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 18:04:46" + date_time_modified="2006-10-16 13:38:44" + approved="1" + record_id="426"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="126.104465" avge_mass="126.1962" composition="H(14) C(8) O"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0386</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0290</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>OCTA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PhosphoHexNAc" full_name="N-acetylglucosamine-1-phosphoryl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 18:15:16" + date_time_modified="2006-10-16 15:48:40" + approved="1" + record_id="428"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other glycosylation" + spec_group="1"/> + <umod:delta mono_mass="283.045704" avge_mass="283.1724" composition="H O(3) P HexNAc"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="8"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0296</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PhosphoHex" full_name="phosphoglycosyl-D-mannose-1-phosphoryl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 18:18:51" + date_time_modified="2006-10-16 15:48:55" + approved="1" + record_id="429"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Other glycosylation" + spec_group="1"/> + <umod:delta mono_mass="242.019154" avge_mass="242.1205" composition="H O(3) P Hex"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="8"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0297</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Palmitoleyl" full_name="palmitoleyl" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 19:57:30" + date_time_modified="2006-10-16 15:36:51" + approved="1" + record_id="431"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="236.214016" avge_mass="236.3929" composition="H(28) C(16) O"> + <umod:element symbol="H" number="28"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0308</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PALE</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cholesterol" full_name="cholesterol ester" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:00:10" + date_time_modified="2006-10-16 16:36:21" + approved="1" + record_id="432"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="368.344302" avge_mass="368.6383" composition="H(44) C(27)"> + <umod:element symbol="H" number="44"/> + <umod:element symbol="C" number="27"/> + </umod:delta> + <umod:xref> + <umod:text>AA0309</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CHOL</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Didehydroretinylidene" full_name="3,4-didehydroretinylidene" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:05:19" + date_time_modified="2006-10-16 15:46:50" + approved="1" + record_id="433"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="264.187801" avge_mass="264.4046" composition="H(24) C(20)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="20"/> + </umod:delta> + <umod:xref> + <umod:text>AA0312</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="CHDH" full_name="cis-14-hydroxy-10,13-dioxo-7-heptadecenoic ester" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:08:49" + date_time_modified="2006-10-16 15:49:28" + approved="1" + record_id="434"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="294.183109" avge_mass="294.3859" composition="H(26) C(17) O(4)"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="17"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>AA0316</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>CHDH</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methylpyrroline" full_name="4-methyl-delta-1-pyrroline-5-carboxyl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:21:00" + date_time_modified="2006-10-16 13:37:33" + approved="1" + record_id="435"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="109.052764" avge_mass="109.1259" composition="H(7) C(6) N O"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0321</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>PYRK</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hydroxyheme" full_name="hydroxyheme" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:29:16" + date_time_modified="2006-10-16 17:10:10" + approved="1" + record_id="436"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="614.161645" avge_mass="614.4714" + composition="H(30) C(34) N(4) O(4) Fe"> + <umod:element symbol="H" number="30"/> + <umod:element symbol="C" number="34"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="Fe" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0324</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="MicrocinC7" + full_name="(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5-adenosine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:36:37" + date_time_modified="2006-10-16 16:40:21" + approved="1" + record_id="437"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="386.110369" avge_mass="386.3003" + composition="H(19) C(13) N(6) O(6) P"> + <umod:element symbol="H" number="19"/> + <umod:element symbol="C" number="13"/> + <umod:element symbol="N" number="6"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0328</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Cyano" full_name="cyano" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:42:40" + date_time_modified="2006-10-14 19:43:48" + approved="1" + record_id="438"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="24.995249" avge_mass="25.0095" composition="H(-1) C N"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0333</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diironsubcluster" full_name="hydrogenase diiron subcluster" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:46:03" + date_time_modified="2006-10-16 16:01:22" + approved="1" + record_id="439"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="342.786916" avge_mass="342.8760" + composition="H(-1) C(5) N(2) O(5) S(2) Fe(2)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="2"/> + <umod:element symbol="Fe" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0334</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Amidino" full_name="amidino" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 20:49:10" + date_time_modified="2006-10-15 19:58:03" + approved="1" + record_id="440"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="42.021798" avge_mass="42.0400" composition="H(2) C N(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>AA0335</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="FMN" full_name="O3-(riboflavin phosphoryl)" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 21:11:32" + date_time_modified="2006-10-16 16:47:27" + approved="1" + record_id="442"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="438.094051" avge_mass="438.3285" + composition="H(19) C(17) N(4) O(8) P"> + <umod:element symbol="H" number="19"/> + <umod:element symbol="C" number="17"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="8"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0350</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0349</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FMN</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="FMNC" full_name="S-(4a-FMN)" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 21:21:47" + date_time_modified="2006-10-16 16:58:10" + approved="1" + record_id="443"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="456.104615" avge_mass="456.3438" + composition="H(21) C(17) N(4) O(9) P"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="17"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="9"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0351</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>FMNC</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="CuSMo" full_name="copper sulfido molybdopterin cytosine dinuncleotide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 21:34:38" + date_time_modified="2006-10-16 17:20:14" + approved="1" + record_id="444"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="922.834855" avge_mass="922.0670" + composition="H(24) C(19) N(8) O(15) P(2) S(3) Cu Mo"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="8"/> + <umod:element symbol="O" number="15"/> + <umod:element symbol="P" number="2"/> + <umod:element symbol="S" number="3"/> + <umod:element symbol="Mo" number="1"/> + <umod:element symbol="Cu" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0355</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hydroxytrimethyl" full_name="5-hydroxy-N6,N6,N6-trimethyl" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 21:40:08" + date_time_modified="2006-10-16 10:28:02" + approved="1" + record_id="445"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="59.049690" avge_mass="59.0871" composition="H(7) C(3) O"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0359</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>TRIMETK</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Deoxy" full_name="reduction" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 22:00:35" + date_time_modified="2006-10-13 17:16:30" + approved="1" + record_id="447"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="3"> + <umod:misc_notes>Beta elimination of O-glycosylation under alkaline conditions followed by reduction</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>Beta elimination of O-glycosylation under alkaline conditions followed by reduction</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="-15.994915" avge_mass="-15.9994" composition="O(-1)"> + <umod:element symbol="O" number="-1"/> + </umod:delta> + <umod:alt_name>Serine to Alanine</umod:alt_name> + <umod:alt_name>Threonine to a-aminobutyrate</umod:alt_name> + <umod:xref> + <umod:text>AA0191</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>14235557</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0373</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Microcin" full_name="microcin E492 siderophore ester from serine" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 22:04:46" + date_time_modified="2006-10-16 17:18:24" + approved="1" + record_id="448"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="831.197041" avge_mass="831.6871" + composition="H(37) C(36) N(3) O(20)"> + <umod:element symbol="H" number="37"/> + <umod:element symbol="C" number="36"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="20"/> + </umod:delta> + <umod:xref> + <umod:text>AA0374</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Decanoyl" full_name="lipid" username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2005-10-15 22:14:11" + date_time_modified="2006-10-16 14:04:24" + approved="1" + record_id="449"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="154.135765" avge_mass="154.2493" composition="H(18) C(10) O"> + <umod:element symbol="H" number="18"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>AA0387</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>AA0385</umod:text> + <umod:source>RESID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>DECA</umod:text> + <umod:source>FindMod</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GluGluGlu" full_name="triglutamyl" username_of_poster="vcavett" + group_of_poster="users" + date_time_posted="2005-10-18 15:21:01" + date_time_modified="2006-10-17 14:11:11" + approved="0" + record_id="452"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:delta mono_mass="387.127779" avge_mass="387.3419" composition="H(21) C(15) N(3) O(9)"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="9"/> + </umod:delta> + <umod:xref> + <umod:text>12356754</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="GluGluGluGlu" full_name="tetraglutamyl" username_of_poster="vcavett" + group_of_poster="users" + date_time_posted="2005-10-18 15:22:24" + date_time_modified="2006-10-17 14:16:56" + approved="0" + record_id="453"> + <umod:specificity hidden="1" site="C-term" position="Protein C-term" + classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:delta mono_mass="516.170373" avge_mass="516.4559" + composition="H(28) C(20) N(4) O(12)"> + <umod:element symbol="H" number="28"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="12"/> + </umod:delta> + <umod:xref> + <umod:text>J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12356754</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="HexN" full_name="Hexosamine" username_of_poster="xyuan" + group_of_poster="users" + date_time_posted="2005-11-08 18:58:20" + date_time_modified="2006-10-16 14:09:11" + approved="1" + record_id="454"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="N-linked glycosylation" + spec_group="4"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" + classification="Synth. pep. protect. gp." + spec_group="1"/> + <umod:delta mono_mass="161.068808" avge_mass="161.1558" composition="H(11) C(6) N O(4)"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:alt_name>Galactosamine</umod:alt_name> + <umod:alt_name>Glucosamine</umod:alt_name> + </umod:mod> + <umod:mod title="Xlink:DMP-s" full_name="One end of crosslink attached, one end free" + username_of_poster="mariana" + group_of_poster="users" + date_time_posted="2005-11-08 20:09:24" + date_time_modified="2006-10-17 13:39:17" + approved="0" + record_id="455"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="154.110613" avge_mass="154.2096" composition="H(14) C(8) N(2) O"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Dimethyl pimelimidate</umod:alt_name> + <umod:xref> + <umod:text>Imidoester Cross-linkers</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/files/0668ss5.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Packman, L.C. and Perhan, R.N. (1982). Quaternary Structures the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus Stearothermophilus Studies by a New Reversible Crosslinking Procedure with Bis(imidoesters). Biochem. 21, 5171-5175.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Xlink:DMP" full_name="Both ends of crosslink attached to same peptide" + username_of_poster="mariana" + group_of_poster="users" + date_time_posted="2005-11-08 20:15:20" + date_time_modified="2006-10-17 13:38:09" + approved="0" + record_id="456"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>Dimethyl pimelimidate, reaction with both ends</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>Dimethyl pimelimidate, reaction with both ends</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="122.084398" avge_mass="122.1677" composition="H(10) C(7) N(2)"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="2"/> + </umod:delta> + <umod:alt_name>Dimethyl pimelimidate</umod:alt_name> + <umod:xref> + <umod:text>Imidoester Cross-linkers</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/files/0668ss5.pdf</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Packman, L.C. and Perhan, R.N. (1982). Quaternary Structures the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus StearothermophilusStudies by a New Reversible Crosslinking Procedure with Bis(imidoesters). Biochem. 21, 5171-5175.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="NDA" full_name="naphthalene-2,3-dicarboxaldehyde" + username_of_poster="Dekker" + group_of_poster="users" + date_time_posted="2005-11-11 11:03:32" + date_time_modified="2006-10-17 13:41:04" + approved="0" + record_id="457"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="175.042199" avge_mass="175.1855" composition="H(5) C(13) N"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="13"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>2081203</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>fluorescent derivative</umod:misc_notes> + </umod:mod> + <umod:mod title="SPITC:13C(6)" full_name="4-sulfophenyl isothiocyanate (Heavy C13)" + username_of_poster="apanchaud" + group_of_poster="users" + date_time_posted="2005-12-19 08:37:57" + date_time_modified="2006-10-16 15:25:36" + approved="1" + record_id="464"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="220.991213" avge_mass="221.2054" + composition="H(5) C 13C(6) N O(3) S(2)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:alt_name>N-terminal / lysine sulfonation</umod:alt_name> + <umod:xref> + <umod:text>16526082</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Lee et al, Rapid Commun Mass Spetrom 2004, 18, 3019-3027</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="TMAB:2H(9)" full_name="d9-4-trimethyllammoniumbutyryl-" + username_of_poster="xwei" + group_of_poster="users" + date_time_posted="2006-02-15 18:36:06" + date_time_modified="2006-10-17 12:08:34" + approved="0" + record_id="477"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"> + <umod:NeutralLoss mono_mass="68.129990" avge_mass="68.1657" flag="false" + composition="2H(9) C(3) N"> + <umod:element symbol="2H" number="9"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:NeutralLoss mono_mass="68.129990" avge_mass="68.1657" flag="false" + composition="2H(9) C(3) N"> + <umod:element symbol="2H" number="9"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:delta mono_mass="137.164030" avge_mass="137.2476" composition="H(5) 2H(9) C(7) N O"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="2H" number="9"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>J. Mass Spectrom. 2005; 40: 238-249</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="TMAB" full_name="4-trimethyllammoniumbutyryl-" username_of_poster="xwei" + group_of_poster="users" + date_time_posted="2006-02-15 03:10:16" + date_time_modified="2006-10-17 12:08:04" + approved="0" + record_id="476"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"> + <umod:NeutralLoss mono_mass="59.073499" avge_mass="59.1103" flag="false" + composition="H(9) C(3) N"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:NeutralLoss mono_mass="59.073499" avge_mass="59.1103" flag="false" + composition="H(9) C(3) N"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + </umod:NeutralLoss> + </umod:specificity> + <umod:delta mono_mass="128.107539" avge_mass="128.1922" composition="H(14) C(7) N O"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>J. Mass Spectrom. 2005; 40: 238-249</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="FTC" full_name="fluorescein-5-thiosemicarbazide" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2006-02-20 11:15:03" + date_time_modified="2006-10-16 16:45:27" + approved="1" + record_id="478"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="5"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="4"/> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="421.073241" avge_mass="421.4259" + composition="H(15) C(21) N(3) O(5) S"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="21"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Ahn, B., Rhee, S.G., and Stadtmann, E. R. (1987) Anal. Biochem.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="AEC-MAEC" full_name="aminoethylcysteine" username_of_poster="mpcusack" + group_of_poster="users" + date_time_posted="2006-01-20 00:46:08" + date_time_modified="2007-09-26 22:43:16" + approved="0" + record_id="472"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>pT gives beta-methylaminoethylcysteine</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>pS gives aminoethylcysteine</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="59.019355" avge_mass="59.1334" composition="H(5) C(2) N O(-1) S"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>beta-methylaminoethylcysteine</umod:alt_name> + <umod:xref> + <umod:text>Z. A. Knight et al, Nature Biotech., 21(9) 1047-1054 (2003)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Modification procedure used for phosphopeptide mapping</umod:misc_notes> + </umod:mod> + <umod:mod title="BADGE" full_name="Bisphenol A diglycidyl ether derivative" + username_of_poster="TNO" + group_of_poster="users" + date_time_posted="2006-03-27 09:30:54" + date_time_modified="2006-10-17 14:09:11" + approved="0" + record_id="493"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Non-standard residue" + spec_group="1"> + <umod:misc_notes>found in canned food products</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="340.167459" avge_mass="340.4129" composition="H(24) C(21) O(4)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="21"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>Berger U, Oehme M, Girardin L., Fresenius J Anal Chem. 2001 Jan 2;369(2):115-23.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Found in canned food products</umod:misc_notes> + </umod:mod> + <umod:mod title="Label:2H(4)" full_name="4,4,5,5-D4 Lysine" username_of_poster="yunwah" + group_of_poster="users" + date_time_posted="2006-02-20 11:44:19" + date_time_modified="2006-10-17 11:52:44" + approved="0" + record_id="481"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="4.025107" avge_mass="4.0246" composition="H(-4) 2H(4)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="2H" number="4"/> + </umod:delta> + <umod:alt_name>K4</umod:alt_name> + <umod:misc_notes>For SILAC experiments</umod:misc_notes> + </umod:mod> + <umod:mod title="Hep" full_name="Heptose" username_of_poster="anikolakakis" + group_of_poster="users" + date_time_posted="2006-03-24 15:59:43" + date_time_modified="2006-10-16 15:08:16" + approved="1" + record_id="490"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="6"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="O-linked glycosylation" + spec_group="5"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="N-linked glycosylation" + spec_group="4"/> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="N-linked glycosylation" + spec_group="3"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="N-linked glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="N-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="192.063388" avge_mass="192.1666" composition="Hep"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + </umod:mod> + <umod:mod title="CyDye-Cy5" full_name="Cy5 CyDye DIGE Fluor saturation dye" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2006-03-27 11:53:04" + date_time_modified="2006-10-17 14:18:49" + approved="0" + record_id="495"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="684.298156" avge_mass="684.8442" + composition="H(44) C(38) N(4) O(6) S"> + <umod:element symbol="H" number="44"/> + <umod:element symbol="C" number="38"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Amersham (GE Healthcare) instruction leaflet 25800983PL Rev-B, 2003</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>12872219</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="DHP" + full_name="Dehydropyrrolizidine alkaloid (dehydroretronecine) on cysteines" + username_of_poster="rowanrainbow" + group_of_poster="users" + date_time_posted="2006-03-07 08:40:13" + date_time_modified="2006-10-17 12:07:19" + approved="0" + record_id="488"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="118.065674" avge_mass="118.1558" composition="H(8) C(8) N"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:alt_name>Dehydroretronecine</umod:alt_name> + <umod:xref> + <umod:text>16222722</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="BHTOH" + full_name="Michael addition of t-butyl hydroxylated BHT (BHTOH) to C, H or K" + username_of_poster="rkupfer" + group_of_poster="users" + date_time_posted="2006-04-10 19:27:51" + date_time_modified="2006-10-17 13:42:22" + approved="0" + record_id="498"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Other" spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="1"> + <umod:misc_notes>primary adduct</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="3"/> + <umod:delta mono_mass="234.161980" avge_mass="234.3340" composition="H(22) C(15) O(2)"> + <umod:element symbol="H" number="22"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>t-butyl hydroxylated BHT</umod:alt_name> + <umod:xref> + <umod:text>16533022</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>BHTOH is formed upon metabolism of BHT with P450 enzymes. The BHTOH is further metabolized to its quinone methide (electrophile) which reacts with -SH and -NH2 groups</umod:misc_notes> + </umod:mod> + <umod:mod title="IGBP:13C(2)" full_name="Heavy IDBEST tag for quantitation" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2006-04-14 18:44:41" + date_time_modified="2006-10-19 10:48:25" + approved="1" + record_id="499"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="298.022748" avge_mass="299.1331" + composition="H(13) C(10) 13C(2) N(2) O(2) Br"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="13C" number="2"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="Br" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Under construction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.targetdiscovery.com/index.php?topic=prod.idbe</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Target discovery , Inc. IDBEST IGBP user manual</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Nmethylmaleimide+water" full_name="Nmethylmaleimidehydrolysis" + username_of_poster="whaskins" + group_of_poster="users" + date_time_posted="2006-04-14 22:58:34" + date_time_modified="2006-10-17 12:12:40" + approved="0" + record_id="500"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="129.042593" avge_mass="129.1140" composition="H(7) C(5) N O(3)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:xref> + <umod:text>Chemistry of Protein Conjugation and Crosslinking by Shan S. Wong, 1991, pg.32</umod:text> + <umod:source>Book</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="PyMIC" full_name="3-methyl-2-pyridyl isocyanate" + username_of_poster="TING" + group_of_poster="users" + date_time_posted="2006-04-18 20:46:17" + date_time_modified="2006-10-17 12:19:15" + approved="0" + record_id="501"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="134.048013" avge_mass="134.1353" composition="H(6) C(7) N(2) O"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="LG-lactam-K" full_name="Levuglandinyl - lysine lactam adduct" + username_of_poster="alexparf" + group_of_poster="users" + date_time_posted="2006-04-27 17:56:39" + date_time_modified="2006-11-14 12:04:37" + approved="0" + record_id="503"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="332.198760" avge_mass="332.4339" composition="H(28) C(20) O(4)"> + <umod:element symbol="H" number="28"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15650407</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15752459</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="BisANS" + full_name="4,4\'-dianilino-1,1\'-binaphthyl-5,5\'-disulfonic acid" + username_of_poster="app95d" + group_of_poster="users" + date_time_posted="2006-07-05 23:31:08" + date_time_modified="2006-10-17 14:18:24" + approved="0" + record_id="519"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="592.076278" avge_mass="592.6410" + composition="H(20) C(32) N(2) O(6) S(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="32"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Pierce, A., Dewaal, E., Vanremmen, H., Richardson, A. & Chaudhuri, A. (2006). A Novel Approach for Screening the Proteome for Changes in Protein Conformation. Biochemistry 45, 3077-3085.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Piperidine" full_name="Piperidination" username_of_poster="PhilipHsu" + group_of_poster="users" + date_time_posted="2006-07-20 08:37:21" + date_time_modified="2006-10-17 12:05:44" + approved="0" + record_id="520"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="68.062600" avge_mass="68.1170" composition="H(8) C(5)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>Jue-Liang Hsu, Sheng-Yu Huang, and Shu-Hui Chen. Stable-Isotope based Multiplex Labeling Coupled with LC-MS/MS, HUPO 3rd ANNUAL WORLD CONGRESS, Bejing (China) 2004</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Diethyl" full_name="Diethylation, analogous to Dimethylation" + username_of_poster="PhilipHsu" + group_of_poster="users" + date_time_posted="2006-06-15 07:18:26" + date_time_modified="2006-10-17 12:00:33" + approved="0" + record_id="518"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="56.062600" avge_mass="56.1063" composition="H(8) C(4)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>J. Proteome Res. 2005, 4, 101-108.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="LG-Hlactam-K" full_name="Levuglandinyl - lysine hydroxylactam adduct" + username_of_poster="alexparf" + group_of_poster="users" + date_time_posted="2006-04-27 18:02:17" + date_time_modified="2006-11-14 12:04:47" + approved="0" + record_id="504"> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Post-translational" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="348.193674" avge_mass="348.4333" composition="H(28) C(20) O(5)"> + <umod:element symbol="H" number="28"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15650407</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15752459</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Dimethyl:2H(4)13C(2)" full_name="DiMethyl-C13HD2" + username_of_poster="oded" + group_of_poster="users" + date_time_posted="2006-05-08 22:03:41" + date_time_modified="2006-10-15 18:26:15" + approved="1" + record_id="510"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="34.063117" avge_mass="34.0631" composition="2H(4) 13C(2)"> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="13C" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>16335955</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>J Proteome Res. 2005 Nov-Dec;4(6):2099-108</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="C8-QAT" + full_name="[3-(2,5)-Dioxopyrrolidin-1-yloxycarbonyl)-propyl]dimethyloctylammonium" + username_of_poster="amadian" + group_of_poster="users" + date_time_posted="2006-05-13 20:55:20" + date_time_modified="2006-12-03 19:43:27" + approved="0" + record_id="513"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="227.224915" avge_mass="227.3862" composition="H(29) C(14) N O"> + <umod:element symbol="H" number="29"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>16771548</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Hex(2)" full_name="Lactosylation" username_of_poster="molle" + group_of_poster="users" + date_time_posted="2006-05-11 13:21:17" + date_time_modified="2006-10-17 13:44:30" + approved="0" + record_id="512"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Other glycosylation" + spec_group="2"> + <umod:misc_notes>Maillard reaction (first event)</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other glycosylation" + spec_group="1"> + <umod:misc_notes>Maillard reaction (first event)</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="324.105647" avge_mass="324.2812" composition="Hex(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="O" number="10"/> + </umod:delta> + <umod:alt_name>lac</umod:alt_name> + <umod:xref> + <umod:text>ANALYTICAL BIOCHEMISTRY 259, 152-161 (1998)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>BIOCHIMECAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 236, 413-417 (1997)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Lactosylation of bovine Beta-Lactoglobulin</umod:misc_notes> + </umod:mod> + <umod:mod title="LG-lactam-R" full_name="Levuglandinyl - arginine lactam adduct" + username_of_poster="alexparf" + group_of_poster="users" + date_time_posted="2006-04-27 18:05:11" + date_time_modified="2006-10-17 14:08:20" + approved="0" + record_id="505"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="290.176961" avge_mass="290.3939" + composition="H(26) C(19) N(-2) O(4)"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>15650407</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15752459</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="CLIP_TRAQ_1" full_name="CLIP_TRAQ_1" username_of_poster="overalllab" + group_of_poster="users" + date_time_posted="2006-09-15 02:21:17" + date_time_modified="2006-10-17 18:03:21" + approved="0" + record_id="524"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Side reaction, low abundance</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="140.094963" avge_mass="140.1830" composition="H(12) C(7) N(2) O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>CLIP_TRAQ_single</umod:alt_name> + <umod:misc_notes>CLIP-TRAQ-1 H(17) C(11) N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 140.0949 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode is 113 m/z. (See also CLIP-TRAQ-2).</umod:misc_notes> + </umod:mod> + <umod:mod title="CLIP_TRAQ_2" full_name="CLIP_TRAQ_2" username_of_poster="overalllab" + group_of_poster="users" + date_time_posted="2006-09-15 02:25:46" + date_time_modified="2006-10-17 18:04:46" + approved="0" + record_id="525"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Side reaction, low abundance</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="141.098318" avge_mass="141.1756" composition="H(12) C(6) 13C N(2) O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="13C" number="1"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>CLIP_TRAQ_double</umod:alt_name> + <umod:misc_notes>CLIP-TRAQ-2 H(17) C(10) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 141.0983 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 113 or 114 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation).</umod:misc_notes> + </umod:mod> + <umod:mod title="LG-Hlactam-R" full_name="Levuglandinyl - arginine hydroxylactam adduct" + username_of_poster="alexparf" + group_of_poster="users" + date_time_posted="2006-04-27 18:08:11" + date_time_modified="2006-10-17 14:08:30" + approved="0" + record_id="506"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="306.171876" avge_mass="306.3933" + composition="H(26) C(19) N(-2) O(5)"> + <umod:element symbol="H" number="26"/> + <umod:element symbol="C" number="19"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>15650407</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15752459</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Maleimide-PEO2-Biotin" full_name="Maleimide-PEO2-Biotin" + username_of_poster="ericjohansen" + group_of_poster="users" + date_time_posted="2006-08-11 02:49:51" + date_time_modified="2006-10-17 14:17:58" + approved="0" + record_id="522"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="525.225719" avge_mass="525.6183" + composition="H(35) C(23) N(5) O(7) S"> + <umod:element symbol="H" number="35"/> + <umod:element symbol="C" number="23"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="7"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Maleimide-PEG-Biotin</umod:alt_name> + <umod:xref> + <umod:text>EZ-Link Maleimide PEOn-Biotin</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=01031005</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Sulfo-NHS-LC-LC-Biotin" full_name="Sulfo-NHS-LC-LC-Biotin" + username_of_poster="unimod" + group_of_poster="admin" + date_time_posted="2006-08-31 18:01:50" + date_time_modified="2006-10-17 14:16:14" + approved="0" + record_id="523"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="452.245726" avge_mass="452.6106" + composition="H(36) C(22) N(4) O(4) S"> + <umod:element symbol="H" number="36"/> + <umod:element symbol="C" number="22"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>EZ-Link Sulfo-NHS-Biotin Reagents</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=8D38BA83-EFDC-421A-853F-E96EBA380612</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="FNEM" full_name="fluorescein-5-maleimide" username_of_poster="shure" + group_of_poster="users" + date_time_posted="2006-06-08 10:07:56" + date_time_modified="2006-10-17 14:15:03" + approved="0" + record_id="515"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>photosensitive</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="427.069202" avge_mass="427.3625" composition="H(13) C(24) N O(7)"> + <umod:element symbol="H" number="13"/> + <umod:element symbol="C" number="24"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="7"/> + </umod:delta> + <umod:alt_name>fluorescein-NEM</umod:alt_name> + <umod:xref> + <umod:text>9325338</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11665566</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Thiol-Reactive Probes</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://probes.invitrogen.com/media/pis/mp00003.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="PropylNAGthiazoline" + full_name="propyl-1,2-dideoxy-2\'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2\'-thiazoline" + username_of_poster="mmacaule" + group_of_poster="users" + date_time_posted="2006-05-18 18:44:52" + date_time_modified="2006-11-14 10:35:19" + approved="0" + record_id="514"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other glycosylation" + spec_group="1"/> + <umod:delta mono_mass="232.064354" avge_mass="232.2768" composition="H(14) C(9) N O(4) S"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>15795231</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>In a recent publication (see reference), we have shown that family 84 glycoside hydrolases contain a deep pocket beneath the 2-acetamido group of its substrate (N-acetyl-glucosamine). With this strucual feature in mind, we have designed a specific inhibitor that contains a chloride group appended to the end of the propyl chain on a known inhibitor termed propyl-NAG-thiazoline. We have shown kinetically that this molecule is a potent suicide inhibitor of this enzyme famiy and now wish to know the precise residue which is acting as the nucleophile to dispace the choride atom. We have included all residues that are in the vacinity of the chloride atom that could potentially act in a nucleophilic manner.</umod:misc_notes> + </umod:mod> + <umod:mod title="Dethiomethyl" full_name="Prompt loss of side chain from oxidised Met" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-13 15:14:55" + date_time_modified="2006-10-13 17:02:27" + approved="1" + record_id="526"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="Artefact" + spec_group="1"/> + <umod:delta mono_mass="-48.003371" avge_mass="-48.1075" composition="H(-4) C(-1) S(-1)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>9004526</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>More commonly seen as a neutral loss</umod:misc_notes> + </umod:mod> + <umod:mod title="iTRAQ4plex114" full_name="Accurate mass for 114" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-16 13:46:49" + date_time_modified="2006-12-09 18:48:09" + approved="0" + record_id="532"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="144.105918" avge_mass="144.1680" + composition="H(12) C(5) 13C(2) N(2) 18O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="13C" number="2"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="18O" number="1"/> + </umod:delta> + <umod:alt_name>Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry</umod:alt_name> + <umod:xref> + <umod:text>Applied Biosystems Chemistry Reference Guide</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf</umod:url> + </umod:xref> + <umod:misc_notes>Different channels have the same nominal mass but slightly different exact masses.</umod:misc_notes> + </umod:mod> + <umod:mod title="iTRAQ4plex115" full_name="Accurate mass for 115" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-16 13:48:16" + date_time_modified="2006-12-09 18:47:52" + approved="0" + record_id="533"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="144.099599" avge_mass="144.1688" + composition="H(12) C(6) 13C N 15N 18O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="13C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="15N" number="1"/> + <umod:element symbol="18O" number="1"/> + </umod:delta> + <umod:alt_name>Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry</umod:alt_name> + <umod:xref> + <umod:text>Applied Biosystems Chemistry Reference Guide</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf</umod:url> + </umod:xref> + <umod:misc_notes>Different channels have the same nominal mass but slightly different exact masses.</umod:misc_notes> + </umod:mod> + <umod:mod title="Dibromo" full_name="Dibromo" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-16 14:06:38" + date_time_modified="2006-10-16 14:06:38" + approved="1" + record_id="534"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="155.821022" avge_mass="157.7921" composition="H(-2) Br(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="Br" number="2"/> + </umod:delta> + </umod:mod> + <umod:mod title="LeuArgGlyGly" full_name="Ubiquitination" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-10-16 16:39:05" + date_time_modified="2006-10-16 16:39:05" + approved="1" + record_id="535"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="383.228103" avge_mass="383.4460" composition="H(29) C(16) N(7) O(4)"> + <umod:element symbol="H" number="29"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="N" number="7"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:alt_name>Addition of LRGG</umod:alt_name> + </umod:mod> + <umod:mod title="CLIP_TRAQ_3" full_name="CLIP_TRAQ_3" username_of_poster="overall" + group_of_poster="" + date_time_posted="2006-10-17 18:08:00" + date_time_modified="2006-10-17 18:11:03" + approved="0" + record_id="536"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="271.148736" avge_mass="271.2976" + composition="H(20) C(11) 13C N(3) O(4)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="13C" number="1"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:misc_notes>CLIP_TRAQ_3 (H(20) C(11) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 155.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 127 or 128 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation).</umod:misc_notes> + </umod:mod> + <umod:mod title="CLIP_TRAQ_4" full_name="CLIP_TRAQ_4" username_of_poster="overall" + group_of_poster="" + date_time_posted="2006-10-17 18:09:22" + date_time_modified="2006-10-17 18:10:05" + approved="0" + record_id="537"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="244.101452" avge_mass="244.2292" + composition="H(15) C(9) 13C N(2) O(5)"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="13C" number="1"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="5"/> + </umod:delta> + <umod:misc_notes>CLIP_TRAQ_4 is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 128.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 100 or 101 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation).</umod:misc_notes> + </umod:mod> + <umod:mod title="15dB-biotin" + full_name="15-deoxy-delta 12,14-Prostaglandin J2-biotinimide" + username_of_poster="sevgh" + group_of_poster="" + date_time_posted="2006-10-17 18:13:45" + date_time_modified="2006-10-17 18:13:45" + approved="0" + record_id="538"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="626.386577" avge_mass="626.8927" + composition="H(54) C(35) N(4) O(4) S"> + <umod:element symbol="H" number="54"/> + <umod:element symbol="C" number="35"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Cayman Chemical data sheet</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.caymanchem.com/pdfs/10141.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="PGA1-biotin" full_name="Prostaglandin A1-biotinimide" + username_of_poster="sevgh" + group_of_poster="" + date_time_posted="2006-10-17 18:24:06" + date_time_modified="2006-10-17 18:24:06" + approved="0" + record_id="539"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="660.428442" avge_mass="660.9504" + composition="H(60) C(36) N(4) O(5) S"> + <umod:element symbol="H" number="60"/> + <umod:element symbol="C" number="36"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="5"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Cayman Chemical data sheet</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.caymanchem.com/pdfs/10013.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Ala->Ser" full_name="Ala->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:07:30" + date_time_modified="2006-11-09 10:07:30" + approved="0" + record_id="540"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="15.994915" avge_mass="15.9994" composition="O"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Thr" full_name="Ala->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:13:43" + date_time_modified="2006-11-09 10:13:43" + approved="0" + record_id="541"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="30.010565" avge_mass="30.0260" composition="H(2) C O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Asp" full_name="Ala->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:15:05" + date_time_modified="2006-11-09 10:15:05" + approved="0" + record_id="542"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="43.989829" avge_mass="44.0095" composition="C O(2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Pro" full_name="Ala->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:16:03" + date_time_modified="2006-11-09 10:16:03" + approved="0" + record_id="543"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="26.015650" avge_mass="26.0373" composition="H(2) C(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Gly" full_name="Ala->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:16:35" + date_time_modified="2006-11-09 10:16:35" + approved="0" + record_id="544"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.015650" avge_mass="-14.0266" composition="H(-2) C(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Glu" full_name="Ala->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:19:56" + date_time_modified="2006-11-09 10:19:56" + approved="0" + record_id="545"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="58.005479" avge_mass="58.0361" composition="H(2) C(2) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ala->Val" full_name="Ala->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:20:15" + date_time_modified="2006-11-09 10:20:15" + approved="0" + record_id="546"> + <umod:specificity hidden="1" site="A" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="28.031300" avge_mass="28.0532" composition="H(4) C(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Phe" full_name="Cys->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:20:41" + date_time_modified="2006-11-09 10:20:41" + approved="0" + record_id="547"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="44.059229" avge_mass="44.0310" composition="H(4) C(6) S(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Ser" full_name="Cys->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:21:13" + date_time_modified="2006-11-09 10:21:13" + approved="0" + record_id="548"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-15.977156" avge_mass="-16.0656" composition="O S(-1)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Trp" full_name="Cys->Trp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:21:37" + date_time_modified="2006-11-09 10:21:37" + approved="0" + record_id="549"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="83.070128" avge_mass="83.0670" composition="H(5) C(8) N S(-1)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Tyr" full_name="Cys->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:22:04" + date_time_modified="2006-11-09 10:22:04" + approved="0" + record_id="550"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="60.054144" avge_mass="60.0304" composition="H(4) C(6) O S(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Arg" full_name="Cys->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:22:25" + date_time_modified="2006-11-09 10:22:25" + approved="0" + record_id="551"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="53.091927" avge_mass="53.0428" composition="H(7) C(3) N(3) S(-1)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Cys->Gly" full_name="Cys->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:22:43" + date_time_modified="2006-11-09 10:22:43" + approved="0" + record_id="552"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-45.987721" avge_mass="-46.0916" composition="H(-2) C(-1) S(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Ala" full_name="Asp->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:53:54" + date_time_modified="2006-11-09 10:53:54" + approved="0" + record_id="553"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-43.989829" avge_mass="-44.0095" composition="C(-1) O(-2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->His" full_name="Asp->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:55:25" + date_time_modified="2006-11-09 10:55:25" + approved="0" + record_id="554"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="22.031969" avge_mass="22.0519" composition="H(2) C(2) N(2) O(-2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Asn" full_name="Asp->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:55:49" + date_time_modified="2006-11-09 10:55:49" + approved="0" + record_id="555"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-0.984016" avge_mass="-0.9848" composition="H N O(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Gly" full_name="Asp->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:56:52" + date_time_modified="2006-11-09 10:56:52" + approved="0" + record_id="556"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-58.005479" avge_mass="-58.0361" composition="H(-2) C(-2) O(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Tyr" full_name="Asp->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:58:23" + date_time_modified="2006-11-09 10:58:23" + approved="0" + record_id="557"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="48.036386" avge_mass="48.0859" composition="H(4) C(5) O(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Glu" full_name="Asp->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:58:44" + date_time_modified="2006-11-09 10:58:44" + approved="0" + record_id="558"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.015650" avge_mass="14.0266" composition="H(2) C"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asp->Val" full_name="Asp->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 10:59:02" + date_time_modified="2006-11-09 10:59:02" + approved="0" + record_id="559"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-15.958529" avge_mass="-15.9563" composition="H(4) C O(-2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Ala" full_name="Glu->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:00:54" + date_time_modified="2006-11-09 11:00:54" + approved="0" + record_id="560"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-58.005479" avge_mass="-58.0361" composition="H(-2) C(-2) O(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Gln" full_name="Glu->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:01:29" + date_time_modified="2006-11-09 11:01:29" + approved="0" + record_id="561"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-0.984016" avge_mass="-0.9848" composition="H N O(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Asp" full_name="Glu->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:01:53" + date_time_modified="2006-11-09 11:01:53" + approved="0" + record_id="562"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.015650" avge_mass="-14.0266" composition="H(-2) C(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Lys" full_name="Glu->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:02:15" + date_time_modified="2006-11-09 11:02:15" + approved="0" + record_id="563"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-0.947630" avge_mass="-0.9417" composition="H(5) C N O(-2)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Gly" full_name="Glu->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:02:36" + date_time_modified="2006-11-09 11:02:36" + approved="0" + record_id="564"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-72.021129" avge_mass="-72.0627" composition="H(-4) C(-3) O(-2)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Glu->Val" full_name="Glu->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:03:02" + date_time_modified="2006-11-09 11:03:02" + approved="0" + record_id="565"> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-29.974179" avge_mass="-29.9829" composition="H(2) O(-2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phe->Ser" full_name="Phe->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:03:29" + date_time_modified="2006-11-09 11:03:29" + approved="0" + record_id="566"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-60.036386" avge_mass="-60.0966" composition="H(-4) C(-6) O"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phe->Cys" full_name="Phe->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:04:01" + date_time_modified="2006-11-09 11:04:01" + approved="0" + record_id="567"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-44.059229" avge_mass="-44.0310" composition="H(-4) C(-6) S"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phe->Ile" full_name="Phe->Ile or Phe->Leu substitution" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:05:41" + date_time_modified="2006-11-09 11:05:41" + approved="0" + record_id="568"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-33.984350" avge_mass="-34.0162" composition="H(2) C(-3)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phe->Tyr" full_name="Phe->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:06:56" + date_time_modified="2006-11-09 11:06:56" + approved="0" + record_id="569"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="15.994915" avge_mass="15.9994" composition="O"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Phe->Val" full_name="Phe->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:07:20" + date_time_modified="2006-11-09 11:07:20" + approved="0" + record_id="570"> + <umod:specificity hidden="1" site="F" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-48.000000" avge_mass="-48.0428" composition="C(-4)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="-4"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Ala" full_name="Gly->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:07:51" + date_time_modified="2006-11-09 11:07:51" + approved="0" + record_id="571"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.015650" avge_mass="14.0266" composition="H(2) C"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Ser" full_name="Gly->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:08:13" + date_time_modified="2006-11-09 11:08:13" + approved="0" + record_id="572"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="30.010565" avge_mass="30.0260" composition="H(2) C O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Trp" full_name="Gly->Trp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:08:33" + date_time_modified="2006-11-09 11:08:33" + approved="0" + record_id="573"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="129.057849" avge_mass="129.1586" composition="H(7) C(9) N"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Glu" full_name="Gly->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:08:57" + date_time_modified="2006-11-09 11:08:57" + approved="0" + record_id="574"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="72.021129" avge_mass="72.0627" composition="H(4) C(3) O(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Val" full_name="Gly->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:09:18" + date_time_modified="2006-11-09 11:09:18" + approved="0" + record_id="575"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="42.046950" avge_mass="42.0797" composition="H(6) C(3)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Asp" full_name="Gly->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:09:44" + date_time_modified="2006-11-09 11:09:44" + approved="0" + record_id="576"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="58.005479" avge_mass="58.0361" composition="H(2) C(2) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Cys" full_name="Gly->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:10:03" + date_time_modified="2006-11-09 11:10:03" + approved="0" + record_id="577"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="45.987721" avge_mass="46.0916" composition="H(2) C S"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gly->Arg" full_name="Gly->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:10:23" + date_time_modified="2006-11-09 11:10:23" + approved="0" + record_id="578"> + <umod:specificity hidden="1" site="G" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="99.079647" avge_mass="99.1344" composition="H(9) C(4) N(3)"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="dNIC" full_name="deuterated Nicotinic Acid" + username_of_poster="verena-meyer" + group_of_poster="" + date_time_posted="2006-12-04 16:12:54" + date_time_modified="2006-12-09 17:32:46" + approved="0" + record_id="698"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="109.048119" avge_mass="109.1205" composition="H 2H(3) C(6) N O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Nature Biotechnology 22, 450 - 454 (2004)</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.nature.com/nbt/journal/v22/n4/abs/nbt947.html</umod:url> + </umod:xref> + <umod:xref> + <umod:text>15004565</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="His->Pro" full_name="His->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:11:29" + date_time_modified="2006-11-09 11:11:29" + approved="0" + record_id="580"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-40.006148" avge_mass="-40.0241" composition="C(-1) N(-2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="His->Tyr" full_name="His->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:11:50" + date_time_modified="2006-11-09 11:11:50" + approved="0" + record_id="581"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="26.004417" avge_mass="26.0340" composition="H(2) C(3) N(-2) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="His->Gln" full_name="His->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:14:42" + date_time_modified="2006-11-09 11:14:42" + approved="0" + record_id="582"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-9.000334" avge_mass="-9.0101" composition="H C(-1) N(-1) O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="NIC" full_name="Nicotinic Acid" username_of_poster="verena-meyer" + group_of_poster="" + date_time_posted="2006-12-04 16:04:56" + date_time_modified="2006-12-09 17:31:30" + approved="0" + record_id="697"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="105.021464" avge_mass="105.0941" composition="H(3) C(6) N O"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Nature Biotechnology 22, 450 - 454 (2004)</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.nature.com/nbt/journal/v22/n4/abs/nbt947.html</umod:url> + </umod:xref> + <umod:xref> + <umod:text>15004565</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="His->Arg" full_name="His->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:15:26" + date_time_modified="2006-11-09 11:15:26" + approved="0" + record_id="584"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="19.042199" avge_mass="19.0464" composition="H(5) N"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="His->Leu" full_name="His->Leu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:15:51" + date_time_modified="2006-11-09 11:15:51" + approved="0" + record_id="585"> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-23.974848" avge_mass="-23.9816" composition="H(4) N(-2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Phe" full_name="Ile->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:17:16" + date_time_modified="2006-11-09 11:17:16" + approved="0" + record_id="586"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="33.984350" avge_mass="34.0162" composition="H(-2) C(3)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Ser" full_name="Ile->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:17:49" + date_time_modified="2006-11-09 11:17:49" + approved="0" + record_id="587"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-26.052036" avge_mass="-26.0803" composition="H(-6) C(-3) O"> + <umod:element symbol="H" number="-6"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Thr" full_name="Ile->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:18:09" + date_time_modified="2006-11-09 11:18:09" + approved="0" + record_id="588"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-12.036386" avge_mass="-12.0538" composition="H(-4) C(-2) O"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Asn" full_name="Ile->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:18:31" + date_time_modified="2006-11-09 11:18:31" + approved="0" + record_id="589"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="0.958863" avge_mass="0.9450" composition="H(-5) C(-2) N O"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Lys" full_name="Ile->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:18:57" + date_time_modified="2006-11-09 11:18:57" + approved="0" + record_id="590"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="15.010899" avge_mass="15.0146" composition="H N"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Val" full_name="Ile->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:19:17" + date_time_modified="2006-11-09 11:19:17" + approved="0" + record_id="591"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.015650" avge_mass="-14.0266" composition="H(-2) C(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Met" full_name="Ile->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:19:40" + date_time_modified="2006-11-09 11:19:40" + approved="0" + record_id="592"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="17.956421" avge_mass="18.0384" composition="H(-2) C(-1) S"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ile->Arg" full_name="Ile->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:20:00" + date_time_modified="2006-11-09 11:20:00" + approved="0" + record_id="593"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="43.017047" avge_mass="43.0280" composition="H N(3)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Thr" full_name="Lys->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:20:28" + date_time_modified="2006-11-09 11:20:28" + approved="0" + record_id="594"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-27.047285" avge_mass="-27.0684" composition="H(-5) C(-2) N(-1) O"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Asn" full_name="Lys->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:20:51" + date_time_modified="2006-11-09 11:20:51" + approved="0" + record_id="595"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.052036" avge_mass="-14.0696" composition="H(-6) C(-2) O"> + <umod:element symbol="H" number="-6"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Glu" full_name="Lys->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:21:12" + date_time_modified="2006-11-09 11:21:12" + approved="0" + record_id="596"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="0.947630" avge_mass="0.9417" composition="H(-5) C(-1) N(-1) O(2)"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Gln" full_name="Lys->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:21:32" + date_time_modified="2006-11-09 11:21:32" + approved="0" + record_id="597"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-0.036386" avge_mass="-0.0431" composition="H(-4) C(-1) O"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Met" full_name="Lys->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:21:56" + date_time_modified="2006-11-09 11:21:56" + approved="0" + record_id="598"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="2.945522" avge_mass="3.0238" composition="H(-3) C(-1) N(-1) S"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Arg" full_name="Lys->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:22:15" + date_time_modified="2006-11-09 11:22:15" + approved="0" + record_id="599"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="28.006148" avge_mass="28.0134" composition="N(2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Lys->Ile" full_name="Lys->Ile substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:22:38" + date_time_modified="2006-11-09 11:22:38" + approved="0" + record_id="600"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-15.010899" avge_mass="-15.0146" composition="H(-1) N(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Ser" full_name="Leu->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:23:01" + date_time_modified="2006-11-09 11:23:01" + approved="0" + record_id="601"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-26.052036" avge_mass="-26.0803" composition="H(-6) C(-3) O"> + <umod:element symbol="H" number="-6"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Phe" full_name="Leu->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:23:22" + date_time_modified="2006-11-09 11:23:22" + approved="0" + record_id="602"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="33.984350" avge_mass="34.0162" composition="H(-2) C(3)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Trp" full_name="Leu->Trp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:23:48" + date_time_modified="2006-11-09 11:23:48" + approved="0" + record_id="603"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="72.995249" avge_mass="73.0523" composition="H(-1) C(5) N"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Pro" full_name="Leu->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:24:06" + date_time_modified="2006-11-09 11:24:06" + approved="0" + record_id="604"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-16.031300" avge_mass="-16.0425" composition="H(-4) C(-1)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Val" full_name="Leu->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:24:28" + date_time_modified="2006-11-09 11:24:28" + approved="0" + record_id="605"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.015650" avge_mass="-14.0266" composition="H(-2) C(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->His" full_name="Leu->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:24:50" + date_time_modified="2006-11-09 11:24:50" + approved="0" + record_id="606"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="23.974848" avge_mass="23.9816" composition="H(-4) N(2)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Gln" full_name="Leu->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:25:14" + date_time_modified="2006-11-09 11:25:14" + approved="0" + record_id="607"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.974514" avge_mass="14.9716" composition="H(-3) C(-1) N O"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Met" full_name="Leu->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:25:59" + date_time_modified="2006-11-09 11:25:59" + approved="0" + record_id="608"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="17.956421" avge_mass="18.0384" composition="H(-2) C(-1) S"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Leu->Arg" full_name="Leu->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:26:21" + date_time_modified="2006-11-09 11:26:21" + approved="0" + record_id="609"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="43.017047" avge_mass="43.0280" composition="H N(3)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Thr" full_name="Met->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:26:47" + date_time_modified="2006-11-09 11:26:47" + approved="0" + record_id="610"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-29.992806" avge_mass="-30.0922" composition="H(-2) C(-1) O S(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Arg" full_name="Met->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:27:10" + date_time_modified="2006-11-09 11:27:10" + approved="0" + record_id="611"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="25.060626" avge_mass="24.9896" composition="H(3) C N(3) S(-1)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Ile" full_name="Met->Ile substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:27:27" + date_time_modified="2006-11-09 11:27:48" + approved="0" + record_id="612"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-17.956421" avge_mass="-18.0384" composition="H(2) C S(-1)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Lys" full_name="Met->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:28:29" + date_time_modified="2006-11-09 11:28:29" + approved="0" + record_id="613"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-2.945522" avge_mass="-3.0238" composition="H(3) C N S(-1)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Leu" full_name="Met->Leu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:28:56" + date_time_modified="2006-11-09 11:28:56" + approved="0" + record_id="614"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-17.956421" avge_mass="-18.0384" composition="H(2) C S(-1)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Met->Val" full_name="Met->Val substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:29:27" + date_time_modified="2006-11-09 11:29:27" + approved="0" + record_id="615"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-31.972071" avge_mass="-32.0650" composition="S(-1)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Ser" full_name="Asn->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:29:57" + date_time_modified="2006-11-09 11:29:57" + approved="0" + record_id="616"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-27.010899" avge_mass="-27.0253" composition="H(-1) C(-1) N(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Thr" full_name="Asn->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:34:11" + date_time_modified="2006-11-09 11:34:11" + approved="0" + record_id="617"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-12.995249" avge_mass="-12.9988" composition="H N(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Lys" full_name="Asn->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:34:31" + date_time_modified="2006-11-09 11:34:31" + approved="0" + record_id="618"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.052036" avge_mass="14.0696" composition="H(6) C(2) O(-1)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Tyr" full_name="Asn->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:34:56" + date_time_modified="2006-11-09 11:34:56" + approved="0" + record_id="619"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="49.020401" avge_mass="49.0706" composition="H(3) C(5) N(-1)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->His" full_name="Asn->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:35:18" + date_time_modified="2006-11-09 11:35:18" + approved="0" + record_id="620"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="23.015984" avge_mass="23.0366" composition="H C(2) N O(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Asp" full_name="Asn->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:35:42" + date_time_modified="2006-11-09 11:35:42" + approved="0" + record_id="621"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="0.984016" avge_mass="0.9848" composition="H(-1) N(-1) O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Asn->Ile" full_name="Asn->Ile substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:36:02" + date_time_modified="2006-11-09 11:36:02" + approved="0" + record_id="622"> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-0.958863" avge_mass="-0.9450" composition="H(5) C(2) N(-1) O(-1)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Ser" full_name="Pro->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:36:26" + date_time_modified="2006-11-09 11:36:26" + approved="0" + record_id="623"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-10.020735" avge_mass="-10.0379" composition="H(-2) C(-2) O"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Ala" full_name="Pro->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:37:56" + date_time_modified="2006-11-09 11:37:56" + approved="0" + record_id="624"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-26.015650" avge_mass="-26.0373" composition="H(-2) C(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->His" full_name="Pro->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:38:18" + date_time_modified="2006-11-09 11:38:18" + approved="0" + record_id="625"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="40.006148" avge_mass="40.0241" composition="C N(2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Gln" full_name="Pro->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:38:40" + date_time_modified="2006-11-09 11:38:40" + approved="0" + record_id="626"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="31.005814" avge_mass="31.0140" composition="H N O"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Thr" full_name="Pro->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:39:02" + date_time_modified="2006-11-09 11:39:02" + approved="0" + record_id="627"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="3.994915" avge_mass="3.9887" composition="C(-1) O"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Arg" full_name="Pro->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:39:29" + date_time_modified="2006-11-09 11:39:29" + approved="0" + record_id="628"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="59.048347" avge_mass="59.0705" composition="H(5) C N(3)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Pro->Leu" full_name="Pro->Leu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:39:47" + date_time_modified="2006-11-09 11:39:47" + approved="0" + record_id="629"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="16.031300" avge_mass="16.0425" composition="H(4) C"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->Pro" full_name="Gln->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:40:19" + date_time_modified="2006-11-09 11:40:19" + approved="0" + record_id="630"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-31.005814" avge_mass="-31.0140" composition="H(-1) N(-1) O(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->Lys" full_name="Gln->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:42:17" + date_time_modified="2006-11-09 11:42:17" + approved="0" + record_id="631"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="0.036386" avge_mass="0.0431" composition="H(4) C O(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->Glu" full_name="Gln->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:42:38" + date_time_modified="2006-11-09 11:42:38" + approved="0" + record_id="632"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="0.984016" avge_mass="0.9848" composition="H(-1) N(-1) O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->His" full_name="Gln->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:42:58" + date_time_modified="2006-11-09 11:42:58" + approved="0" + record_id="633"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="9.000334" avge_mass="9.0101" composition="H(-1) C N O(-1)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->Arg" full_name="Gln->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:43:25" + date_time_modified="2006-11-09 11:43:25" + approved="0" + record_id="634"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="28.042534" avge_mass="28.0565" composition="H(4) C N(2) O(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Gln->Leu" full_name="Gln->Leu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:43:47" + date_time_modified="2006-11-09 11:43:47" + approved="0" + record_id="635"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.974514" avge_mass="-14.9716" composition="H(3) C N(-1) O(-1)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Ser" full_name="Arg->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:44:13" + date_time_modified="2006-11-09 11:44:13" + approved="0" + record_id="636"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-69.069083" avge_mass="-69.1084" composition="H(-7) C(-3) N(-3) O"> + <umod:element symbol="H" number="-7"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Trp" full_name="Arg->Trp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:44:36" + date_time_modified="2006-11-09 11:44:36" + approved="0" + record_id="637"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="29.978202" avge_mass="30.0242" composition="H(-2) C(5) N(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Thr" full_name="Arg->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:44:59" + date_time_modified="2006-11-09 11:44:59" + approved="0" + record_id="638"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-55.053433" avge_mass="-55.0818" composition="H(-5) C(-2) N(-3) O"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Pro" full_name="Arg->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:45:18" + date_time_modified="2006-11-09 11:45:18" + approved="0" + record_id="639"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-59.048347" avge_mass="-59.0705" composition="H(-5) C(-1) N(-3)"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Lys" full_name="Arg->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:45:37" + date_time_modified="2006-11-09 11:45:37" + approved="0" + record_id="640"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-28.006148" avge_mass="-28.0134" composition="N(-2)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->His" full_name="Arg->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:45:56" + date_time_modified="2006-11-09 11:45:56" + approved="0" + record_id="641"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-19.042199" avge_mass="-19.0464" composition="H(-5) N(-1)"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Gln" full_name="Arg->Gln substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:46:17" + date_time_modified="2006-11-09 11:46:17" + approved="0" + record_id="642"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-28.042534" avge_mass="-28.0565" composition="H(-4) C(-1) N(-2) O"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Met" full_name="Arg->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:46:37" + date_time_modified="2006-11-09 11:46:37" + approved="0" + record_id="643"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-25.060626" avge_mass="-24.9896" composition="H(-3) C(-1) N(-3) S"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Cys" full_name="Arg->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:47:00" + date_time_modified="2006-11-09 11:47:00" + approved="0" + record_id="644"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-53.091927" avge_mass="-53.0428" composition="H(-7) C(-3) N(-3) S"> + <umod:element symbol="H" number="-7"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Ile" full_name="Arg->Ile or Arg->Leu substitution" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:47:36" + date_time_modified="2006-11-09 11:47:36" + approved="0" + record_id="645"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-43.017047" avge_mass="-43.0280" composition="H(-1) N(-3)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Arg->Gly" full_name="Arg->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 11:48:00" + date_time_modified="2006-11-09 11:48:00" + approved="0" + record_id="646"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-99.079647" avge_mass="-99.1344" composition="H(-9) C(-4) N(-3)"> + <umod:element symbol="H" number="-9"/> + <umod:element symbol="C" number="-4"/> + <umod:element symbol="N" number="-3"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Phe" full_name="Ser->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:32:55" + date_time_modified="2006-11-09 12:32:55" + approved="0" + record_id="647"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="60.036386" avge_mass="60.0966" composition="H(4) C(6) O(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Ala" full_name="Ser->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:33:14" + date_time_modified="2006-11-09 12:33:14" + approved="0" + record_id="648"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-15.994915" avge_mass="-15.9994" composition="O(-1)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Trp" full_name="Ser->Trp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:33:32" + date_time_modified="2006-11-09 12:33:32" + approved="0" + record_id="649"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="99.047285" avge_mass="99.1326" composition="H(5) C(8) N O(-1)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Thr" full_name="Ser->Thr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:33:51" + date_time_modified="2006-11-09 12:33:51" + approved="0" + record_id="650"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.015650" avge_mass="14.0266" composition="H(2) C"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Asn" full_name="Ser->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:34:12" + date_time_modified="2006-11-09 12:34:12" + approved="0" + record_id="651"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="27.010899" avge_mass="27.0253" composition="H C N"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Pro" full_name="Ser->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:34:34" + date_time_modified="2006-11-09 12:34:34" + approved="0" + record_id="652"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="10.020735" avge_mass="10.0379" composition="H(2) C(2) O(-1)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Tyr" full_name="Ser->Tyr substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:35:00" + date_time_modified="2006-11-09 12:35:00" + approved="0" + record_id="653"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="76.031300" avge_mass="76.0960" composition="H(4) C(6)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Cys" full_name="Ser->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:35:22" + date_time_modified="2006-11-09 12:35:22" + approved="0" + record_id="654"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="15.977156" avge_mass="16.0656" composition="O(-1) S"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Arg" full_name="Ser->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:35:40" + date_time_modified="2006-11-09 12:35:40" + approved="0" + record_id="655"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="69.069083" avge_mass="69.1084" composition="H(7) C(3) N(3) O(-1)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Ile" full_name="Ser->Ile or Ser->Leu substitution" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:36:10" + date_time_modified="2006-11-09 12:36:10" + approved="0" + record_id="656"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="26.052036" avge_mass="26.0803" composition="H(6) C(3) O(-1)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Ser->Gly" full_name="Ser->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:36:34" + date_time_modified="2006-11-09 12:36:34" + approved="0" + record_id="657"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-30.010565" avge_mass="-30.0260" composition="H(-2) C(-1) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Ser" full_name="Thr->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:36:57" + date_time_modified="2006-11-09 12:36:57" + approved="0" + record_id="658"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-14.015650" avge_mass="-14.0266" composition="H(-2) C(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Ala" full_name="Thr->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:37:15" + date_time_modified="2006-11-09 12:37:15" + approved="0" + record_id="659"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-30.010565" avge_mass="-30.0260" composition="H(-2) C(-1) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Asn" full_name="Thr->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:37:37" + date_time_modified="2006-11-09 12:37:37" + approved="0" + record_id="660"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="12.995249" avge_mass="12.9988" composition="H(-1) N"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Lys" full_name="Thr->Lys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:37:55" + date_time_modified="2006-11-09 12:37:55" + approved="0" + record_id="661"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="27.047285" avge_mass="27.0684" composition="H(5) C(2) N O(-1)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Pro" full_name="Thr->Pro substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:38:14" + date_time_modified="2006-11-09 12:38:14" + approved="0" + record_id="662"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-3.994915" avge_mass="-3.9887" composition="C O(-1)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Met" full_name="Thr->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:38:34" + date_time_modified="2006-11-09 12:38:34" + approved="0" + record_id="663"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="29.992806" avge_mass="30.0922" composition="H(2) C O(-1) S"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Ile" full_name="Thr->Ile substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:38:56" + date_time_modified="2006-11-09 12:38:56" + approved="0" + record_id="664"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="12.036386" avge_mass="12.0538" composition="H(4) C(2) O(-1)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Thr->Arg" full_name="Thr->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:39:14" + date_time_modified="2006-11-09 12:39:14" + approved="0" + record_id="665"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="55.053433" avge_mass="55.0818" composition="H(5) C(2) N(3) O(-1)"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Phe" full_name="Val->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:39:35" + date_time_modified="2006-11-09 12:39:35" + approved="0" + record_id="666"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="48.000000" avge_mass="48.0428" composition="C(4)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Ala" full_name="Val->Ala substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:40:00" + date_time_modified="2006-11-09 12:40:00" + approved="0" + record_id="667"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-28.031300" avge_mass="-28.0532" composition="H(-4) C(-2)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Glu" full_name="Val->Glu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:40:19" + date_time_modified="2006-11-09 12:40:19" + approved="0" + record_id="668"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="29.974179" avge_mass="29.9829" composition="H(-2) O(2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Met" full_name="Val->Met substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:40:36" + date_time_modified="2006-11-09 12:40:36" + approved="0" + record_id="669"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="31.972071" avge_mass="32.0650" composition="S"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Asp" full_name="Val->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:41:04" + date_time_modified="2006-11-09 12:41:04" + approved="0" + record_id="670"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="15.958529" avge_mass="15.9563" composition="H(-4) C(-1) O(2)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Ile" full_name="Val->Ile or Val->Leu substitution" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:41:27" + date_time_modified="2006-11-24 15:29:33" + approved="0" + record_id="671"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="14.015650" avge_mass="14.0266" composition="H(2) C"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Val->Gly" full_name="Val->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:41:45" + date_time_modified="2006-11-09 12:41:45" + approved="0" + record_id="672"> + <umod:specificity hidden="1" site="V" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-42.046950" avge_mass="-42.0797" composition="H(-6) C(-3)"> + <umod:element symbol="H" number="-6"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Trp->Ser" full_name="Trp->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:42:22" + date_time_modified="2006-11-09 12:42:22" + approved="0" + record_id="673"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-99.047285" avge_mass="-99.1326" composition="H(-5) C(-8) N(-1) O"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-8"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Trp->Cys" full_name="Trp->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:42:46" + date_time_modified="2006-11-09 12:42:46" + approved="0" + record_id="674"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-83.070128" avge_mass="-83.0670" composition="H(-5) C(-8) N(-1) S"> + <umod:element symbol="H" number="-5"/> + <umod:element symbol="C" number="-8"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="Trp->Arg" full_name="Trp->Arg substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:43:10" + date_time_modified="2006-11-09 12:43:10" + approved="0" + record_id="675"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-29.978202" avge_mass="-30.0242" composition="H(2) C(-5) N(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Trp->Gly" full_name="Trp->Gly substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:43:29" + date_time_modified="2006-11-09 12:43:29" + approved="0" + record_id="676"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-129.057849" avge_mass="-129.1586" composition="H(-7) C(-9) N(-1)"> + <umod:element symbol="H" number="-7"/> + <umod:element symbol="C" number="-9"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Trp->Leu" full_name="Trp->Leu substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:43:49" + date_time_modified="2006-11-09 12:43:49" + approved="0" + record_id="677"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-72.995249" avge_mass="-73.0523" composition="H C(-5) N(-1)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->Phe" full_name="Tyr->Phe substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:44:13" + date_time_modified="2006-11-09 12:44:13" + approved="0" + record_id="678"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-15.994915" avge_mass="-15.9994" composition="O(-1)"> + <umod:element symbol="H" number="0"/> + <umod:element symbol="C" number="0"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->Ser" full_name="Tyr->Ser substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:44:37" + date_time_modified="2006-11-09 12:44:37" + approved="0" + record_id="679"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-76.031300" avge_mass="-76.0960" composition="H(-4) C(-6)"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->Asn" full_name="Tyr->Asn substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:44:59" + date_time_modified="2006-11-09 12:44:59" + approved="0" + record_id="680"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-49.020401" avge_mass="-49.0706" composition="H(-3) C(-5) N"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="0"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->His" full_name="Tyr->His substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:45:22" + date_time_modified="2006-11-09 12:45:22" + approved="0" + record_id="681"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-26.004417" avge_mass="-26.0340" + composition="H(-2) C(-3) N(2) O(-1)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->Asp" full_name="Tyr->Asp substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:45:44" + date_time_modified="2006-11-09 12:45:44" + approved="0" + record_id="682"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-48.036386" avge_mass="-48.0859" composition="H(-4) C(-5) O"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="0"/> + </umod:delta> + </umod:mod> + <umod:mod title="Tyr->Cys" full_name="Tyr->Cys substitution" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-09 12:46:03" + date_time_modified="2006-11-09 12:46:03" + approved="0" + record_id="683"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="AA substitution" + spec_group="1"/> + <umod:delta mono_mass="-60.054144" avge_mass="-60.0304" composition="H(-4) C(-6) O(-1) S"> + <umod:element symbol="H" number="-4"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="N" number="0"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="BDMAPP" full_name="Mass Defect Tag on lysine e-amino" + username_of_poster="LVSchneid" + group_of_poster="" + date_time_posted="2006-11-13 18:51:11" + date_time_modified="2006-11-13 18:52:47" + approved="0" + record_id="684"> + <umod:specificity hidden="1" site="W" position="Anywhere" classification="Artefact" + spec_group="5"> + <umod:misc_notes>Low efficiency</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Artefact" + spec_group="4"> + <umod:misc_notes>Low efficiency</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Protein N-term" + classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Artefact" + spec_group="1"> + <umod:misc_notes>Low efficiency</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="253.010225" avge_mass="254.1231" composition="H(12) C(11) N O Br"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="Br" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Isotope-differentiated binding energy shift tags</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.targetdiscovery.com/article.php?topic=crpc.prst&story=20060321132643690</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="NA-LNO2" full_name="Nitroalkylation by Nitro Linoleic Acid" + username_of_poster="cbatthya" + group_of_poster="" + date_time_posted="2006-11-13 18:59:35" + date_time_modified="2006-11-13 18:59:35" + approved="0" + record_id="685"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:delta mono_mass="325.225309" avge_mass="325.4430" composition="H(31) C(18) N O(4)"> + <umod:element symbol="H" number="31"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:alt_name>Michael addition of nitro-linoleic acid to Cys and His</umod:alt_name> + <umod:xref> + <umod:text>JBC 281(29):20450-63; 2006</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Reversible post-translational modification of proteins by nitrated fatty acids</umod:misc_notes> + </umod:mod> + <umod:mod title="NA-OA-NO2" full_name="Nitroalkylation by Nitro Oleic Acid" + username_of_poster="cbatthya" + group_of_poster="" + date_time_posted="2006-11-13 19:01:33" + date_time_modified="2006-11-13 19:01:33" + approved="0" + record_id="686"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Post-translational" + spec_group="2"/> + <umod:delta mono_mass="327.240959" avge_mass="327.4589" composition="H(33) C(18) N O(4)"> + <umod:element symbol="H" number="33"/> + <umod:element symbol="C" number="18"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:alt_name>Michael addition of nitro-oleic acid to Cys and His</umod:alt_name> + <umod:xref> + <umod:text>JBC 281(29):20450-63; 2006</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Reversible post-translational modification of proteins by nitrated fatty acids</umod:misc_notes> + </umod:mod> + <umod:mod title="ICPL:2H(4)" + full_name="Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form" + username_of_poster="suckau" + group_of_poster="" + date_time_posted="2006-11-13 19:05:12" + date_time_modified="2008-09-03 15:26:54" + approved="0" + record_id="687"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Use when labelling post-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>Use when labelling pre-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="109.046571" avge_mass="109.1188" composition="H(-1) 2H(4) C(6) N O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Bruker Daltonics order reference</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15602776</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.</umod:misc_notes> + </umod:mod> + <umod:mod title="iTRAQ8plex" + full_name="Representative mass and accurate mass for 113, 114, 116 & 117" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2007-01-11 09:53:13" + date_time_modified="2007-01-13 21:00:08" + approved="0" + record_id="730"> + <umod:specificity hidden="0" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="304.205360" avge_mass="304.3074" + composition="H(24) C(7) 13C(7) N(3) 15N O(3)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="13C" number="7"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="15N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:alt_name>AKA iTRAQ8plex:13C(7)15N(1)</umod:alt_name> + <umod:alt_name>Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry</umod:alt_name> + <umod:misc_notes>Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use this entry for all channels</umod:misc_notes> + </umod:mod> + <umod:mod title="Label:13C(6)15N(1)" full_name="13C(6) 15N(1) Silac label" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2006-11-29 15:10:53" + date_time_modified="2007-08-22 18:30:49" + approved="1" + record_id="695"> + <umod:specificity hidden="1" site="I" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="7.017164" avge_mass="6.9493" composition="C(-6) 13C(6) N(-1) 15N"> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="15N" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:2H(9)13C(6)15N(2)" full_name="13C(6) 15N(2) (D)9 SILAC label" + username_of_poster="striker2000" + group_of_poster="" + date_time_posted="2006-12-01 22:36:25" + date_time_modified="2007-08-22 18:48:35" + approved="0" + record_id="696"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="17.070690" avge_mass="16.9982" + composition="H(-9) 2H(9) C(-6) 13C(6) N(-2) 15N(2)"> + <umod:element symbol="H" number="-9"/> + <umod:element symbol="2H" number="9"/> + <umod:element symbol="C" number="-6"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="15N" number="2"/> + </umod:delta> + <umod:alt_name>heavy D9 lysine</umod:alt_name> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>CDNLM-6810</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.isotope.com/cil/products/displayproduct.cfm?prod_id=8635</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="HNE-Delta:H(2)O" full_name="Dehydrated 4-hydroxynonenal" + username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-01-08 18:29:46" + date_time_modified="2007-01-21 18:27:18" + approved="0" + record_id="720"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="138.104465" avge_mass="138.2069" composition="H(14) C(9) O"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Liu Z, Minkler P, and Sayre L. Chem. Res. Toxicology 2003 16 901-911</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Mass Spectroscopic Characterization of Protein Modification by 4-Hydroxy-2-(E)-nonenal and 4-Oxo-2-(E)-nonenal.</umod:misc_notes> + </umod:mod> + <umod:mod title="4-ONE" full_name="4-Oxononenal (ONE)" username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-01-08 19:41:28" + date_time_modified="2007-01-21 18:26:54" + approved="0" + record_id="721"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="154.099380" avge_mass="154.2063" composition="H(14) C(9) O(2)"> + <umod:element symbol="H" number="14"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Chemico-Biological Interactions 143-144(2003) 93-100.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Covalent adduction of nucleophilic amino acids by 4-hydroxynonenal and 4-oxononenal</umod:misc_notes> + </umod:mod> + <umod:mod title="O-Dimethylphosphate" full_name="O-Dimethylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-09 21:25:28" + date_time_modified="2007-01-13 21:01:15" + approved="0" + record_id="723"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="107.997631" avge_mass="108.0331" composition="H(5) C(2) O(3) P"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="O-Methylphosphate" full_name="O-Methylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-09 21:35:38" + date_time_modified="2007-01-21 18:13:01" + approved="0" + record_id="724"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="93.981981" avge_mass="94.0065" composition="H(3) C O(3) P"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Created by auto-catalytic dealkylation of the O-Dimethylphosphate adduct.</umod:misc_notes> + </umod:mod> + <umod:mod title="O-Diethylphosphate" full_name="O-Diethylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-09 21:44:04" + date_time_modified="2007-01-13 21:03:17" + approved="0" + record_id="725"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="136.028931" avge_mass="136.0862" composition="H(9) C(4) O(3) P"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="O-Ethylphosphate" full_name="O-Ethylphosphorylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-09 21:46:17" + date_time_modified="2007-01-21 18:12:23" + approved="0" + record_id="726"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="107.997631" avge_mass="108.0331" composition="H(5) C(2) O(3) P"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Created by auto-catalytic dealkylation of the O-Diethylphosphate adduct.</umod:misc_notes> + </umod:mod> + <umod:mod title="O-pinacolylmethylphosphonate" + full_name="O-pinacolylmethylphosphonylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-10 16:04:46" + date_time_modified="2007-01-13 21:06:41" + approved="0" + record_id="727"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="162.080967" avge_mass="162.1666" composition="H(15) C(7) O(2) P"> + <umod:element symbol="H" number="15"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Methylphosphonate" full_name="Methylphosphonylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-10 16:07:37" + date_time_modified="2007-01-21 18:11:36" + approved="0" + record_id="728"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="77.987066" avge_mass="78.0071" composition="H(3) C O(2) P"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="1"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Created by auto-catalytic dealkylation of either the O-pinacolylmethylphosphonate adduct, or the O-isopropylmethylphosphonate adduct.</umod:misc_notes> + </umod:mod> + <umod:mod title="O-Isopropylmethylphosphonate" + full_name="O-Isopropylmethylphosphonylation" + username_of_poster="lmschopfer" + group_of_poster="" + date_time_posted="2007-01-10 16:10:55" + date_time_modified="2007-01-13 21:02:02" + approved="0" + record_id="729"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="120.034017" avge_mass="120.0868" composition="H(9) C(4) O(2) P"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="iTRAQ8plex:13C(6)15N(2)" + full_name="Accurate mass for 115, 118, 119 & 121" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2007-01-11 09:56:21" + date_time_modified="2007-01-13 20:59:54" + approved="0" + record_id="731"> + <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Low abundance</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="304.199040" avge_mass="304.3081" + composition="H(24) C(8) 13C(6) N(2) 15N(2) O(3)"> + <umod:element symbol="H" number="24"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="15N" number="2"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + <umod:alt_name>Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry</umod:alt_name> + <umod:misc_notes>Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use iTRAQ8plex for all channels</umod:misc_notes> + </umod:mod> + <umod:mod title="DTT_ST" full_name="Dithiothreitol (DTT)" + username_of_poster="stephenaw777" + group_of_poster="" + date_time_posted="2007-02-10 00:00:43" + date_time_modified="2007-02-11 19:39:11" + approved="0" + record_id="735"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>The addition of DTT adds 136.2 not 154.2 to Serine due to loss of water in reaction</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative" + spec_group="2"> + <umod:misc_notes>The addition of DTT adds 136.2 not 154.2 to Threonine due to loss of water in reaction</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="136.001656" avge_mass="136.2357" composition="H(8) C(4) O S(2)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:alt_name>threo-1,4-dimercaptobutane-2,3-diol</umod:alt_name> + <umod:alt_name>Cleland's reagent</umod:alt_name> + <umod:xref> + <umod:text>Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>17116471</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Mol Cell Proteomics. 2002 Oct;1(10):791-804. rnMapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications.Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, Hart GW.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>12438562</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Proteomics. 2005 Feb;5(2):388-98. Links rnQuantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>15648052</umod:url> + </umod:xref> + <umod:misc_notes>Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2.</umod:misc_notes> + </umod:mod> + <umod:mod title="Ethanolamine" full_name="Carboxyl modification with ethanolamine" + username_of_poster="overalllab" + group_of_poster="" + date_time_posted="2007-01-31 22:04:44" + date_time_modified="2007-02-11 19:39:59" + approved="0" + record_id="734"> + <umod:specificity hidden="1" site="D" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C-term" position="Any C-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="E" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:delta mono_mass="43.042199" avge_mass="43.0678" composition="H(5) C(2) N"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + <umod:misc_notes>Carbodiimide mediated blocking of free carboxylic acids (Asp/Glu sidechains and C-termini) with ethanolamine; reaction yields an amide-bond between the carboxylic acid of the peptide/protein and the primary amine of ethanolamine; reaction irreversibly modifies carboxylic acids. Shown above is the composition of the mass adduct, after substraction of water.</umod:misc_notes> + </umod:mod> + <umod:mod title="TMT6plex" full_name="Sixplex Tandem Mass Tag®" + username_of_poster="JUergen.schaefer" + group_of_poster="" + date_time_posted="2007-03-01 13:44:23" + date_time_modified="2007-03-03 18:24:35" + approved="0" + record_id="737"> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:delta mono_mass="229.162932" avge_mass="229.2634" + composition="H(20) C(8) 13C(4) N 15N O(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="8"/> + <umod:element symbol="13C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="15N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Tandem Mass Tag sixplex labelling kit Proteome Sciences</umod:alt_name> + <umod:alt_name>Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.</umod:alt_name> + <umod:xref> + <umod:text>Juergen.Schaefer@Proteomics.com</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Sixplex-TMT® reagents 6TMT-126, 6TMT-127, 6TMT-128, 6TMT-129, 6TMT-130, 6TMT-131 Masses of the TMT® fragment ions to be quantified:126.1283 127.1316 128.1350 129.1383 130.1417 131.1387</umod:misc_notes> + </umod:mod> + <umod:mod title="DTT_C" full_name="Dithiothreitol (DTT) on Cys" + username_of_poster="stephenaw777" + group_of_poster="" + date_time_posted="2007-02-10 03:12:41" + date_time_modified="2007-02-11 19:38:59" + approved="0" + record_id="736"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="120.024500" avge_mass="120.1701" composition="H(8) C(4) O(2) S"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Cleland's reagent</umod:alt_name> + <umod:xref> + <umod:text>Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>17116471</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Mol Cell Proteomics. 2006 May;5(5):923-34. Epub 2006 Feb 1. Links rnO-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>16452088</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Mol Cell Proteomics. 2002 Oct;1(10):791-804. Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications.Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, Hart GW.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>12438562</umod:url> + </umod:xref> + <umod:misc_notes>When the beta-elimination and Michael addition of dithiothreitol (DTT) (BEMAD) reaction is used with alkylated cysteine a sulfur group is lost leaving the addition of approximately 120.2 in the chemical reaction.</umod:misc_notes> + </umod:mod> + <umod:mod title="TMT2plex" full_name="Duplex Tandem Mass Tag®" + username_of_poster="JUergen.schaefer" + group_of_poster="" + date_time_posted="2007-03-01 13:53:36" + date_time_modified="2007-03-03 18:23:19" + approved="0" + record_id="738"> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="225.155833" avge_mass="225.2921" + composition="H(20) C(11) 13C N(2) O(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="13C" number="1"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.</umod:alt_name> + <umod:alt_name>Tandem Mass Tag Duplex labelling kit Proteome Sciences</umod:alt_name> + <umod:xref> + <umod:text>Juergen.Schaefer@Proteomics.com</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Duplex-TMT® reagents 2TMT-126, 2TMT-127 Masses of the TMT® fragment ions to be quantified: 126.1283 127.1316</umod:misc_notes> + </umod:mod> + <umod:mod title="TMT" full_name="Native Tandem Mass Tag®" + username_of_poster="JUergen.schaefer" + group_of_poster="" + date_time_posted="2007-03-02 09:29:50" + date_time_modified="2007-03-03 18:21:42" + approved="0" + record_id="739"> + <umod:specificity hidden="0" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="224.152478" avge_mass="224.2994" composition="H(20) C(12) N(2) O(2)"> + <umod:element symbol="H" number="20"/> + <umod:element symbol="C" number="12"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.</umod:alt_name> + <umod:xref> + <umod:text>Juergen.Schaefer@Proteomics.com</umod:text> + <umod:source>Other</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>This modification describes the \"native\" TMT Reagent without isotopic label.</umod:misc_notes> + </umod:mod> + <umod:mod title="ExacTagThiol" full_name="ExacTag Thiol label mass for 2-4-7-10 plex" + username_of_poster="cparman" + group_of_poster="" + date_time_posted="2007-03-02 17:24:48" + date_time_modified="2007-03-03 18:28:20" + approved="0" + record_id="740"> + <umod:specificity hidden="0" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="972.365219" avge_mass="972.7268" + composition="H(50) C(23) 13C(12) N(8) 15N(6) O(18)"> + <umod:element symbol="H" number="50"/> + <umod:element symbol="C" number="23"/> + <umod:element symbol="13C" number="12"/> + <umod:element symbol="N" number="8"/> + <umod:element symbol="15N" number="6"/> + <umod:element symbol="O" number="18"/> + </umod:delta> + <umod:alt_name>PerkinElmer ExacTag Thiol kit</umod:alt_name> + <umod:xref> + <umod:text>PerkinElmer ExacTag product page</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.perkinelmer.com/exactag</umod:url> + </umod:xref> + <umod:misc_notes>Accurate mass for Exactag Thiol labels</umod:misc_notes> + </umod:mod> + <umod:mod title="ExacTagAmine" full_name="ExacTag Amine label mass for 2-4-7-10 plex" + username_of_poster="cparman" + group_of_poster="" + date_time_posted="2007-03-02 17:28:02" + date_time_modified="2007-05-02 14:15:44" + approved="0" + record_id="741"> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="1046.347854" avge_mass="1046.8285" + composition="H(52) C(25) 13C(12) N(8) 15N(6) O(19) S"> + <umod:element symbol="H" number="52"/> + <umod:element symbol="C" number="25"/> + <umod:element symbol="13C" number="12"/> + <umod:element symbol="N" number="8"/> + <umod:element symbol="15N" number="6"/> + <umod:element symbol="O" number="19"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>PerkinElmer ExacTag Amine kit</umod:alt_name> + <umod:xref> + <umod:text>PerkinElmer ExacTag product page</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.perkinelmer.com/exactag</umod:url> + </umod:xref> + <umod:misc_notes>Accurate mass for Exactag Amine labels. Includes the mass of the conjugation reagent</umod:misc_notes> + </umod:mod> + <umod:mod title="NO_SMX_SEMD" + full_name="Nitroso Sulfamethoxazole Sulphenamide thiol adduct" + username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-04-17 23:28:29" + date_time_modified="2007-04-21 16:55:48" + approved="0" + record_id="744"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="252.044287" avge_mass="252.2697" + composition="H(10) C(10) N(3) O(3) S"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.</umod:misc_notes> + </umod:mod> + <umod:mod title="4-ONE+Delta:H(-2)O(-1)" + full_name="Dehydrated 4-Oxononenal Michael adduct" + username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-03-21 21:21:34" + date_time_modified="2007-04-08 18:56:36" + approved="0" + record_id="743"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="136.088815" avge_mass="136.1910" composition="H(12) C(9) O"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Liu. Z., Minkler, P. E., and Sayre, L. M. Chem. Res. Toxico. 2003, 16, 901-911.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Mass Spectorscopic Characterization of Protein Modification by 4-hydroxy-2-(E)-nonenal and 4-oxo-2-(E)-nonenal</umod:misc_notes> + </umod:mod> + <umod:mod title="NO_SMX_SMCT" + full_name="Nitroso Sulfamethoxazole semimercaptal thiol adduct" + username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-04-18 21:37:48" + date_time_modified="2007-04-21 16:56:19" + approved="0" + record_id="745"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="268.039202" avge_mass="268.2691" + composition="H(10) C(10) N(3) O(4) S"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.</umod:misc_notes> + </umod:mod> + <umod:mod title="NO_SMX_SIMD" + full_name="Nitroso Sulfamethoxazole Sulfinamide thiol adduct" + username_of_poster="stewartb" + group_of_poster="" + date_time_posted="2007-04-18 21:39:11" + date_time_modified="2007-04-21 16:56:07" + approved="0" + record_id="746"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="267.031377" avge_mass="267.2612" + composition="H(9) C(10) N(3) O(4) S"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.</umod:misc_notes> + </umod:mod> + <umod:mod title="Malonyl" full_name="Malonylation of C and S residues" + username_of_poster="massy" + group_of_poster="" + date_time_posted="2007-05-17 14:17:42" + date_time_modified="2007-05-25 18:34:43" + approved="0" + record_id="747"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:delta mono_mass="86.000394" avge_mass="86.0462" composition="H(2) C(3) O(3)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="3"/> + </umod:delta> + </umod:mod> + <umod:mod title="3sulfo" + full_name="derivatization by N-term modification using 3-Sulfobenzoic succinimidyl ester" + username_of_poster="MaxWis" + group_of_poster="" + date_time_posted="2007-05-31 10:15:48" + date_time_modified="2007-06-24 19:58:07" + approved="0" + record_id="748"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="183.983029" avge_mass="184.1693" composition="H(4) C(7) O(4) S"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="7"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="trifluoro" full_name="trifluoroleucine replacement of leucine" + username_of_poster="UKMSF" + group_of_poster="" + date_time_posted="2007-06-13 17:10:33" + date_time_modified="2007-06-24 19:56:32" + approved="0" + record_id="750"> + <umod:specificity hidden="1" site="L" position="Anywhere" classification="Non-standard residue" + spec_group="1"/> + <umod:delta mono_mass="53.971735" avge_mass="53.9714" composition="H(-3) F(3)"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="F" number="3"/> + </umod:delta> + </umod:mod> + <umod:mod title="TNBS" full_name="tri nitro benzene" username_of_poster="DelphineP" + group_of_poster="" + date_time_posted="2007-06-21 13:36:03" + date_time_modified="2007-06-24 19:58:58" + approved="0" + record_id="751"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="210.986535" avge_mass="211.0886" composition="H C(6) N(3) O(6)"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="6"/> + </umod:delta> + </umod:mod> + <umod:mod title="Biotin-phenacyl" + full_name="Alkylation by biotinylated form of phenacyl bromide" + username_of_poster="Sandeep" + group_of_poster="" + date_time_posted="2007-09-14 23:07:12" + date_time_modified="2007-10-03 15:42:46" + approved="0" + record_id="774"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:specificity hidden="1" site="H" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:delta mono_mass="626.263502" avge_mass="626.7270" + composition="H(38) C(29) N(8) O(6) S"> + <umod:element symbol="H" number="38"/> + <umod:element symbol="C" number="29"/> + <umod:element symbol="N" number="8"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>4-bromophenacyl bromide [99-73-0]</umod:text> + <umod:source>CAS Registry</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>428399</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>phenacyl bromide conjugated with a linker and biotin tag, details not published yet</umod:misc_notes> + </umod:mod> + <umod:mod title="DTT_C:2H(6)" + full_name="Isotopically labeled Dithiothreitol (DTT) modification of cysteines" + username_of_poster="chalkley" + group_of_poster="" + date_time_posted="2007-07-10 20:44:56" + date_time_modified="2007-07-10 21:10:28" + approved="0" + record_id="764"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="126.062161" avge_mass="126.2071" + composition="H(2) 2H(6) C(4) O(2) S"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Cleland's reagent</umod:alt_name> + <umod:xref> + <umod:text>Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Proteomics. 2005 5(2):388-98. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>15648052</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Can be used for quantitative analysis of cysteine-containing peptides. Same reaction can be used for quantitative analysis of O-linked post-translational modifications to serines and threonines, but then the modification is 16 Da more in mass; i.e. isotopically labeled reagent adds 142 Da in mass.</umod:misc_notes> + </umod:mod> + <umod:mod title="lapachenole" full_name="lapachenole photochemically added to cysteine" + username_of_poster="hmfales" + group_of_poster="" + date_time_posted="2007-08-17 22:22:15" + date_time_modified="2007-09-07 16:52:37" + approved="0" + record_id="771"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>Simple cyclic compound C16H16O2 adds to cysteine forming fluorescent derivative.</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="240.115030" avge_mass="240.2970" composition="H(16) C(16) O(2)"> + <umod:element symbol="H" number="16"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Biochemistry 2005 vol 44 pp 1833-1845</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1021/bi048228c</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(5)" full_name="13C(5) Silac label" username_of_poster="unimod" + group_of_poster="" + date_time_posted="2007-08-22 18:36:11" + date_time_modified="2007-08-22 18:36:11" + approved="1" + record_id="772"> + <umod:specificity hidden="1" site="P" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Result of Arg to Pro conversion of 13C(6) labelled Arg</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="5.016774" avge_mass="4.9633" composition="C(-5) 13C(5)"> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="13C" number="5"/> + </umod:delta> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="maleimide" full_name="maleimide" username_of_poster="mjayson" + group_of_poster="" + date_time_posted="2007-09-05 23:31:52" + date_time_modified="2007-09-06 11:28:09" + approved="0" + record_id="773"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="97.016378" avge_mass="97.0721" composition="H(3) C(4) N O(2)"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + </umod:mod> + <umod:mod title="IDEnT" full_name="Isotope Distribution Encoded Tag" + username_of_poster="chalkley" + group_of_poster="" + date_time_posted="2007-07-10 20:14:50" + date_time_modified="2007-07-15 20:04:29" + approved="0" + record_id="762"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="214.990469" avge_mass="216.0640" composition="H(7) C(9) N O Cl(2)"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="Cl" number="2"/> + </umod:delta> + <umod:alt_name>2,4-dichlorobenzylcarbamidomethyl</umod:alt_name> + <umod:xref> + <umod:text>Analytical Chemistry (2000) 72 6 1112-1118</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>10740847</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Modified peptides identified by isotope pattern. Restriction to cysteine-containing peptides combined with high mass accuracy allows peptide identification.</umod:misc_notes> + </umod:mod> + <umod:mod title="DTT_ST:2H(6)" + full_name="Isotopically labeled Dithiothreitol (DTT) modification of serines or threonines" + username_of_poster="chalkley" + group_of_poster="" + date_time_posted="2007-07-10 20:34:46" + date_time_modified="2007-07-10 21:11:44" + approved="0" + record_id="763"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="142.039317" avge_mass="142.2727" + composition="H(2) 2H(6) C(4) O S(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="2"/> + </umod:delta> + <umod:alt_name>Cleland's reagent</umod:alt_name> + <umod:xref> + <umod:text>15648052</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Proteomics. 2005 5(2):388-98. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Can be used for quantitative analysis of O-linked post-translational modifications. Same reaction can be used for quantitative analysis of cysteine-containing peptides, but then the modification is 16 Da less in mass; i.e. isotopically labeled reagent adds 126 Da in mass.</umod:misc_notes> + </umod:mod> + <umod:mod title="Met-loss" + full_name="Removal of initiator methionine from protein N-terminus" + username_of_poster="chalkley" + group_of_poster="" + date_time_posted="2007-07-10 22:40:00" + date_time_modified="2007-07-15 20:01:35" + approved="0" + record_id="765"> + <umod:specificity hidden="1" site="M" position="Protein N-term" classification="Co-translational" + spec_group="1"/> + <umod:delta mono_mass="-131.040485" avge_mass="-131.1961" + composition="H(-9) C(-5) N(-1) O(-1) S(-1)"> + <umod:element symbol="H" number="-9"/> + <umod:element symbol="C" number="-5"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>Biochemistry (1987) 26 8242-8246</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>3327521</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins where the residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. This is generally the final N-terminal state for proteins where the following residue was a Cys, Pro or Val.</umod:misc_notes> + </umod:mod> + <umod:mod title="Met-loss+Acetyl" + full_name="Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus" + username_of_poster="chalkley" + group_of_poster="" + date_time_posted="2007-07-10 22:57:12" + date_time_modified="2007-07-15 20:01:06" + approved="0" + record_id="766"> + <umod:specificity hidden="1" site="M" position="Protein N-term" classification="Co-translational" + spec_group="1"/> + <umod:delta mono_mass="-89.029920" avge_mass="-89.1594" + composition="H(-7) C(-3) N(-1) S(-1)"> + <umod:element symbol="H" number="-7"/> + <umod:element symbol="C" number="-3"/> + <umod:element symbol="N" number="-1"/> + <umod:element symbol="S" number="-1"/> + </umod:delta> + <umod:xref> + <umod:text>3327521</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Biochemistry (1987) 26 8242-8246</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>The N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins whose residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. Proteins whose following residue was Ala, Gly, Ser or Thr are then acetylated by an N(alpha)-acetyltransferase on the new N-terminus.</umod:misc_notes> + </umod:mod> + <umod:mod title="Menadione-HQ" full_name="Menadione hydroquinone derivative" + username_of_poster="catsriku" + group_of_poster="" + date_time_posted="2007-07-12 07:35:07" + date_time_modified="2007-07-15 20:05:56" + approved="0" + record_id="767"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="172.052430" avge_mass="172.1800" composition="H(8) C(11) O(2)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>15939799</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Carboxymethyl:13C(2)" + full_name="Iodoacetic acid derivative w/ 13C label" + username_of_poster="mpcusack" + group_of_poster="" + date_time_posted="2007-09-18 19:26:42" + date_time_modified="2008-06-22 12:00:27" + approved="0" + record_id="775"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="60.012189" avge_mass="60.0214" composition="H(2) 13C(2) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="13C" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>Carboxymethylation w/ 13C label</umod:alt_name> + <umod:xref> + <umod:text>B. Schilling, C.B. Yoo, C.J. Collins, B.W. Gibson, Determining Cysteine Oxidation Status Using Differential Alkylation, Int. J. Mass Spectrom., 2004, 236 (1-3), 117-121</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1016/j.ijms.2004.06.004</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="NEM:2H(5)" full_name="D5 N-ethylmaleimide on cysteines" + username_of_poster="mpcusack" + group_of_poster="" + date_time_posted="2007-09-18 19:49:39" + date_time_modified="2007-09-28 10:37:50" + approved="0" + record_id="776"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="130.079062" avge_mass="130.1561" + composition="H(2) 2H(5) C(6) N O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="5"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>CysNEM D5</umod:alt_name> + <umod:xref> + <umod:text>reaction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.chemistry.ucsc.edu/~fink/231/Image118.gif</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12777388</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>11813307</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Gly-loss+Amide" + full_name="Enzymatic glycine removal leaving an amidated C-terminus" + username_of_poster="timothyr" + group_of_poster="" + date_time_posted="2008-02-06 09:33:39" + date_time_modified="2008-02-15 05:34:31" + approved="0" + record_id="822"> + <umod:specificity hidden="1" site="G" position="Any C-term" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="-58.005479" avge_mass="-58.0361" composition="H(-2) C(-2) O(-2)"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="O" number="-2"/> + </umod:delta> + <umod:alt_name>Amidation requires presence of glycine at peptide terminus</umod:alt_name> + <umod:xref> + <umod:text>Bradbury, A.F. and D.G. Smyth, Peptide amidation. Trends Biochem Sci, 1991. 16(3): p. 112-5.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="TMPP-Ac" + full_name="tris(2,4,6-trimethoxyphenyl)phosphonium acetic acid N-hydroxysuccinimide ester derivative" + username_of_poster="unimod" + group_of_poster="" + date_time_posted="2008-02-20 14:12:31" + date_time_modified="2008-02-20 14:23:30" + approved="0" + record_id="827"> + <umod:specificity hidden="1" site="N-term" position="Any N-term" + classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="573.188959" avge_mass="573.5480" composition="H(34) C(29) O(10) P"> + <umod:element symbol="H" number="34"/> + <umod:element symbol="C" number="29"/> + <umod:element symbol="O" number="10"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Weibin Chen et. al., Anal. Chem.2007, 79,1583-1590</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1021/ac061670b</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)+GlyGly" full_name="13C6 labeled ubiquitinylation residue" + username_of_poster="glick2" + group_of_poster="" + date_time_posted="2007-12-02 22:45:39" + date_time_modified="2008-07-04 19:11:02" + approved="0" + record_id="799"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="120.063056" avge_mass="120.0586" + composition="H(6) C(-2) 13C(6) N(2) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12716131&itool=pubmed_docsum</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. + +Nat Biotechnol. 2003 Aug;21(8):921-6</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12872131&itool=pubmed_docsum</umod:url> + </umod:xref> + <umod:misc_notes>The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion</umod:misc_notes> + </umod:mod> + <umod:mod title="Arg->Npo" full_name="Arginine replacement by Nitropyrimidyl ornithine" + username_of_poster="Kramerh" + group_of_poster="" + date_time_posted="2008-04-10 15:35:22" + date_time_modified="2008-04-21 18:30:45" + approved="0" + record_id="837"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="80.985078" avge_mass="81.0297" composition="H(-1) C(3) N O(2)"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>JBC 258(1) 203-207 1983</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.jbc.org/cgi/reprint/258/1/203.pdf</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:2H(4)+Acetyl" full_name="Acetyl 4,4,5,5-D4 Lysine" + username_of_poster="Raghothama" + group_of_poster="" + date_time_posted="2008-03-24 17:25:15" + date_time_modified="2008-04-02 10:17:08" + approved="0" + record_id="834"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Both isotopiclabel and post translational mod</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="46.035672" avge_mass="46.0613" composition="H(-2) 2H(4) C(2) O"> + <umod:element symbol="H" number="-2"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Acetyl_K4</umod:alt_name> + <umod:misc_notes>For SILAC experiments, + PTM</umod:misc_notes> + </umod:mod> + <umod:mod title="Pentylamine" + full_name="Labeling transglutaminase substrate on glutamine side chain" + username_of_poster="mengyi" + group_of_poster="" + date_time_posted="2007-12-05 11:08:02" + date_time_modified="2007-12-14 17:52:16" + approved="0" + record_id="801"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="85.089149" avge_mass="85.1475" composition="H(11) C(5) N"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="PentylamineBiotin" + full_name="Used for labeling glutamine-donor substrate of transglutaminase" + username_of_poster="mengyi" + group_of_poster="" + date_time_posted="2007-12-03 13:56:58" + date_time_modified="2007-12-04 09:00:49" + approved="0" + record_id="800"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="311.166748" avge_mass="311.4429" + composition="H(25) C(15) N(3) O(2) S"> + <umod:element symbol="H" number="25"/> + <umod:element symbol="C" number="15"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="2"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Pierce EZ-Link Pentylamine-Biotin</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=01031206</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Dihydroxyimidazolidine" full_name="Dihydroxy methylglyoxal adduct" + username_of_poster="kimzey" + group_of_poster="" + date_time_posted="2008-03-04 00:00:29" + date_time_modified="2008-05-22 00:32:41" + approved="0" + record_id="830"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Multiple" + spec_group="1"/> + <umod:delta mono_mass="72.021129" avge_mass="72.0627" composition="H(4) C(3) O(2)"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>J. Mass. Spectrom. 2007; 42:89-100.</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1002/jms.1144</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="DFDNB" full_name="Addition of DFDNB crosslinker" + username_of_poster="Larsenmarsen" + group_of_poster="" + date_time_posted="2008-02-13 15:35:40" + date_time_modified="2008-03-05 16:48:47" + approved="0" + record_id="825"> + <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Chemical derivative" + spec_group="3"/> + <umod:specificity hidden="1" site="N" position="Anywhere" classification="Chemical derivative" + spec_group="4"/> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="2"/> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="203.998263" avge_mass="204.0879" + composition="H(2) C(6) N(2) O(4) F(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="4"/> + <umod:element symbol="F" number="2"/> + </umod:delta> + <umod:xref> + <umod:text>Chen, X., et al. (1999). Anal. Biochem. 273, 192-203.</umod:text> + <umod:source>Other</umod:source> + <umod:url>http://www.piercenet.com/products/browse.cfm?fldID=02030220</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Kornblatt, J.A. and Lake, D.F. (1980). Crosslinking of cytochrome oxidase subunits with difluorodinitrobenzene. Can J. Biochem. 58, 219-224.</umod:text> + <umod:source>Other</umod:source> + <umod:url>http://www.piercenet.com/products/browse.cfm?fldID=02030220</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Cy3b-maleimide" full_name="fluorescent dye that labels cysteines" + username_of_poster="kfinan" + group_of_poster="" + date_time_posted="2008-02-01 16:03:09" + date_time_modified="2008-02-15 14:09:55" + approved="0" + record_id="821"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="796.238984" avge_mass="796.8086" + composition="H(39) C(39) N(4) O(9) F(3) S"> + <umod:element symbol="H" number="39"/> + <umod:element symbol="C" number="39"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="9"/> + <umod:element symbol="F" number="3"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:alt_name>Cy3b meleimide reacted with Cysteine</umod:alt_name> + <umod:xref> + <umod:text>Article describing design of Cy3B</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://www.springerlink.com/content/q3u3271467573733/</umod:url> + </umod:xref> + <umod:xref> + <umod:text>Amersham website for chemical</umod:text> + <umod:source>Other</umod:source> + <umod:url>http://www1.gelifesciences.com/APTRIX/upp01077.nsf/Content/Products?OpenDocument&parentid=658513&moduleid=166300</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Hex1HexNAc1" full_name="Hex1HexNAc1" username_of_poster="julienjardin" + group_of_poster="" + date_time_posted="2007-10-12 13:16:23" + date_time_modified="2007-10-20 19:28:06" + approved="0" + record_id="793"> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="O-linked glycosylation" + spec_group="2"/> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="O-linked glycosylation" + spec_group="1"/> + <umod:delta mono_mass="365.132196" avge_mass="365.3331" composition="Hex HexNAc"> + <umod:element symbol="H" number="23"/> + <umod:element symbol="C" number="14"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="10"/> + </umod:delta> + <umod:xref> + <umod:text>Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="AEC-MAEC:2H(4)" full_name="deuterium cysteamine modification to S or T" + username_of_poster="zwang23" + group_of_poster="" + date_time_posted="2007-10-03 19:41:19" + date_time_modified="2007-10-08 13:44:02" + approved="0" + record_id="792"> + <umod:specificity hidden="1" site="S" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="1" site="T" position="Anywhere" classification="Isotopic label" + spec_group="2"/> + <umod:delta mono_mass="63.044462" avge_mass="63.1580" composition="H 2H(4) C(2) N O(-1) S"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="-1"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + </umod:mod> + <umod:mod title="BMOE" full_name="Addition of BMOE crosslinker" + username_of_poster="Larsenmarsen" + group_of_poster="" + date_time_posted="2008-02-13 15:28:55" + date_time_modified="2008-03-05 16:47:02" + approved="0" + record_id="824"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="220.048407" avge_mass="220.1815" composition="H(8) C(10) N(2) O(4)"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>Chen, L.L., Rosa, J.J., Turner, S. and Pepinsky, R.B. (1991). Production of multimeric forms of CD4 through a sugar-based crosslinking strategy. J. Biol. Chem. 266(27), 18237-18243</umod:text> + <umod:source>Other</umod:source> + <umod:url>http://www.piercenet.com/Products/Browse.cfm?fldID=02030208</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Biotin-PEO4-hydrazide" + full_name="Pierce EZ link biotin hydrazide prod no. 21360" + username_of_poster="MCole18" + group_of_poster="" + date_time_posted="2007-12-12 15:23:23" + date_time_modified="2007-12-14 18:09:17" + approved="0" + record_id="811"> + <umod:specificity hidden="1" site="C-term" position="Anywhere" + classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>hydrazide reacts at any activated carboxyl group</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="487.246455" avge_mass="487.6134" + composition="H(37) C(21) N(5) O(6) S"> + <umod:element symbol="H" number="37"/> + <umod:element symbol="C" number="21"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="S" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Pierce product page</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.piercenet.com/products/browse.cfm?fldID=C4FE82D4-DD06-493C-8EC4-9C1D7F83211B</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)+Acetyl" full_name="Acetyl 13C(6) Silac label" + username_of_poster="Raghothama" + group_of_poster="" + date_time_posted="2008-03-24 17:33:44" + date_time_modified="2008-04-02 10:14:57" + approved="0" + record_id="835"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>SILAC and PTM</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="48.030694" avge_mass="47.9926" composition="H(2) C(-4) 13C(6) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="-4"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)15N(2)+Acetyl" full_name="Acetyl_13C(6) 15N(2) Silac label" + username_of_poster="Raghothama" + group_of_poster="" + date_time_posted="2008-03-24 17:35:52" + date_time_modified="2008-04-02 10:13:59" + approved="0" + record_id="836"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="50.024764" avge_mass="49.9794" + composition="H(2) C(-4) 13C(6) N(-2) 15N(2) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="-4"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="15N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>Acetyl_heavy lysine</umod:alt_name> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="EQIGG" full_name="Sumo mutant Smt3-WT tail following trypsin digestion" + username_of_poster="Magnojunqueira" + group_of_poster="" + date_time_posted="2008-05-13 16:56:23" + date_time_modified="2008-05-17 18:58:13" + approved="0" + record_id="846"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="484.228162" avge_mass="484.5035" composition="H(32) C(20) N(6) O(8)"> + <umod:element symbol="H" number="32"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="6"/> + <umod:element symbol="O" number="8"/> + </umod:delta> + <umod:alt_name>Sumoylation</umod:alt_name> + <umod:xref> + <umod:text>Wohlschlegel, J. A. et al., J Proteome Res. 5 761 2006</umod:text> + <umod:source>Journal</umod:source> + <umod:url>http://dx.doi.org/10.1021/pr050451o</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="cGMP" full_name="S-guanylation" username_of_poster="atsushiirie" + group_of_poster="" + date_time_posted="2008-06-21 09:02:53" + date_time_modified="2008-07-04 19:14:47" + approved="0" + record_id="849"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="344.039610" avge_mass="344.1974" + composition="H(11) C(10) N(5) O(7) P"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="10"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="7"/> + <umod:element symbol="P" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Nat Chem Biol. 3: 727-735, 2007</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>17906641</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Protein which is posttranslationally modified by the attachment of cGMP on the sulfur atom of one or more cysteine residues.</umod:misc_notes> + </umod:mod> + <umod:mod title="cGMP+RMP-loss" full_name="S-guanylation-2" + username_of_poster="atsushiirie" + group_of_poster="" + date_time_posted="2008-06-21 09:06:56" + date_time_modified="2008-07-04 19:22:39" + approved="0" + record_id="851"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="150.041585" avge_mass="150.1182" composition="H(4) C(5) N(5) O"> + <umod:element symbol="H" number="4"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="5"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>17906641</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Nat Chem Biol. 3: 727-735, 2007</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:misc_notes>Protein which is posttranslationally modified by the attachment of cGMP that has lost ribose 3\',5\'-cyclic monophosphate moiety on the sulfur atom of one or more cysteine residues.</umod:misc_notes> + </umod:mod> + <umod:mod title="Arg2PG" full_name="Adduct of phenylglyoxal with Arg" + username_of_poster="Kramerh" + group_of_poster="" + date_time_posted="2008-05-16 11:07:51" + date_time_modified="2008-05-17 19:01:10" + approved="0" + record_id="848"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Chemical derivative" + spec_group="1"> + <umod:misc_notes>The reaction product of Arg with phenylglyoxal has been shown to be a 2:1 adduct</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="266.057909" avge_mass="266.2482" composition="H(10) C(16) O(4)"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="16"/> + <umod:element symbol="O" number="4"/> + </umod:delta> + <umod:xref> + <umod:text>PMID 11698400rnLigand-selective modulation of the permeability transition pore by arginine modification. Opposing effects of p-hydroxyphenylglyoxal and phenylglyoxal.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/pubmed/11698400?ordinalpos=39&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum</umod:url> + </umod:xref> + <umod:xref> + <umod:text>PMID 5723461rnThe reaction of phenylglyoxal with arginine residues in proteins.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/pubmed/5723461?ordinalpos=517&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum</umod:url> + </umod:xref> + <umod:xref> + <umod:text>PMID 11945751rnReaction of arginine residues in basic pancreatic trypsin inhibitor with phenylglyoxal.</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url>http://www.ncbi.nlm.nih.gov/pubmed/11945751?ordinalpos=514&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="Label:2H(4)+GlyGly" full_name="Ubiquitination 2H4 lysine" + username_of_poster="Raghothama" + group_of_poster="" + date_time_posted="2008-06-27 14:28:36" + date_time_modified="2008-08-13 20:29:26" + approved="0" + record_id="853"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Post-translational" + spec_group="1"/> + <umod:delta mono_mass="118.068034" avge_mass="118.1273" + composition="H(2) 2H(4) C(4) N(2) O(2)"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + </umod:mod> + <umod:mod title="Label:13C(8)15N(2)" full_name="13C(8) 15N(2) Silac label" + username_of_poster="nedamoc" + group_of_poster="" + date_time_posted="2008-06-30 20:11:08" + date_time_modified="2008-07-04 19:07:25" + approved="0" + record_id="854"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:delta mono_mass="10.020909" avge_mass="9.9281" + composition="C(-8) 13C(8) N(-2) 15N(2)"> + <umod:element symbol="C" number="-8"/> + <umod:element symbol="13C" number="8"/> + <umod:element symbol="N" number="-2"/> + <umod:element symbol="15N" number="2"/> + </umod:delta> + </umod:mod> + <umod:mod title="Label:13C(1)2H(3)" full_name="SILAC" username_of_poster="msalek" + group_of_poster="" + date_time_posted="2008-08-11 13:43:25" + date_time_modified="2008-08-14 18:16:30" + approved="0" + record_id="862"> + <umod:specificity hidden="1" site="M" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Isotopic labeled methionine SILAC</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="4.022185" avge_mass="4.0111" composition="H(-3) 2H(3) C(-1) 13C"> + <umod:element symbol="H" number="-3"/> + <umod:element symbol="2H" number="3"/> + <umod:element symbol="C" number="-1"/> + <umod:element symbol="13C" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="ZGB" full_name="NHS ester linked Green Fluorescent Bodipy Dye" + username_of_poster="JBowden" + group_of_poster="" + date_time_posted="2008-07-30 14:51:06" + date_time_modified="2008-08-14 18:13:03" + approved="0" + record_id="861"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"/> + <umod:specificity hidden="1" site="N-term" position="Any N-term" classification="Other" + spec_group="2"/> + <umod:delta mono_mass="757.373016" avge_mass="757.7182" + composition="H(52) B C(37) N(6) O(6) F(2) S"> + <umod:element symbol="H" number="52"/> + <umod:element symbol="C" number="37"/> + <umod:element symbol="N" number="6"/> + <umod:element symbol="O" number="6"/> + <umod:element symbol="F" number="2"/> + <umod:element symbol="S" number="1"/> + <umod:element symbol="B" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>Created for Commercial use by ZDye. Being utilized in proteomic and peptidomic research soon to be published</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.zdye.com/</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="MG-H1" full_name="Methylglyoxal-derived hydroimidazolone" + username_of_poster="AndrewW" + group_of_poster="" + date_time_posted="2008-07-24 14:41:07" + date_time_modified="2008-07-31 17:14:35" + approved="0" + record_id="859"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="54.010565" avge_mass="54.0474" composition="H(2) C(3) O"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>15377717</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="G-H1" full_name="Glyoxal-derived hydroimiadazolone" + username_of_poster="AndrewW" + group_of_poster="" + date_time_posted="2008-07-24 14:44:11" + date_time_modified="2008-07-31 17:16:39" + approved="0" + record_id="860"> + <umod:specificity hidden="1" site="R" position="Anywhere" classification="Other" spec_group="1"/> + <umod:delta mono_mass="39.994915" avge_mass="40.0208" composition="C(2) O"> + <umod:element symbol="C" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:xref> + <umod:text>17143934</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + </umod:mod> + <umod:mod title="Label:13C(6)15N(2)+GlyGly" full_name="13C(6) 15N(2) Lysine glygly" + username_of_poster="Raghothama" + group_of_poster="" + date_time_posted="2008-08-13 21:56:52" + date_time_modified="2008-08-14 18:22:40" + approved="0" + record_id="864"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"> + <umod:misc_notes>Used in SILAC PTM (glygly) experiment</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="122.057126" avge_mass="122.0454" + composition="H(6) C(-2) 13C(6) 15N(2) O(2)"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="-2"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="15N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:delta> + <umod:alt_name>heavy glygly lysine</umod:alt_name> + <umod:xref> + <umod:text>12716131</umod:text> + <umod:source>PubMed PMID</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Silac introduction</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.pil.sdu.dk/silac_intro.htm</umod:url> + </umod:xref> + </umod:mod> + <umod:mod title="ICPL:13C(6)2H(4)" + full_name="Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, +10 Da form" + username_of_poster="suckau" + group_of_poster="" + date_time_posted="2008-09-03 15:17:21" + date_time_modified="2008-09-12 11:59:23" + approved="0" + record_id="866"> + <umod:specificity hidden="0" site="N-term" position="Any N-term" classification="Isotopic label" + spec_group="3"> + <umod:misc_notes>Use when labelling post-digest</umod:misc_notes> + </umod:specificity> + <umod:specificity hidden="0" site="K" position="Anywhere" classification="Isotopic label" + spec_group="1"/> + <umod:specificity hidden="0" site="N-term" position="Protein N-term" + classification="Isotopic label" + spec_group="2"> + <umod:misc_notes>Use when labelling pre-digest</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="115.066700" avge_mass="115.0747" + composition="H(-1) 2H(4) 13C(6) N O"> + <umod:element symbol="H" number="-1"/> + <umod:element symbol="2H" number="4"/> + <umod:element symbol="13C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:delta> + <umod:alt_name>ICPL_10</umod:alt_name> + <umod:xref> + <umod:text>Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.</umod:text> + <umod:source>Journal</umod:source> + <umod:url/> + </umod:xref> + <umod:xref> + <umod:text>Bruker Daltonics order reference</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html</umod:url> + </umod:xref> + <umod:misc_notes>Attention: As the digest is typically applied AFTER ICPL labeling, only ProteinN-term labeling and Lys-specific labeling is applied.</umod:misc_notes> + </umod:mod> + <umod:mod title="QQQTGG" full_name="SUMOylation by SUMO-2/3" username_of_poster="oosula" + group_of_poster="" + date_time_posted="2008-09-09 17:09:04" + date_time_modified="2008-09-12 18:18:08" + approved="0" + record_id="877"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"> + <umod:misc_notes>This peptide is generated from a trypsin/chymotrypsin dual digest</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="617.276903" avge_mass="617.6095" + composition="H(39) C(23) N(9) O(11)"> + <umod:element symbol="H" number="39"/> + <umod:element symbol="C" number="23"/> + <umod:element symbol="N" number="9"/> + <umod:element symbol="O" number="11"/> + </umod:delta> + <umod:alt_name>GlnGlnGlnThrGlyGly</umod:alt_name> + </umod:mod> + <umod:mod title="QEQTGG" full_name="SUMOylation by SUMO-1" username_of_poster="oosula" + group_of_poster="" + date_time_posted="2008-09-09 17:02:45" + date_time_modified="2008-09-12 18:16:39" + approved="0" + record_id="876"> + <umod:specificity hidden="1" site="K" position="Anywhere" classification="Other" spec_group="1"> + <umod:misc_notes>This peptide is generated from a trypsin/chymotrypsin dual digest.</umod:misc_notes> + </umod:specificity> + <umod:delta mono_mass="618.260919" avge_mass="618.5942" + composition="H(38) C(23) N(8) O(12)"> + <umod:element symbol="H" number="38"/> + <umod:element symbol="C" number="23"/> + <umod:element symbol="N" number="8"/> + <umod:element symbol="O" number="12"/> + </umod:delta> + <umod:alt_name>GlnGluGlnThrGlyGly</umod:alt_name> + </umod:mod> + <umod:mod title="Bodipy" full_name="Bodipy modifications onto cysteine" + username_of_poster="anikolakakis" + group_of_poster="" + date_time_posted="2008-09-10 20:24:53" + date_time_modified="2008-09-12 18:30:57" + approved="0" + record_id="878"> + <umod:specificity hidden="1" site="C" position="Anywhere" classification="Chemical derivative" + spec_group="1"/> + <umod:delta mono_mass="414.167478" avge_mass="414.2135" + composition="H(21) B C(20) N(4) O(3) F(2)"> + <umod:element symbol="H" number="21"/> + <umod:element symbol="C" number="20"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="3"/> + <umod:element symbol="F" number="2"/> + <umod:element symbol="B" number="1"/> + </umod:delta> + <umod:alt_name>Which one?</umod:alt_name> + <umod:xref> + <umod:text>Invitrogen BODIPY Handbook</umod:text> + <umod:source>Misc. URL</umod:source> + <umod:url>http://probes.invitrogen.com/handbook/sections/0104.html</umod:url> + </umod:xref> + </umod:mod> + </umod:modifications> + <umod:amino_acids> + <umod:aa title="-" three_letter="" full_name="" mono_mass="0.0" avge_mass="0.0"/> + <umod:aa title="A" three_letter="Ala" full_name="Alanine" mono_mass="71.037114" + avge_mass="71.0779"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="R" three_letter="Arg" full_name="Arginine" mono_mass="156.101111" + avge_mass="156.1857"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="4"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="N" three_letter="Asn" full_name="Asparagine" mono_mass="114.042927" + avge_mass="114.1026"> + <umod:element symbol="H" number="6"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:aa> + <umod:aa title="D" three_letter="Asp" full_name="Aspartic acid" mono_mass="115.026943" + avge_mass="115.0874"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:aa> + <umod:aa title="C" three_letter="Cys" full_name="Cysteine" mono_mass="103.009185" + avge_mass="103.1429"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:aa> + <umod:aa title="E" three_letter="Glu" full_name="Glutamic acid" mono_mass="129.042593" + avge_mass="129.114"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:aa> + <umod:aa title="Q" three_letter="Gln" full_name="Glutamine" mono_mass="128.058578" + avge_mass="128.1292"> + <umod:element symbol="H" number="8"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="2"/> + </umod:aa> + <umod:aa title="G" three_letter="Gly" full_name="Glycine" mono_mass="57.021464" + avge_mass="57.0513"> + <umod:element symbol="H" number="3"/> + <umod:element symbol="C" number="2"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="H" three_letter="His" full_name="Histidine" mono_mass="137.058912" + avge_mass="137.1393"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="3"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="I" three_letter="Ile" full_name="Isoleucine" mono_mass="113.084064" + avge_mass="113.1576"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="L" three_letter="Leu" full_name="Leucine" mono_mass="113.084064" + avge_mass="113.1576"> + <umod:element symbol="H" number="11"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="K" three_letter="Lys" full_name="Lysine" mono_mass="128.094963" + avge_mass="128.1723"> + <umod:element symbol="H" number="12"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="M" three_letter="Met" full_name="Methionine" mono_mass="131.040485" + avge_mass="131.1961"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + <umod:element symbol="S" number="1"/> + </umod:aa> + <umod:aa title="F" three_letter="Phe" full_name="Phenylalanine" mono_mass="147.068414" + avge_mass="147.1739"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="P" three_letter="Pro" full_name="Proline" mono_mass="97.052764" + avge_mass="97.1152"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="S" three_letter="Ser" full_name="Serine" mono_mass="87.032028" + avge_mass="87.0773"> + <umod:element symbol="H" number="5"/> + <umod:element symbol="C" number="3"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:aa> + <umod:aa title="T" three_letter="Thr" full_name="Threonine" mono_mass="101.047679" + avge_mass="101.1039"> + <umod:element symbol="H" number="7"/> + <umod:element symbol="C" number="4"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:aa> + <umod:aa title="W" three_letter="Trp" full_name="Tryptophan" mono_mass="186.079313" + avge_mass="186.2099"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="11"/> + <umod:element symbol="N" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="Y" three_letter="Tyr" full_name="Tyrosine" mono_mass="163.063329" + avge_mass="163.1733"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="9"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="2"/> + </umod:aa> + <umod:aa title="V" three_letter="Val" full_name="Valine" mono_mass="99.068414" + avge_mass="99.1311"> + <umod:element symbol="H" number="9"/> + <umod:element symbol="C" number="5"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + <umod:aa title="N-term" three_letter="N-term" full_name="N-term" mono_mass="1.007825" + avge_mass="1.0079"> + <umod:element symbol="H" number="1"/> + </umod:aa> + <umod:aa title="C-term" three_letter="C-term" full_name="C-term" mono_mass="17.00274" + avge_mass="17.0073"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="O" number="1"/> + </umod:aa> + </umod:amino_acids> + <umod:mod_bricks> + <umod:brick title="-" full_name="" mono_mass="0" avge_mass="0"/> + <umod:brick title="H" full_name="Hydrogen" mono_mass="1.007825035" avge_mass="1.00794"> + <umod:element symbol="H" number="1"/> + </umod:brick> + <umod:brick title="C" full_name="Carbon" mono_mass="12" avge_mass="12.0107"> + <umod:element symbol="C" number="1"/> + </umod:brick> + <umod:brick title="N" full_name="Nitrogen" mono_mass="14.003074" avge_mass="14.0067"> + <umod:element symbol="N" number="1"/> + </umod:brick> + <umod:brick title="O" full_name="Oxygen" mono_mass="15.99491463" avge_mass="15.9994"> + <umod:element symbol="O" number="1"/> + </umod:brick> + <umod:brick title="P" full_name="Phosphorous" mono_mass="30.973762" avge_mass="30.973761"> + <umod:element symbol="P" number="1"/> + </umod:brick> + <umod:brick title="S" full_name="Sulphur" mono_mass="31.9720707" avge_mass="32.065"> + <umod:element symbol="S" number="1"/> + </umod:brick> + <umod:brick title="2H" full_name="Deuterium" mono_mass="2.014101779" + avge_mass="2.014101779"> + <umod:element symbol="2H" number="1"/> + </umod:brick> + <umod:brick title="18O" full_name="Oxygen 18" mono_mass="17.9991603" avge_mass="17.9991603"> + <umod:element symbol="18O" number="1"/> + </umod:brick> + <umod:brick title="F" full_name="Fluorine" mono_mass="18.99840322" avge_mass="18.9984032"> + <umod:element symbol="F" number="1"/> + </umod:brick> + <umod:brick title="Na" full_name="Sodium" mono_mass="22.9897677" avge_mass="22.98977"> + <umod:element symbol="Na" number="1"/> + </umod:brick> + <umod:brick title="Se" full_name="Selenium" mono_mass="79.9165196" avge_mass="78.96"> + <umod:element symbol="Se" number="1"/> + </umod:brick> + <umod:brick title="Hex" full_name="Hexose" mono_mass="162.0528235" avge_mass="162.1406"> + <umod:element symbol="H" number="10"/> + <umod:element symbol="C" number="6"/> + <umod:element symbol="O" number="5"/> + </umod:brick> + <umod:brick title="HexNAc" full_name="N-Acetyl Hexosamine" mono_mass="203.079372605" + avge_mass="203.19252"> + <umod:element symbol="C" number="8"/> + <umod:element symbol="H" number="13"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="5"/> + </umod:brick> + <umod:brick title="Ac" full_name="Acetate" mono_mass="42.0105647" avge_mass="42.03668"> + <umod:element symbol="C" number="2"/> + <umod:element symbol="H" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:brick> + <umod:brick title="dHex" full_name="Deoxy-hexose" mono_mass="146.05790887" + avge_mass="146.1412"> + <umod:element symbol="C" number="6"/> + <umod:element symbol="H" number="10"/> + <umod:element symbol="O" number="4"/> + </umod:brick> + <umod:brick title="HexA" full_name="Hexosamine" mono_mass="176.03208806" + avge_mass="176.12412"> + <umod:element symbol="C" number="6"/> + <umod:element symbol="H" number="8"/> + <umod:element symbol="O" number="6"/> + </umod:brick> + <umod:brick title="Kdn" full_name="3-deoxy-d-glycero-D-galacto-nonulosonic acid" + mono_mass="250.06886753" + avge_mass="250.20265999999998"> + <umod:element symbol="C" number="9"/> + <umod:element symbol="H" number="14"/> + <umod:element symbol="O" number="8"/> + </umod:brick> + <umod:brick title="Kdo" full_name="2-keto-3-deoxyoctulosonic acid" mono_mass="220.05830283" + avge_mass="220.17668"> + <umod:element symbol="C" number="8"/> + <umod:element symbol="H" number="12"/> + <umod:element symbol="O" number="7"/> + </umod:brick> + <umod:brick title="Me" full_name="Methyl" mono_mass="14.01565007" avge_mass="14.02658"> + <umod:element symbol="C" number="1"/> + <umod:element symbol="H" number="2"/> + </umod:brick> + <umod:brick title="NeuAc" full_name="N-acetyl neuraminic acid" mono_mass="291.095416635" + avge_mass="291.25458000000003"> + <umod:element symbol="C" number="11"/> + <umod:element symbol="H" number="17"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="8"/> + </umod:brick> + <umod:brick title="NeuGc" full_name="N-glycoyl neuraminic acid" + mono_mass="307.09033126500003" + avge_mass="307.25398"> + <umod:element symbol="C" number="11"/> + <umod:element symbol="H" number="17"/> + <umod:element symbol="N" number="1"/> + <umod:element symbol="O" number="9"/> + </umod:brick> + <umod:brick title="Water" full_name="Water" mono_mass="18.0105647" avge_mass="18.01528"> + <umod:element symbol="H" number="2"/> + <umod:element symbol="O" number="1"/> + </umod:brick> + <umod:brick title="Phos" full_name="Phosphate" mono_mass="79.96633092500001" + avge_mass="79.979901"> + <umod:element symbol="H" number="1"/> + <umod:element symbol="P" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:brick> + <umod:brick title="Sulf" full_name="Sulfate" mono_mass="79.95681459000001" + avge_mass="80.0632"> + <umod:element symbol="S" number="1"/> + <umod:element symbol="O" number="3"/> + </umod:brick> + <umod:brick title="Pent" full_name="Pentose" mono_mass="132.0422588" avge_mass="132.11462"> + <umod:element symbol="C" number="5"/> + <umod:element symbol="H" number="8"/> + <umod:element symbol="O" number="4"/> + </umod:brick> + <umod:brick title="Li" full_name="Lithium" mono_mass="7.016003" avge_mass="6.941"> + <umod:element symbol="Li" number="1"/> + </umod:brick> + <umod:brick title="13C" full_name="Carbon 13" mono_mass="13.00335483" + avge_mass="13.00335483"> + <umod:element symbol="13C" number="1"/> + </umod:brick> + <umod:brick title="15N" full_name="Nitrogen 15" mono_mass="15.00010897" + avge_mass="15.00010897"> + <umod:element symbol="15N" number="1"/> + </umod:brick> + <umod:brick title="Cl" full_name="Chlorine" mono_mass="34.96885272" avge_mass="35.453"> + <umod:element symbol="Cl" number="1"/> + </umod:brick> + <umod:brick title="K" full_name="Potassium" mono_mass="38.9637074" avge_mass="39.0983"> + <umod:element symbol="K" number="1"/> + </umod:brick> + <umod:brick title="Ca" full_name="Calcium" mono_mass="39.9625906" avge_mass="40.078"> + <umod:element symbol="Ca" number="1"/> + </umod:brick> + <umod:brick title="Fe" full_name="Iron" mono_mass="55.9349393" avge_mass="55.845"> + <umod:element symbol="Fe" number="1"/> + </umod:brick> + <umod:brick title="Ni" full_name="Nickel" mono_mass="57.9353462" avge_mass="58.6934"> + <umod:element symbol="Ni" number="1"/> + </umod:brick> + <umod:brick title="Zn" full_name="Zinc" mono_mass="63.9291448" avge_mass="65.409"> + <umod:element symbol="Zn" number="1"/> + </umod:brick> + <umod:brick title="Br" full_name="Bromine" mono_mass="78.9183361" avge_mass="79.904"> + <umod:element symbol="Br" number="1"/> + </umod:brick> + <umod:brick title="Ag" full_name="Silver" mono_mass="106.905092" avge_mass="107.8682"> + <umod:element symbol="Ag" number="1"/> + </umod:brick> + <umod:brick title="Hg" full_name="Mercury" mono_mass="201.970617" avge_mass="200.59"> + <umod:element symbol="Hg" number="1"/> + </umod:brick> + <umod:brick title="Au" full_name="Gold" mono_mass="196.966543" avge_mass="196.96655"> + <umod:element symbol="Au" number="1"/> + </umod:brick> + <umod:brick title="I" full_name="Iodine" mono_mass="126.904473" avge_mass="126.90447"> + <umod:element symbol="I" number="1"/> + </umod:brick> + <umod:brick title="Mo" full_name="Molybdenum" mono_mass="97.9054073" avge_mass="95.94"> + <umod:element symbol="Mo" number="1"/> + </umod:brick> + <umod:brick title="Cu" full_name="Copper" mono_mass="62.9295989" avge_mass="63.546"> + <umod:element symbol="Cu" number="1"/> + </umod:brick> + <umod:brick title="Hep" full_name="Heptose" mono_mass="192.06338820000002" + avge_mass="192.16658"> + <umod:element symbol="C" number="7"/> + <umod:element symbol="H" number="12"/> + <umod:element symbol="O" number="6"/> + </umod:brick> + <umod:brick title="B" full_name="Boron" mono_mass="11.0093055" avge_mass="10.811"> + <umod:element symbol="B" number="1"/> + </umod:brick> + <umod:brick title="As" full_name="Arsenic" mono_mass="74.9215942" avge_mass="74.9215942"> + <umod:element symbol="As" number="1"/> + </umod:brick> + </umod:mod_bricks> +</umod:unimod> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xtandem_adapter.xml Fri May 10 17:31:05 2013 -0400 @@ -0,0 +1,94 @@ +<tool id="xtandem_adapter" version="0.1.0" name="X! Tandem (OpenMS)"> + <description> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires"> + <requirement type="package">tandem</requirement> + </expand> + <command interpreter="python"> + openms_wrapper.py + --executable 'XTandemAdapter' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=$input1 +out=$out +database=$database +xtandem_executable=@WHICH(tandem)@ +variable_modifications=${variable_modifications or ''} +fixed_modifications=${fixed_modifications or ''} +precursor_mass_tolerance=$precursor_mass_tolerance +precursor_error_units=$precursor_mass_tolerance_unit +fragment_mass_tolerance=$fragment_mass_tolerance +fragment_error_units=$fragment_mass_tolerance_unit +min_precursor_charge=$min_precursor_charge +max_precursor_charge=$max_precursor_charge +cleavage_site=$cleavage_site +minimum_fragment_mz=$minimum_fragment_mz +max_valid_expect=$max_valid_expect +refinement=$refinement +semi_cleavage=$semi_cleavage +</configfile> + </configfiles> + <inputs> + <expand macro="id_inputs" /> + <expand macro="fixed_modifications_param" /> + <expand macro="variable_modifications_param" /> + <expand macro="precursor_mass_tolerance_param" /> + <expand macro="precursor_mass_tolerance_unit_param" /> + <expand macro="fragment_mass_tolerance_param" /> + <expand macro="fragment_mass_tolerance_unit_param" /> + <expand macro="precursor_charge_params" /> + <param name="cleavage_site" label="Cleavage Site" type="select"> + <option value="[R]|{P}">argc</option> + <option value="[X]|[D]">aspn</option> + <option value="[FMWY]|{P}">chymotrypsin</option> + <option value="[R]|[X]">clostripain</option> + <option value="[M]|{P}">cnbr</option> + <option value="[AGILV]|{P}">elastase</option> + <option value="[D]|{P}">formicacid</option> + <option value="[DE]|{P}">gluc</option> + <option value="[E]|{P}">gluc_bicarb</option> + <option value="[W]|[X]">iodosobenzoate</option> + <option value="[K]|[P]">lysc</option> + <option value="[K]|[X]">lysc-p</option> + <option value="[X]|[K]">lysn</option> + <option value="[X]|[AKRS]">lysn_promisc</option> + <option value="[X]|[X]">nonspecific</option> + <option value="[FL]|[X]">pepsina</option> + <option value="[P]|[X]">protein_endopeptidase</option> + <option value="[E]|[X]">staph_protease</option> + <option value="[KR]|{P}" selected="true">trypsin</option> + <option value="[DEKR]|{P}">trypsin_gluc</option> + <option value="[K]|{P}">trypsin_k</option> + <option value="[R]|{P}">trypsin_r</option> + <sanitizer> + <valid> + <add value="{"/> + <add value="}"/> + <add value="|"/> + <add value="["/> + <add value="]"/> + </valid> + </sanitizer> + </param> + <param name="minimum_fragment_mz" label="Minimum Fragment m/z" value="150" type="float" /> + <param name="max_valid_expect" label="Maximum Valid E-Value to be Reported" value=".1" type="float" /> + <param name="semi_cleavage" type="boolean" label="Enable Semi-Cleavage" checked="false" truevalue="true" falsevalue="false" help="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." /> + <param name="refinement" type="boolean" label="Enable Refinement" checked="false" truevalue="true" falsevalue="false" help="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." /> + </inputs> + <expand macro="id_outputs" /> + <help> +**What it does** + + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>