# HG changeset patch # User galaxyp # Date 1368220971 14400 # Node ID d4b6c9eae6358d89cf8fdf9ecee917fa3e6c38a9 Initial commit. diff -r 000000000000 -r d4b6c9eae635 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,11 @@ +--2012-09-19 08:46:18-- http://www.apache.org/licenses/LICENSE-2.0.txt +Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229 +Connecting to www.apache.org|140.211.11.131|:80... connected. +HTTP request sent, awaiting response... 200 OK +Length: 11358 (11K) [text/plain] +Saving to: “LICENSE-2.0.txt” + + 0K .......... . 100% 200K=0.06s + +2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358] + diff -r 000000000000 -r d4b6c9eae635 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,34 @@ +Tool wrapper for MaxQuant. + +MaxQuant is a Windows only program and so you will likely need to +deploy this tool to run on a remote Windows system via the LWR +(https://lwr.readthedocs.org). + +The sample mods file maxquant_mods.loc.sample corresponds to the +default modifications MaxQuant is configured with. The Galaxy-P +project uses a MaxQuant that has been extended with all of Unimod. To +modify MaxQuant in this fashion replace MaxQuant's modifications.xml +file with the extended_modifications.xml distributed with this tool +and configure Galaxy with the maxquant_mods.loc.sample.extended loc +file.# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. diff -r 000000000000 -r d4b6c9eae635 README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. diff -r 000000000000 -r d4b6c9eae635 README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,13 @@ +Tool wrapper for MaxQuant. + +MaxQuant is a Windows only program and so you will likely need to +deploy this tool to run on a remote Windows system via the LWR +(https://lwr.readthedocs.org). + +The sample mods file maxquant_mods.loc.sample corresponds to the +default modifications MaxQuant is configured with. The Galaxy-P +project uses a MaxQuant that has been extended with all of Unimod. To +modify MaxQuant in this fashion replace MaxQuant's modifications.xml +file with the extended_modifications.xml distributed with this tool +and configure Galaxy with the maxquant_mods.loc.sample.extended loc +file. \ No newline at end of file diff -r 000000000000 -r d4b6c9eae635 augment_maxquant_mods.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augment_maxquant_mods.py Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,166 @@ +#!/usr/bin/env python +""" +Usage: + python augment_maxquant_mods.py + +Assuming Unimod XML file (unimod.xml) and stock MaxQuant modifications +file (modifications.xml) are in this same directory, this script will +create a new MaxQuant modifications file (extended_modifications.xml) +with an a new modification for each unimod entry. These new entires +will be suffixed with [Unimod] to distinguish them from existing +MaxQuant entries. This file should be copied to +\bin\conf\modifications.xml + +""" +import xml.etree.ElementTree as ET +import re + +FAKE_DATE = "2012-06-11T21:21:24.4946343+02:00" + +POSITION_MAP = { + "Anywhere": "anywhere", + "Any N-term": "anyNterm", + "Any C-term": "anyCterm", + "Protein N-term": "proteinNterm", + "Protein C-term": "proteinCterm", +} + +unimod_tree = ET.parse('unimod.xml') +unimod_ns = '{http://www.unimod.org/xmlns/schema/unimod_2}' +unimod_modifications_el = unimod_tree.getroot().find('%smodifications' % unimod_ns) +mq_tree = ET.parse("modifications.xml") +mq_root = mq_tree.getroot() + + +def to_label(title, site): + return "%s (%s) [Unimod]" % (title, site) + + +def copy_modification(unimod_modification): + if unimod_modification.hidden: + return False + if unimod_modification.delta_el is None: + return False + comp_array = unimod_modification.composition_array + for aa, count in comp_array: + if len(aa) > 1 and aa not in COMP_REPLACES.keys(): + # Complex stuff like Hep, that I cannot translate into MaxQuant. + return False + return True + + +COMP_REPLACES = { + "15N": "Nx", + "13C": "Cx", + "18O": "Ox", + "2H": "Hx", +} + +## HEP? + + +def convert_composition(unimod_composition): + """ + Convert Unimod representation of composition to MaxQuant + """ + composition = unimod_composition + for key, value in COMP_REPLACES.iteritems(): + composition = composition.replace(key, value) + print composition + return composition + + +def populate_modification(modification, unimod_modification): + """ + Copy unimod entry ``unimod_modification`` to MaxQuant entry ``modification``. + """ + attrib = modification.attrib + attrib["create_date"] = FAKE_DATE + attrib["last_modified_date"] = FAKE_DATE + attrib["reporterCorrectionM1"] = str(0) + attrib["reporterCorrectionM2"] = str(0) + attrib["reporterCorrectionP1"] = str(0) + attrib["reporterCorrectionP2"] = str(0) + attrib["user"] = "build_mods_script" + label = unimod_modification.label + attrib["title"] = label + attrib["description"] = label + attrib["composition"] = convert_composition(unimod_modification.raw_composition) + unimod_position = unimod_modification.position + maxquant_position = POSITION_MAP[unimod_position] + assert maxquant_position != None + position_el = ET.SubElement(modification, "position") + position_el.text = maxquant_position + modification_site_el = ET.SubElement(modification, "modification_site") + modification_site_el.attrib["index"] = "0" + unimod_site = unimod_modification.site + modification_site_el.attrib["site"] = "-" if len(unimod_site) > 1 else unimod_site + type_el = ET.SubElement(modification, "type") + type_el.text = "standard" + return modification + + +class UnimodModification: + + def __init__(self, modification, specificity): + self.modification = modification + self.specificity = specificity + + @property + def title(self): + return self.modification.attrib["title"] + + @property + def site(self): + return self.specificity.attrib["site"] + + @property + def label(self): + return "%s (%s) [Unimod]" % (self.title, self.site) + + @property + def delta_el(self): + return self.modification.find("%sdelta" % unimod_ns) + + @property + def raw_composition(self): + return self.delta_el.attrib["composition"] + + @property + def composition_array(self): + raw_composition = self.raw_composition + aa_and_counts = re.split("\s+", raw_composition) + comp_array = [] + for aa_and_count in aa_and_counts: + match = re.match(r"(\w+)(\((-?\d+)\))?", aa_and_count) + aa = match.group(1) + count = match.group(3) or 1 + comp_array.append((aa, count)) + return comp_array + + @property + def position(self): + return self.specificity.attrib["position"] + + @property + def hidden(self): + return self.specificity.attrib["hidden"] == "true" + +unimod_modifications = [] +for mod in unimod_modifications_el.findall('%smod' % unimod_ns): + for specificity in mod.findall('%sspecificity' % unimod_ns): + unimod_modifications.append(UnimodModification(mod, specificity)) + +max_index = 0 +for modification in mq_root.getchildren(): + index = int(modification.attrib["index"]) + max_index = max(max_index, index) + +for unimod_modification in unimod_modifications: + if copy_modification(unimod_modification): + print unimod_modification.composition_array + max_index += 1 + modification = ET.SubElement(mq_root, "modification", attrib={"index": str(max_index)}) + populate_modification(modification, unimod_modification) + +mq_tree.write("extended_modifications.xml") diff -r 000000000000 -r d4b6c9eae635 build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_mods_loc.py Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,17 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +mods_path = "extended_modifications.xml" + +if not exists(mods_path): + mods_path = "modifications.xml" + +tree = ET.parse(mods_path) +modifications_el = tree.getroot() + +with open("maxquant_mods.loc", "w") as output: + for mod in modifications_el.getchildren(): + if mod.find("type").text.strip() == "standard": + output.write("%s\n" % mod.attrib["title"]) diff -r 000000000000 -r d4b6c9eae635 build_proteases_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_proteases_loc.py Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,14 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +proteases_path = "proteases.xml" + +tree = ET.parse(proteases_path) +proteases_el = tree.getroot() + +with open("maxquant_proteases.loc", "w") as output: + for protease in proteases_el.getchildren(): + output.write("%s\n" % protease.attrib["name"]) + diff -r 000000000000 -r d4b6c9eae635 extended_modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extended_modifications.xml Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,2579 @@ + + + notCterm + + + + + + + standard + + + proteinNterm + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + + + + + + + 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\ No newline at end of file diff -r 000000000000 -r d4b6c9eae635 maxquant.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant.xml Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,331 @@ + + + + + maxquant + windows + + + ##Describe inputs +#set $type = str($analysis_type.type) +#if $type == "single" +#set $groups = [$analysis_type] +#elif $type == "multi_same" +#set $groups = $analysis_type.groups +#end if +#for $i, $group in enumerate($groups) +num:${str(i + 1)} +#for $input in $group.inputs +name:${input.display_name} +path:${input} +#end for +#end for + + + maxquant_wrapper.py + --input_groups=$inputs_config + --database="${database}" + --database_name="${database.name}" + --protease=$analysis_type.protease + --first_search_tol=$analysis_type.first_search_tol + --main_search_tol=$analysis_type.main_search_tol + --max_missed_cleavages=$analysis_type.max_missed_cleavages + --max_n_mods=$analysis_type.max_n_mods + --variable_mods="${analysis_type.variable_modifications or ''}" + #if $analysis_type.advanced_group_parameters.specify + --do_mass_filtering=$analysis_type.advanced_group_parameters.do_mass_filtering + --max_charge=$analysis_type.advanced_group_parameters.max_charge + #end if + #set $run = $analysis_type.run + #set $lcms_run_type = $run.lcms_run_type + --lcms_run_type=$lcms_run_type + #if str($lcms_run_type) != "3" + ## i.e. is not reporter ion type + #if $run.labels_conditional.labeled + #for $label_group in $run.labels_conditional.label_groups + --labels="${label_group.labels or ''}" + #end for + --max_labeled_aa=$run.labels_conditional.max_labeled_aa + #end if + #else + --reporter_type=$run.reporter_type + #end if + #set $sp = $advanced_sequence_parameters + #if $sp.specify + --include_contamiants=${str(sp['include_contamiants']).lower()} + --equal_il=${str(sp['equal_il']).lower()} + --randomize=${str(sp['randomize'])} + #end if + #if $quantification.specify + #set $restrict = $quantification.restrict.restrict_protein_quantification + --restrict_protein_quantification=${str(restrict).lower()} + #if $quantification.restrict.restrict_protein_quantification + --restrict_mods="${quantification.restrict.restrict_modifications or ''}" + #end if + --quant_mode=$quantification.quant_mode + --use_counterparts=$quantification.use_counterparts + --min_ratio_count=$quantification.min_ratio_count + #end if + #if $site_quantification.specify + --site_quant_mode=$site_quantification.site_quant_mode + --use_norm_ratios_for_occupancy=$site_quantification.use_norm_ratios_for_occupancy + #end if + #set $identification_type = str($identification.options_type) + #if $identification_type != "none" + --protein_fdr=$identification.protein_fdr + --peptide_fdr=$identification.peptide_fdr + --site_fdr=$identification.site_fdr + #if $identification_type != "simple" + --peptide_pep=$identification.peptide_pep + #end if + #end if + #if $misc.specify + --re_quantify="$misc.re_quantify" + #end if + --fixed_mods="${fixed_modifications or ''}" + --output_protein_groups=$output_protein_groups + --output_peptides=$output_peptides + --output_evidence=$output_evidence + --output_parameters=$output_parameters + --output_msms=$output_msms + --output_mqpar=$output_mqpar + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,1234 @@ +Acetyl (K) +Acetyl (Protein N-term) +Carbamidomethyl (C) +Oxidation (M) +Phospho (STY) +GlyGly (K) +Methyl (KR) +Dimethyl (KR) +Trimethyl (K) +Pro5 +Pro6 +Glu->pyro-Glu +Gln->pyro-Glu +OHexNAc +QQTGG (K) +Deamidation (N) +Deamidation 18O (N) +Deamidation (NQ) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Xle +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Arg->Ala +Arg->Asn +Arg->Asp +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +His->Ala +His->Arg +His->Asn +His->Asp +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Ala->CamCys +Arg->CamCys +Asn->CamCys +Asp->CamCys +Gln->CamCys +Glu->CamCys +Gly->CamCys +His->CamCys +Lys->CamCys +Met->CamCys +Phe->CamCys +Pro->CamCys +Ser->CamCys +Thr->CamCys +Trp->CamCys +Tyr->CamCys +Val->CamCys +Xle->CamCys +Acetyl (T) [Unimod] +Acetyl (N-term) [Unimod] +Acetyl (S) [Unimod] +Acetyl (C) [Unimod] +Acetyl (N-term) [Unimod] +Acetyl (K) [Unimod] +Acetyl (Y) [Unimod] +Acetyl (H) [Unimod] +Amidated (C-term) [Unimod] +Amidated (C-term) [Unimod] +Biotin (N-term) [Unimod] +Biotin (K) [Unimod] +Carbamidomethyl (D) [Unimod] +Carbamidomethyl (H) [Unimod] +Carbamidomethyl (N-term) [Unimod] +Carbamidomethyl (K) [Unimod] +Carbamidomethyl (C) [Unimod] +Carbamidomethyl (E) [Unimod] +Carbamyl (C) [Unimod] +Carbamyl (R) [Unimod] +Carbamyl (N-term) [Unimod] +Carbamyl (K) [Unimod] +Carbamyl (M) [Unimod] +Carboxymethyl (N-term) [Unimod] +Carboxymethyl (K) [Unimod] +Carboxymethyl (C) [Unimod] +Carboxymethyl (W) [Unimod] +Deamidated (R) [Unimod] +Deamidated (N) [Unimod] +Deamidated (Q) [Unimod] +Deamidated (F) [Unimod] +ICAT-G (C) [Unimod] +ICAT-G:2H(8) (C) [Unimod] +Met->Hse (M) [Unimod] +Met->Hsl (M) [Unimod] +ICAT-D:2H(8) (C) [Unimod] +ICAT-D (C) [Unimod] +NIPCAM (C) [Unimod] +PEO-Iodoacetyl-LC-Biotin (C) [Unimod] +Phospho (R) [Unimod] +Phospho (C) [Unimod] +Phospho (D) [Unimod] +Phospho (Y) [Unimod] +Phospho (H) [Unimod] +Phospho (T) [Unimod] +Phospho (S) [Unimod] +Dehydrated (D) [Unimod] +Dehydrated (Y) [Unimod] +Dehydrated (T) [Unimod] +Dehydrated (S) [Unimod] +Dehydrated (N) [Unimod] +Dehydrated (Q) [Unimod] +Dehydrated (C) [Unimod] +Propionamide (C) [Unimod] +Pyridylacetyl (N-term) [Unimod] +Pyridylacetyl (K) [Unimod] +Pyro-carbamidomethyl (C) [Unimod] +Glu->pyro-Glu (E) [Unimod] +Gln->pyro-Glu (Q) [Unimod] +SMA (N-term) [Unimod] +SMA (K) [Unimod] +Pyridylethyl (C) [Unimod] +Methyl (T) [Unimod] +Methyl (S) [Unimod] +Methyl (N-term) [Unimod] +Methyl (E) [Unimod] +Methyl (D) [Unimod] +Methyl (C-term) [Unimod] +Methyl (L) [Unimod] +Methyl (I) [Unimod] +Methyl (R) [Unimod] +Methyl (N-term) [Unimod] +Methyl (Q) [Unimod] +Methyl (N) [Unimod] +Methyl (K) [Unimod] +Methyl (H) [Unimod] +Methyl (C) [Unimod] +Oxidation (W) [Unimod] +Oxidation (H) [Unimod] +Oxidation (C) [Unimod] +Oxidation (M) [Unimod] +Oxidation (R) [Unimod] +Oxidation (Y) [Unimod] +Oxidation (F) [Unimod] +Oxidation (P) [Unimod] +Oxidation (N) [Unimod] +Oxidation (K) [Unimod] +Oxidation (D) [Unimod] +Oxidation (G) [Unimod] +Dimethyl (N) [Unimod] +Dimethyl (N-term) [Unimod] +Dimethyl (R) [Unimod] +Dimethyl (K) [Unimod] +Dimethyl (P) [Unimod] +Trimethyl (A) [Unimod] +Trimethyl (R) [Unimod] +Trimethyl (K) [Unimod] +Methylthio (C) [Unimod] +Methylthio (N) [Unimod] +Methylthio (D) [Unimod] +Sulfo (Y) [Unimod] +Sulfo (T) [Unimod] +Sulfo (S) [Unimod] +Sulfo (C) [Unimod] +Lipoyl (K) [Unimod] +Farnesyl (C) [Unimod] +Myristoyl (C) [Unimod] +Myristoyl (K) [Unimod] +Myristoyl (G) [Unimod] +PyridoxalPhosphate (K) [Unimod] +Palmitoyl (T) [Unimod] +Palmitoyl (S) [Unimod] +Palmitoyl (K) [Unimod] +Palmitoyl (C) [Unimod] +Palmitoyl (N-term) [Unimod] +GeranylGeranyl (C) [Unimod] +Phosphopantetheine (S) [Unimod] +FAD (Y) [Unimod] +FAD (H) [Unimod] +FAD (C) [Unimod] +Tripalmitate (C) [Unimod] +Guanidinyl (K) [Unimod] +HNE (K) [Unimod] +HNE (H) [Unimod] +HNE (C) [Unimod] +Glucuronyl (N-term) [Unimod] +Glucuronyl (S) [Unimod] +Glutathione (C) [Unimod] +Acetyl:2H(3) (N-term) [Unimod] +Acetyl:2H(3) (K) [Unimod] +Propionyl (N-term) [Unimod] +Propionyl (K) [Unimod] +Propionyl:13C(3) (N-term) [Unimod] +Propionyl:13C(3) (K) [Unimod] +GIST-Quat (N-term) [Unimod] +GIST-Quat (K) [Unimod] +GIST-Quat:2H(3) (N-term) [Unimod] +GIST-Quat:2H(3) (K) [Unimod] +GIST-Quat:2H(6) (N-term) [Unimod] +GIST-Quat:2H(6) (K) [Unimod] +GIST-Quat:2H(9) (N-term) [Unimod] +GIST-Quat:2H(9) (K) [Unimod] +Succinyl (N-term) [Unimod] +Succinyl (N-term) [Unimod] +Succinyl (K) [Unimod] +Succinyl:2H(4) (N-term) [Unimod] +Succinyl:2H(4) (K) [Unimod] +Succinyl:13C(4) (N-term) [Unimod] +Succinyl:13C(4) (K) [Unimod] +probiotinhydrazide (P) [Unimod] +Pro->pyro-Glu (P) [Unimod] +His->Asn (H) [Unimod] +His->Asp (H) [Unimod] +Trp->Hydroxykynurenin (W) [Unimod] +Delta:H(4)C(3) (K) [Unimod] +Delta:H(4)C(3) (H) [Unimod] +Delta:H(4)C(2) (K) [Unimod] +Delta:H(4)C(2) (H) [Unimod] +Cys->Dha (C) [Unimod] +Arg->GluSA (R) [Unimod] +Trioxidation (C) [Unimod] +Iminobiotin (N-term) [Unimod] +Iminobiotin (K) [Unimod] +ESP (N-term) [Unimod] +ESP (K) [Unimod] +ESP:2H(10) (N-term) [Unimod] +ESP:2H(10) (K) [Unimod] +NHS-LC-Biotin (N-term) [Unimod] +NHS-LC-Biotin (K) [Unimod] +EDT-maleimide-PEO-biotin (T) [Unimod] +EDT-maleimide-PEO-biotin (S) [Unimod] +IMID (K) [Unimod] +IMID:2H(4) (K) [Unimod] +Lysbiotinhydrazide (K) [Unimod] +Propionamide:2H(3) (C) [Unimod] +Nitro (Y) [Unimod] +Nitro (W) [Unimod] +ICAT-C (C) [Unimod] +Delta:H(2)C(2) (K) [Unimod] +Delta:H(2)C(2) (H) [Unimod] +Trp->Kynurenin (W) [Unimod] +Lys->Allysine (K) [Unimod] +ICAT-C:13C(9) (C) [Unimod] +FormylMet (N-term) [Unimod] +Nethylmaleimide (C) [Unimod] +OxLysBiotinRed (K) [Unimod] +IBTP (C) [Unimod] +OxLysBiotin (K) [Unimod] +OxProBiotinRed (P) [Unimod] +OxProBiotin (P) [Unimod] +OxArgBiotin (R) [Unimod] +OxArgBiotinRed (R) [Unimod] +EDT-iodoacetyl-PEO-biotin (T) [Unimod] +EDT-iodoacetyl-PEO-biotin (S) [Unimod] +GlyGly (T) [Unimod] +GlyGly (S) [Unimod] +GlyGly (C) [Unimod] +GlyGly (K) [Unimod] +Formyl (N-term) [Unimod] +Formyl (T) [Unimod] +Formyl (K) [Unimod] +Formyl (N-term) [Unimod] +Formyl (S) [Unimod] +Cation:K (C-term) [Unimod] +Cation:K (E) [Unimod] +Cation:K (D) [Unimod] +Thioacyl (N-term) [Unimod] +Thioacyl (K) [Unimod] +Fluoro (W) [Unimod] +Fluoro (F) [Unimod] +Fluoro (Y) [Unimod] +Fluorescein (C) [Unimod] +Iodo (H) [Unimod] +Iodo (Y) [Unimod] +Diiodo (Y) [Unimod] +Triiodo (Y) [Unimod] +Myristoleyl (G) [Unimod] +Pro->Pyrrolidinone (P) [Unimod] +Myristoyl+Delta:H(-4) (G) [Unimod] +Benzoyl (N-term) [Unimod] +Benzoyl (K) [Unimod] +Dansyl (N-term) [Unimod] +Dansyl (K) [Unimod] +a-type-ion (C-term) [Unimod] +Amidine (N-term) [Unimod] +Amidine (K) [Unimod] +NBS:13C(6) (W) [Unimod] +Methyl:2H(3)13C(1) (R) [Unimod] +Dimethyl:2H(6)13C(2) (R) [Unimod] +NBS (W) [Unimod] +Delta:H(1)O(-1)18O(1) (N) [Unimod] +QAT (C) [Unimod] +BHT (H) [Unimod] +BHT (K) [Unimod] +BHT (C) [Unimod] +Delta:H(4)C(2)O(-1)S(1) (S) [Unimod] +DAET (T) [Unimod] +DAET (S) [Unimod] +Pro->Pyrrolidone (P) [Unimod] +Label:13C(9) (Y) [Unimod] +Label:13C(9) (F) [Unimod] +Label:13C(9)+Phospho (Y) [Unimod] +Label:13C(6) (I) [Unimod] +Label:13C(6) (L) [Unimod] +Label:13C(6) (K) [Unimod] +Label:13C(6) (R) [Unimod] +HPG (R) [Unimod] +2HPG (R) [Unimod] +QAT:2H(3) (C) [Unimod] +Label:18O(2) (C-term) [Unimod] +AccQTag (N-term) [Unimod] +AccQTag (K) [Unimod] +Dimethyl:2H(4) (N-term) [Unimod] +Dimethyl:2H(4) (N-term) [Unimod] +Dimethyl:2H(4) (K) [Unimod] +EQAT (C) [Unimod] +EQAT:2H(5) (C) [Unimod] +Ethanedithiol (T) [Unimod] +Ethanedithiol (S) [Unimod] +NEIAA:2H(5) (Y) [Unimod] +NEIAA:2H(5) (C) [Unimod] +Delta:H(6)C(6)O(1) (K) [Unimod] +Delta:H(4)C(3)O(1) (K) [Unimod] +Delta:H(4)C(3)O(1) (H) [Unimod] +Delta:H(4)C(3)O(1) (C) [Unimod] +Delta:H(2)C(3) (K) [Unimod] +Delta:H(4)C(6) (K) [Unimod] +Delta:H(8)C(6)O(2) (K) [Unimod] +ADP-Ribosyl (E) [Unimod] +ADP-Ribosyl (S) [Unimod] +ADP-Ribosyl (N) [Unimod] +ADP-Ribosyl (C) [Unimod] +ADP-Ribosyl (R) [Unimod] +NEIAA (Y) [Unimod] +NEIAA (C) [Unimod] +iTRAQ4plex (Y) [Unimod] +iTRAQ4plex (N-term) [Unimod] +iTRAQ4plex (K) [Unimod] +Crotonaldehyde (K) [Unimod] +Crotonaldehyde (H) [Unimod] +Crotonaldehyde (C) [Unimod] +Amino (Y) [Unimod] +Argbiotinhydrazide (R) [Unimod] +Label:18O(1) (Y) [Unimod] +Label:18O(1) (T) [Unimod] +Label:18O(1) (S) [Unimod] +Label:18O(1) (C-term) [Unimod] +Label:13C(6)15N(2) (K) [Unimod] +Thiophospho (Y) [Unimod] +Thiophospho (T) [Unimod] +Thiophospho (S) [Unimod] +SPITC (K) [Unimod] +SPITC (N-term) [Unimod] +Cytopiloyne (Y) [Unimod] +Cytopiloyne (S) [Unimod] +Cytopiloyne (R) [Unimod] +Cytopiloyne (P) [Unimod] +Cytopiloyne (N-term) [Unimod] +Cytopiloyne (K) [Unimod] +Cytopiloyne (C) [Unimod] +Cytopiloyne+water (Y) [Unimod] +Cytopiloyne+water (T) [Unimod] +Cytopiloyne+water (S) [Unimod] +Cytopiloyne+water (R) [Unimod] +Cytopiloyne+water (N-term) [Unimod] +Cytopiloyne+water (K) [Unimod] +Cytopiloyne+water (C) [Unimod] +Label:13C(6)15N(4) (R) [Unimod] +Label:13C(9)15N(1) (F) [Unimod] +Label:2H(3) (L) [Unimod] +Label:13C(5)15N(1) (V) [Unimod] +PET (T) [Unimod] +PET (S) [Unimod] +CAF (N-term) [Unimod] +Xlink:SSD (K) [Unimod] +Nitrosyl (C) [Unimod] +AEBS (Y) [Unimod] +AEBS (S) [Unimod] +AEBS (N-term) [Unimod] +AEBS (K) [Unimod] +AEBS (H) [Unimod] +Ethanolyl (C) [Unimod] +HMVK (C) [Unimod] +Ethyl (N-term) [Unimod] +Ethyl (K) [Unimod] +Ethyl (E) [Unimod] +Ethyl (N-term) [Unimod] +CoenzymeA (C) [Unimod] +Methyl+Deamidated (Q) [Unimod] +Methyl+Deamidated (N) [Unimod] +Delta:H(5)C(2) (P) [Unimod] +Methyl:2H(2) (K) [Unimod] +SulfanilicAcid (E) [Unimod] +SulfanilicAcid (D) [Unimod] +SulfanilicAcid (C-term) [Unimod] +SulfanilicAcid:13C(6) (E) [Unimod] +SulfanilicAcid:13C(6) (D) [Unimod] +SulfanilicAcid:13C(6) (C-term) [Unimod] +Biotin-PEO-Amine (D) [Unimod] +Biotin-PEO-Amine (C-term) [Unimod] +Biotin-PEO-Amine (E) [Unimod] +Trp->Oxolactone (W) [Unimod] +Biotin-HPDP (C) [Unimod] +IodoU-AMP (Y) [Unimod] +IodoU-AMP (W) [Unimod] +IodoU-AMP (F) [Unimod] +CAMthiopropanoyl (N-term) [Unimod] +CAMthiopropanoyl (K) [Unimod] +IED-Biotin (C) [Unimod] +Methyl:2H(3) (E) [Unimod] +Methyl:2H(3) (D) [Unimod] +Methyl:2H(3) (C-term) [Unimod] +Carboxy (E) [Unimod] +Carboxy (D) [Unimod] +Carboxy (K) [Unimod] +Carboxy (W) [Unimod] +Carboxy (M) [Unimod] +Bromobimane (C) [Unimod] +Menadione (K) [Unimod] +Menadione (C) [Unimod] +DeStreak (C) [Unimod] +Cysteinyl (C) [Unimod] +Lys-loss (K) [Unimod] +Nmethylmaleimide (K) [Unimod] +Nmethylmaleimide (C) [Unimod] +CyDye-Cy3 (C) [Unimod] +DimethylpyrroleAdduct (K) [Unimod] +Delta:H(2)C(5) (K) [Unimod] +Delta:H(2)C(3)O(1) (K) [Unimod] +Delta:H(2)C(3)O(1) (R) [Unimod] +Nethylmaleimide+water (K) [Unimod] +Nethylmaleimide+water (C) [Unimod] +Methyl+Acetyl:2H(3) (K) [Unimod] +Xlink:B10621 (C) [Unimod] +DTBP (N-term) [Unimod] +DTBP (K) [Unimod] +DTBP (R) [Unimod] +DTBP (Q) [Unimod] +DTBP (N) [Unimod] +FP-Biotin (T) [Unimod] +FP-Biotin (Y) [Unimod] +FP-Biotin (S) [Unimod] +Thiophos-S-S-biotin (Y) [Unimod] +Thiophos-S-S-biotin (T) [Unimod] +Thiophos-S-S-biotin (S) [Unimod] +Can-FP-biotin (T) [Unimod] +Can-FP-biotin (Y) [Unimod] +Can-FP-biotin (S) [Unimod] +HNE+Delta:H(2) (K) [Unimod] +HNE+Delta:H(2) (H) [Unimod] +HNE+Delta:H(2) (C) [Unimod] +Thrbiotinhydrazide (T) [Unimod] +Methylamine (T) [Unimod] +Methylamine (S) [Unimod] +Diisopropylphosphate (Y) [Unimod] +Diisopropylphosphate (T) [Unimod] +Diisopropylphosphate (S) [Unimod] +Isopropylphospho (Y) [Unimod] +Isopropylphospho (T) [Unimod] +Isopropylphospho (S) [Unimod] +ICPL:13C(6) (N-term) [Unimod] +ICPL:13C(6) (N-term) [Unimod] +ICPL:13C(6) (K) [Unimod] +ICPL (N-term) [Unimod] +ICPL (K) [Unimod] +ICPL (N-term) [Unimod] +Deamidated:18O(1) (Q) [Unimod] +Deamidated:18O(1) (N) [Unimod] +Arg->Orn (R) [Unimod] +Dehydro (C) [Unimod] +Diphthamide (H) [Unimod] +Hydroxyfarnesyl (C) [Unimod] +Diacylglycerol (C) [Unimod] +Carboxyethyl (K) [Unimod] +Hypusine (K) [Unimod] +Retinylidene (K) [Unimod] +Lys->AminoadipicAcid (K) [Unimod] +Cys->PyruvicAcid (C) [Unimod] +Ammonia-loss (C) [Unimod] +Ammonia-loss (S) [Unimod] +Ammonia-loss (T) [Unimod] +Ammonia-loss (N) [Unimod] +Phycocyanobilin (C) [Unimod] +Phycoerythrobilin (C) [Unimod] +Phytochromobilin (C) [Unimod] +Quinone (W) [Unimod] +Quinone (Y) [Unimod] +GPIanchor (C-term) [Unimod] +PhosphoribosyldephosphoCoA (S) [Unimod] +GlycerylPE (E) [Unimod] +Triiodothyronine (Y) [Unimod] +Thyroxine (Y) [Unimod] +Tyr->Dha (Y) [Unimod] +Didehydro (S) [Unimod] +Didehydro (Y) [Unimod] +Didehydro (T) [Unimod] +Didehydro (K) [Unimod] +Cys->Oxoalanine (C) [Unimod] +Ser->LacticAcid (S) [Unimod] +GluGlu (E) [Unimod] +GluGlu (C-term) [Unimod] +Phosphoadenosine (H) [Unimod] +Phosphoadenosine (T) [Unimod] +Phosphoadenosine (K) [Unimod] +Phosphoadenosine (Y) [Unimod] +Glu (E) [Unimod] +Glu (C-term) [Unimod] +Hydroxycinnamyl (C) [Unimod] +Glycosyl (P) [Unimod] +FMNH (H) [Unimod] +FMNH (C) [Unimod] +Archaeol (C) [Unimod] +Phenylisocyanate (N-term) [Unimod] +Phenylisocyanate:2H(5) (N-term) [Unimod] +Phosphoguanosine (H) [Unimod] +Phosphoguanosine (K) [Unimod] +Hydroxymethyl (N) [Unimod] +Dipyrrolylmethanemethyl (C) [Unimod] +PhosphoUridine (H) [Unimod] +PhosphoUridine (Y) [Unimod] +Glycerophospho (S) [Unimod] +Carboxy->Thiocarboxy (G) [Unimod] +Sulfide (C) [Unimod] +PyruvicAcidIminyl (K) [Unimod] +PyruvicAcidIminyl (V) [Unimod] +PyruvicAcidIminyl (C) [Unimod] +Dioxidation (Y) [Unimod] +Dioxidation (W) [Unimod] +Dioxidation (F) [Unimod] +Dioxidation (M) [Unimod] +Dioxidation (R) [Unimod] +Dioxidation (K) [Unimod] +Dioxidation (P) [Unimod] +Dioxidation (C) [Unimod] +Octanoyl (T) [Unimod] +Octanoyl (S) [Unimod] +Palmitoleyl (C) [Unimod] +Cholesterol (C-term) [Unimod] +Didehydroretinylidene (K) [Unimod] +CHDH (D) [Unimod] +Methylpyrroline (K) [Unimod] +MicrocinC7 (C-term) [Unimod] +Cyano (C) [Unimod] +Amidino (C) [Unimod] +FMN (S) [Unimod] +FMN (T) [Unimod] +FMNC (C) [Unimod] +Hydroxytrimethyl (K) [Unimod] +Deoxy (T) [Unimod] +Deoxy (D) [Unimod] +Deoxy (S) [Unimod] +Microcin (C-term) [Unimod] +Decanoyl (T) [Unimod] +Decanoyl (S) [Unimod] +GluGluGlu (C-term) [Unimod] +GluGluGlu (E) [Unimod] +GluGluGluGlu (C-term) [Unimod] +GluGluGluGlu (E) [Unimod] +HexN (W) [Unimod] +HexN (T) [Unimod] +HexN (N) [Unimod] +HexN (K) [Unimod] +Xlink:DMP-s (N-term) [Unimod] +Xlink:DMP-s (K) [Unimod] +Xlink:DMP (N-term) [Unimod] +Xlink:DMP (K) [Unimod] +NDA (N-term) [Unimod] +NDA (K) [Unimod] +SPITC:13C(6) (N-term) [Unimod] +SPITC:13C(6) (K) [Unimod] +TMAB:2H(9) (N-term) [Unimod] +TMAB:2H(9) (K) [Unimod] +TMAB (N-term) [Unimod] +TMAB (K) [Unimod] +FTC (S) [Unimod] +FTC (R) [Unimod] +FTC (P) [Unimod] +FTC (K) [Unimod] +FTC (C) [Unimod] +AEC-MAEC (T) [Unimod] +AEC-MAEC (S) [Unimod] +BADGE (C) [Unimod] +Label:2H(4) (K) [Unimod] +CyDye-Cy5 (C) [Unimod] +DHP (C) [Unimod] +BHTOH (H) [Unimod] +BHTOH (C) [Unimod] +BHTOH (K) [Unimod] +Nmethylmaleimide+water (C) [Unimod] +PyMIC (N-term) [Unimod] +LG-lactam-K (N-term) [Unimod] +LG-lactam-K (K) [Unimod] +BisANS (K) [Unimod] +Piperidine (N-term) [Unimod] +Piperidine (K) [Unimod] +Diethyl (N-term) [Unimod] +Diethyl (K) [Unimod] +LG-Hlactam-K (N-term) [Unimod] +LG-Hlactam-K (K) [Unimod] +Dimethyl:2H(4)13C(2) (N-term) [Unimod] +Dimethyl:2H(4)13C(2) (K) [Unimod] +C8-QAT (N-term) [Unimod] +C8-QAT (K) [Unimod] +LG-lactam-R (R) [Unimod] +CLIP_TRAQ_1 (N-term) [Unimod] +CLIP_TRAQ_1 (K) [Unimod] +CLIP_TRAQ_1 (Y) [Unimod] +CLIP_TRAQ_2 (N-term) [Unimod] +CLIP_TRAQ_2 (K) [Unimod] +CLIP_TRAQ_2 (Y) [Unimod] +LG-Hlactam-R (R) [Unimod] +Maleimide-PEO2-Biotin (C) [Unimod] +Sulfo-NHS-LC-LC-Biotin (N-term) [Unimod] +Sulfo-NHS-LC-LC-Biotin (K) [Unimod] +FNEM (C) [Unimod] +PropylNAGthiazoline (C) [Unimod] +Dethiomethyl (M) [Unimod] +iTRAQ4plex114 (Y) [Unimod] +iTRAQ4plex114 (N-term) [Unimod] +iTRAQ4plex114 (K) [Unimod] +iTRAQ4plex115 (Y) [Unimod] +iTRAQ4plex115 (N-term) [Unimod] +iTRAQ4plex115 (K) [Unimod] +LeuArgGlyGly (K) [Unimod] +CLIP_TRAQ_3 (Y) [Unimod] +CLIP_TRAQ_3 (N-term) [Unimod] +CLIP_TRAQ_3 (K) [Unimod] +CLIP_TRAQ_4 (N-term) [Unimod] +CLIP_TRAQ_4 (K) [Unimod] +CLIP_TRAQ_4 (Y) [Unimod] +15dB-biotin (C) [Unimod] +PGA1-biotin (C) [Unimod] +Ala->Ser (A) [Unimod] +Ala->Thr (A) [Unimod] +Ala->Asp (A) [Unimod] +Ala->Pro (A) [Unimod] +Ala->Gly (A) [Unimod] +Ala->Glu (A) [Unimod] +Ala->Val (A) [Unimod] +Cys->Phe (C) [Unimod] +Cys->Ser (C) [Unimod] +Cys->Trp (C) [Unimod] +Cys->Tyr (C) [Unimod] +Cys->Arg (C) [Unimod] +Cys->Gly (C) [Unimod] +Asp->Ala (D) [Unimod] +Asp->His (D) [Unimod] +Asp->Asn (D) [Unimod] +Asp->Gly (D) [Unimod] +Asp->Tyr (D) [Unimod] +Asp->Glu (D) [Unimod] +Asp->Val (D) [Unimod] +Glu->Ala (E) [Unimod] +Glu->Gln (E) [Unimod] +Glu->Asp (E) [Unimod] +Glu->Lys (E) [Unimod] +Glu->Gly (E) [Unimod] +Glu->Val (E) [Unimod] +Phe->Ser (F) [Unimod] +Phe->Cys (F) [Unimod] +Phe->Ile (F) [Unimod] +Phe->Tyr (F) [Unimod] +Phe->Val (F) [Unimod] +Gly->Ala (G) [Unimod] +Gly->Ser (G) [Unimod] +Gly->Trp (G) [Unimod] +Gly->Glu (G) [Unimod] +Gly->Val (G) [Unimod] +Gly->Asp (G) [Unimod] +Gly->Cys (G) [Unimod] +Gly->Arg (G) [Unimod] +dNIC (N-term) [Unimod] +His->Pro (H) [Unimod] +His->Tyr (H) [Unimod] +His->Gln (H) [Unimod] +NIC (N-term) [Unimod] +His->Arg (H) [Unimod] +His->Leu (H) [Unimod] +Ile->Phe (I) [Unimod] +Ile->Ser (I) [Unimod] +Ile->Thr (I) [Unimod] +Ile->Asn (I) [Unimod] +Ile->Lys (I) [Unimod] +Ile->Val (I) [Unimod] +Ile->Met (I) [Unimod] +Ile->Arg (I) [Unimod] +Lys->Thr (K) [Unimod] +Lys->Asn (K) [Unimod] +Lys->Glu (K) [Unimod] +Lys->Gln (K) [Unimod] +Lys->Met (K) [Unimod] +Lys->Arg (K) [Unimod] +Lys->Ile (K) [Unimod] +Leu->Ser (L) [Unimod] +Leu->Phe (L) [Unimod] +Leu->Trp (L) [Unimod] +Leu->Pro (L) [Unimod] +Leu->Val (L) [Unimod] +Leu->His (L) [Unimod] +Leu->Gln (L) [Unimod] +Leu->Met (L) [Unimod] +Leu->Arg (L) [Unimod] +Met->Thr (M) [Unimod] +Met->Arg (M) [Unimod] +Met->Ile (M) [Unimod] +Met->Lys (M) [Unimod] +Met->Leu (M) [Unimod] +Met->Val (M) [Unimod] +Asn->Ser (N) [Unimod] +Asn->Thr (N) [Unimod] +Asn->Lys (N) [Unimod] +Asn->Tyr (N) [Unimod] +Asn->His (N) [Unimod] +Asn->Asp (N) [Unimod] +Asn->Ile (N) [Unimod] +Pro->Ser (P) [Unimod] +Pro->Ala (P) [Unimod] +Pro->His (P) [Unimod] +Pro->Gln (P) [Unimod] +Pro->Thr (P) [Unimod] +Pro->Arg (P) [Unimod] +Pro->Leu (P) [Unimod] +Gln->Pro (Q) [Unimod] +Gln->Lys (Q) [Unimod] +Gln->Glu (Q) [Unimod] +Gln->His (Q) [Unimod] +Gln->Arg (Q) [Unimod] +Gln->Leu (Q) [Unimod] +Arg->Ser (R) [Unimod] +Arg->Trp (R) [Unimod] +Arg->Thr (R) [Unimod] +Arg->Pro (R) [Unimod] +Arg->Lys (R) [Unimod] +Arg->His (R) [Unimod] +Arg->Gln (R) [Unimod] +Arg->Met (R) [Unimod] +Arg->Cys (R) [Unimod] +Arg->Ile (R) [Unimod] +Arg->Gly (R) [Unimod] +Ser->Phe (S) [Unimod] +Ser->Ala (S) [Unimod] +Ser->Trp (S) [Unimod] +Ser->Thr (S) [Unimod] +Ser->Asn (S) [Unimod] +Ser->Pro (S) [Unimod] +Ser->Tyr (S) [Unimod] +Ser->Cys (S) [Unimod] +Ser->Arg (S) [Unimod] +Ser->Ile (S) [Unimod] +Ser->Gly (S) [Unimod] +Thr->Ser (T) [Unimod] +Thr->Ala (T) [Unimod] +Thr->Asn (T) [Unimod] +Thr->Lys (T) [Unimod] +Thr->Pro (T) [Unimod] +Thr->Met (T) [Unimod] +Thr->Ile (T) [Unimod] +Thr->Arg (T) [Unimod] +Val->Phe (V) [Unimod] +Val->Ala (V) [Unimod] +Val->Glu (V) [Unimod] +Val->Met (V) [Unimod] +Val->Asp (V) [Unimod] +Val->Ile (V) [Unimod] +Val->Gly (V) [Unimod] +Trp->Ser (W) [Unimod] +Trp->Cys (W) [Unimod] +Trp->Arg (W) [Unimod] +Trp->Gly (W) [Unimod] +Trp->Leu (W) [Unimod] +Tyr->Phe (Y) [Unimod] +Tyr->Ser (Y) [Unimod] +Tyr->Asn (Y) [Unimod] +Tyr->His (Y) [Unimod] +Tyr->Asp (Y) [Unimod] +Tyr->Cys (Y) [Unimod] +NA-LNO2 (C) [Unimod] +NA-LNO2 (H) [Unimod] +NA-OA-NO2 (C) [Unimod] +NA-OA-NO2 (H) [Unimod] +ICPL:2H(4) (N-term) [Unimod] +ICPL:2H(4) (N-term) [Unimod] +ICPL:2H(4) (K) [Unimod] +iTRAQ8plex (Y) [Unimod] +iTRAQ8plex (N-term) [Unimod] +iTRAQ8plex (K) [Unimod] +Label:13C(6)15N(1) (I) [Unimod] +Label:13C(6)15N(1) (L) [Unimod] +Label:2H(9)13C(6)15N(2) (K) [Unimod] +HNE-Delta:H(2)O (K) [Unimod] +HNE-Delta:H(2)O (H) [Unimod] +HNE-Delta:H(2)O (C) [Unimod] +4-ONE (K) [Unimod] +4-ONE (H) [Unimod] +4-ONE (C) [Unimod] +O-Dimethylphosphate (Y) [Unimod] +O-Dimethylphosphate (T) [Unimod] +O-Dimethylphosphate (S) [Unimod] +O-Methylphosphate (Y) [Unimod] +O-Methylphosphate (T) [Unimod] +O-Methylphosphate (S) [Unimod] +O-Diethylphosphate (Y) [Unimod] +O-Diethylphosphate (T) [Unimod] +O-Diethylphosphate (S) [Unimod] +O-Ethylphosphate (Y) [Unimod] +O-Ethylphosphate (T) [Unimod] +O-Ethylphosphate (S) [Unimod] +O-pinacolylmethylphosphonate (Y) [Unimod] +O-pinacolylmethylphosphonate (T) [Unimod] +O-pinacolylmethylphosphonate (S) [Unimod] +Methylphosphonate (Y) [Unimod] +Methylphosphonate (T) [Unimod] +Methylphosphonate (S) [Unimod] +O-Isopropylmethylphosphonate (Y) [Unimod] +O-Isopropylmethylphosphonate (T) [Unimod] +O-Isopropylmethylphosphonate (S) [Unimod] +iTRAQ8plex:13C(6)15N(2) (Y) [Unimod] +iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod] +iTRAQ8plex:13C(6)15N(2) (K) [Unimod] +DTT_ST (S) [Unimod] +DTT_ST (T) [Unimod] +Ethanolamine (D) [Unimod] +Ethanolamine (C-term) [Unimod] +Ethanolamine (E) [Unimod] +TMT6plex (K) [Unimod] +TMT6plex (N-term) [Unimod] +DTT_C (C) [Unimod] +TMT2plex (N-term) [Unimod] +TMT2plex (K) [Unimod] +TMT (N-term) [Unimod] +TMT (K) [Unimod] +ExacTagThiol (C) [Unimod] +ExacTagAmine (K) [Unimod] +NO_SMX_SEMD (C) [Unimod] +4-ONE+Delta:H(-2)O(-1) (K) [Unimod] +4-ONE+Delta:H(-2)O(-1) (H) [Unimod] +4-ONE+Delta:H(-2)O(-1) (C) [Unimod] +NO_SMX_SMCT (C) [Unimod] +NO_SMX_SIMD (C) [Unimod] +Malonyl (C) [Unimod] +Malonyl (S) [Unimod] +3sulfo (N-term) [Unimod] +trifluoro (L) [Unimod] +TNBS (N-term) [Unimod] +TNBS (K) [Unimod] +Biotin-phenacyl (C) [Unimod] +Biotin-phenacyl (H) [Unimod] +Biotin-phenacyl (S) [Unimod] +DTT_C:2H(6) (C) [Unimod] +lapachenole (C) [Unimod] +Label:13C(5) (P) [Unimod] +maleimide (K) [Unimod] +maleimide (C) [Unimod] +DTT_ST:2H(6) (T) [Unimod] +DTT_ST:2H(6) (S) [Unimod] +Met-loss (M) [Unimod] +Met-loss+Acetyl (M) [Unimod] +Menadione-HQ (K) [Unimod] +Menadione-HQ (C) [Unimod] +Carboxymethyl:13C(2) (C) [Unimod] +NEM:2H(5) (C) [Unimod] +Gly-loss+Amide (G) [Unimod] +TMPP-Ac (N-term) [Unimod] +Label:13C(6)+GlyGly (K) [Unimod] +Arg->Npo (R) [Unimod] +Label:2H(4)+Acetyl (K) [Unimod] +Pentylamine (Q) [Unimod] +PentylamineBiotin (Q) [Unimod] +Dihydroxyimidazolidine (R) [Unimod] +DFDNB (Q) [Unimod] +DFDNB (N) [Unimod] +DFDNB (R) [Unimod] +DFDNB (K) [Unimod] +Cy3b-maleimide (C) [Unimod] +AEC-MAEC:2H(4) (S) [Unimod] +AEC-MAEC:2H(4) (T) [Unimod] +BMOE (C) [Unimod] +Biotin-PEO4-hydrazide (C-term) [Unimod] +Label:13C(6)+Acetyl (K) [Unimod] +Label:13C(6)15N(2)+Acetyl (K) [Unimod] +EQIGG (K) [Unimod] +cGMP (C) [Unimod] +cGMP+RMP-loss (C) [Unimod] +Arg2PG (R) [Unimod] +Label:2H(4)+GlyGly (K) [Unimod] +Label:13C(8)15N(2) (R) [Unimod] +Label:13C(1)2H(3) (M) [Unimod] +ZGB (K) [Unimod] +ZGB (N-term) [Unimod] +MG-H1 (R) [Unimod] +G-H1 (R) [Unimod] +Label:13C(6)15N(2)+GlyGly (K) [Unimod] +ICPL:13C(6)2H(4) (N-term) [Unimod] +ICPL:13C(6)2H(4) (K) [Unimod] +ICPL:13C(6)2H(4) (N-term) [Unimod] +QQQTGG (K) [Unimod] +QEQTGG (K) [Unimod] +Bodipy (C) [Unimod] diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,396 @@ +Oxidation (M) +Acetyl (Protein N-term) +Acetyl (K) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->CamCys +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Ala->Xle +Arg->Ala +Arg->Asn +Arg->Asp +Arg->CamCys +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->CamCys +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->CamCys +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Carbamidomethyl (C) +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Deamidation (N) +Deamidation (NQ) +Deamidation 18O (N) +Dimethyl (KR) +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->CamCys +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->pyro-Glu +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->CamCys +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->pyro-Glu +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->CamCys +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +GlyGly (K) +His->Ala +His->Arg +His->Asn +His->Asp +His->CamCys +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->CamCys +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->CamCys +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Methyl (KR) +OHexNAc +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->CamCys +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Phospho (STY) +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->CamCys +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Pro5 +Pro6 +QQTGG (K) +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->CamCys +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->CamCys +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trimethyl (K) +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->CamCys +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->CamCys +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->CamCys +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->CamCys +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample.default --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample.default Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,396 @@ +Oxidation (M) +Acetyl (Protein N-term) +Acetyl (K) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->CamCys +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Ala->Xle +Arg->Ala +Arg->Asn +Arg->Asp +Arg->CamCys +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->CamCys +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->CamCys +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Carbamidomethyl (C) +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Deamidation (N) +Deamidation (NQ) +Deamidation 18O (N) +Dimethyl (KR) +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->CamCys +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->pyro-Glu +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->CamCys +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->pyro-Glu +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->CamCys +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +GlyGly (K) +His->Ala +His->Arg +His->Asn +His->Asp +His->CamCys +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->CamCys +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->CamCys +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Methyl (KR) +OHexNAc +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->CamCys +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Phospho (STY) +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->CamCys +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Pro5 +Pro6 +QQTGG (K) +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->CamCys +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->CamCys +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trimethyl (K) +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->CamCys +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->CamCys +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->CamCys +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->CamCys +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample.extended --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample.extended Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,1308 @@ +Acetyl (K) +Acetyl (Protein N-term) +Carbamidomethyl (C) +Oxidation (M) +Phospho (STY) +Arg6 +Arg10 +Lys4 +Lys6 +Lys8 +GlyGly (K) +Methyl (KR) +Dimethyl (KR) +Trimethyl (K) +Pro5 +Pro6 +Glu->pyro-Glu +Gln->pyro-Glu +OHexNAc +DimethLys0 +DimethNter0 +DimethLys4 +DimethNter4 +DimethLys8 +DimethNter8 +18O +ICAT-0 +ICAT-9 +ICPL-Lys0 +ICPL-Nter0 +ICPL-Lys4 +ICPL-Nter4 +ICPL-Lys6 +ICPL-Nter6 +ICPL-Lys10 +ICPL-Nter10 +mTRAQ-Lys0 +mTRAQ-Nter0 +mTRAQ-Lys4 +mTRAQ-Nter4 +mTRAQ-Lys8 +mTRAQ-Nter8 +DimethLys2 +DimethNter2 +DimethLys6 +DimethNter6 +QQTGG (K) +Deamidation (N) +Deamidation 18O (N) +iTRAQ4plex-Nter114 +iTRAQ4plex-Nter115 +iTRAQ4plex-Nter116 +iTRAQ4plex-Nter117 +iTRAQ4plex-Lys114 +iTRAQ4plex-Lys115 +iTRAQ4plex-Lys116 +iTRAQ4plex-Lys117 +iTRAQ8plex-Nter113 +iTRAQ8plex-Nter114 +iTRAQ8plex-Nter115 +iTRAQ8plex-Nter116 +iTRAQ8plex-Nter117 +iTRAQ8plex-Nter118 +iTRAQ8plex-Nter119 +iTRAQ8plex-Nter121 +iTRAQ8plex-Lys113 +iTRAQ8plex-Lys114 +iTRAQ8plex-Lys115 +iTRAQ8plex-Lys116 +iTRAQ8plex-Lys117 +iTRAQ8plex-Lys118 +iTRAQ8plex-Lys119 +iTRAQ8plex-Lys121 +TMT2plex-Nter126 +TMT2plex-Nter127 +TMT2plex-Lys126 +TMT2plex-Lys127 +TMT6plex-Nter126 +TMT6plex-Nter127 +TMT6plex-Nter128 +TMT6plex-Nter129 +TMT6plex-Nter130 +TMT6plex-Nter131 +TMT6plex-Lys126 +TMT6plex-Lys127 +TMT6plex-Lys128 +TMT6plex-Lys129 +TMT6plex-Lys130 +TMT6plex-Lys131 +Deamidation (NQ) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Xle +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Arg->Ala +Arg->Asn +Arg->Asp +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +His->Ala +His->Arg +His->Asn +His->Asp +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Ala->CamCys +Arg->CamCys +Asn->CamCys +Asp->CamCys +Gln->CamCys +Glu->CamCys +Gly->CamCys +His->CamCys +Lys->CamCys +Met->CamCys +Phe->CamCys +Pro->CamCys +Ser->CamCys +Thr->CamCys +Trp->CamCys +Tyr->CamCys +Val->CamCys +Xle->CamCys +Leu7 +Ile7 +Acetyl (T) [Unimod] +Acetyl (N-term) [Unimod] +Acetyl (S) [Unimod] +Acetyl (C) [Unimod] +Acetyl (N-term) [Unimod] +Acetyl (K) [Unimod] +Acetyl (Y) [Unimod] +Acetyl (H) [Unimod] +Amidated (C-term) [Unimod] +Amidated (C-term) [Unimod] +Biotin (N-term) [Unimod] +Biotin (K) [Unimod] +Carbamidomethyl (D) [Unimod] +Carbamidomethyl (H) [Unimod] +Carbamidomethyl (N-term) [Unimod] +Carbamidomethyl (K) [Unimod] +Carbamidomethyl (C) [Unimod] +Carbamidomethyl (E) [Unimod] +Carbamyl (C) [Unimod] +Carbamyl (R) [Unimod] +Carbamyl (N-term) [Unimod] +Carbamyl (K) [Unimod] +Carbamyl (M) [Unimod] +Carboxymethyl (N-term) [Unimod] +Carboxymethyl (K) [Unimod] +Carboxymethyl (C) [Unimod] +Carboxymethyl (W) [Unimod] +Deamidated (R) [Unimod] +Deamidated (N) [Unimod] +Deamidated (Q) [Unimod] +Deamidated (F) [Unimod] +ICAT-G (C) [Unimod] +ICAT-G:2H(8) (C) [Unimod] +Met->Hse (M) [Unimod] +Met->Hsl (M) [Unimod] +ICAT-D:2H(8) (C) [Unimod] +ICAT-D (C) [Unimod] +NIPCAM (C) [Unimod] +PEO-Iodoacetyl-LC-Biotin (C) [Unimod] +Phospho (R) [Unimod] +Phospho (C) [Unimod] +Phospho (D) [Unimod] +Phospho (Y) [Unimod] +Phospho (H) [Unimod] +Phospho (T) [Unimod] +Phospho (S) [Unimod] +Dehydrated (D) [Unimod] +Dehydrated (Y) [Unimod] +Dehydrated (T) [Unimod] +Dehydrated (S) [Unimod] +Dehydrated (N) [Unimod] +Dehydrated (Q) [Unimod] +Dehydrated (C) [Unimod] +Propionamide (C) [Unimod] +Pyridylacetyl (N-term) [Unimod] +Pyridylacetyl (K) [Unimod] +Pyro-carbamidomethyl (C) [Unimod] +Glu->pyro-Glu (E) [Unimod] +Gln->pyro-Glu (Q) [Unimod] +SMA (N-term) [Unimod] +SMA (K) [Unimod] +Pyridylethyl (C) [Unimod] +Methyl (T) [Unimod] +Methyl (S) [Unimod] +Methyl (N-term) [Unimod] +Methyl (E) [Unimod] +Methyl (D) [Unimod] +Methyl (C-term) [Unimod] +Methyl (L) [Unimod] +Methyl (I) [Unimod] +Methyl (R) [Unimod] +Methyl (N-term) [Unimod] +Methyl (Q) [Unimod] +Methyl (N) [Unimod] +Methyl (K) [Unimod] +Methyl (H) [Unimod] +Methyl (C) [Unimod] +Oxidation (W) [Unimod] +Oxidation (H) [Unimod] +Oxidation (C) [Unimod] +Oxidation (M) [Unimod] +Oxidation (R) [Unimod] +Oxidation (Y) [Unimod] +Oxidation (F) [Unimod] +Oxidation (P) [Unimod] +Oxidation (N) [Unimod] +Oxidation (K) [Unimod] +Oxidation (D) [Unimod] +Oxidation (G) [Unimod] +Dimethyl (N) [Unimod] +Dimethyl (N-term) [Unimod] +Dimethyl (R) [Unimod] +Dimethyl (K) [Unimod] +Dimethyl (P) [Unimod] +Trimethyl (A) [Unimod] +Trimethyl (R) [Unimod] +Trimethyl (K) [Unimod] +Methylthio (C) [Unimod] +Methylthio (N) [Unimod] +Methylthio (D) [Unimod] +Sulfo (Y) [Unimod] +Sulfo (T) [Unimod] +Sulfo (S) [Unimod] +Sulfo (C) [Unimod] +Lipoyl (K) [Unimod] +Farnesyl (C) [Unimod] +Myristoyl (C) [Unimod] +Myristoyl (K) [Unimod] +Myristoyl (G) [Unimod] +PyridoxalPhosphate (K) [Unimod] +Palmitoyl (T) [Unimod] +Palmitoyl (S) [Unimod] +Palmitoyl (K) [Unimod] +Palmitoyl (C) [Unimod] +Palmitoyl (N-term) [Unimod] +GeranylGeranyl (C) [Unimod] +Phosphopantetheine (S) [Unimod] +FAD (Y) [Unimod] +FAD (H) [Unimod] +FAD (C) [Unimod] +Tripalmitate (C) [Unimod] +Guanidinyl (K) [Unimod] +HNE (K) [Unimod] +HNE (H) [Unimod] +HNE (C) [Unimod] +Glucuronyl (N-term) [Unimod] +Glucuronyl (S) [Unimod] +Glutathione (C) [Unimod] +Acetyl:2H(3) (N-term) [Unimod] +Acetyl:2H(3) (K) [Unimod] +Propionyl (N-term) [Unimod] +Propionyl (K) [Unimod] +Propionyl:13C(3) (N-term) [Unimod] +Propionyl:13C(3) (K) [Unimod] +GIST-Quat (N-term) [Unimod] +GIST-Quat (K) [Unimod] +GIST-Quat:2H(3) (N-term) [Unimod] +GIST-Quat:2H(3) (K) [Unimod] +GIST-Quat:2H(6) (N-term) [Unimod] +GIST-Quat:2H(6) (K) [Unimod] +GIST-Quat:2H(9) (N-term) [Unimod] +GIST-Quat:2H(9) (K) [Unimod] +Succinyl (N-term) [Unimod] +Succinyl (N-term) [Unimod] +Succinyl (K) [Unimod] +Succinyl:2H(4) (N-term) [Unimod] +Succinyl:2H(4) (K) [Unimod] +Succinyl:13C(4) (N-term) [Unimod] +Succinyl:13C(4) (K) [Unimod] +probiotinhydrazide (P) [Unimod] +Pro->pyro-Glu (P) [Unimod] +His->Asn (H) [Unimod] +His->Asp (H) [Unimod] +Trp->Hydroxykynurenin (W) [Unimod] +Delta:H(4)C(3) (K) [Unimod] +Delta:H(4)C(3) (H) [Unimod] +Delta:H(4)C(2) (K) [Unimod] +Delta:H(4)C(2) (H) [Unimod] +Cys->Dha (C) [Unimod] +Arg->GluSA (R) [Unimod] +Trioxidation (C) [Unimod] +Iminobiotin (N-term) [Unimod] +Iminobiotin (K) [Unimod] +ESP (N-term) [Unimod] +ESP (K) [Unimod] +ESP:2H(10) (N-term) [Unimod] +ESP:2H(10) (K) [Unimod] +NHS-LC-Biotin (N-term) [Unimod] +NHS-LC-Biotin (K) [Unimod] +EDT-maleimide-PEO-biotin (T) [Unimod] +EDT-maleimide-PEO-biotin (S) [Unimod] +IMID (K) [Unimod] +IMID:2H(4) (K) [Unimod] +Lysbiotinhydrazide (K) [Unimod] +Propionamide:2H(3) (C) [Unimod] +Nitro (Y) [Unimod] +Nitro (W) [Unimod] +ICAT-C (C) [Unimod] +Delta:H(2)C(2) (K) [Unimod] +Delta:H(2)C(2) (H) [Unimod] +Trp->Kynurenin (W) [Unimod] +Lys->Allysine (K) [Unimod] +ICAT-C:13C(9) (C) [Unimod] +FormylMet (N-term) [Unimod] +Nethylmaleimide (C) [Unimod] +OxLysBiotinRed (K) [Unimod] +IBTP (C) [Unimod] +OxLysBiotin (K) [Unimod] +OxProBiotinRed (P) [Unimod] +OxProBiotin (P) [Unimod] +OxArgBiotin (R) [Unimod] +OxArgBiotinRed (R) [Unimod] +EDT-iodoacetyl-PEO-biotin (T) [Unimod] +EDT-iodoacetyl-PEO-biotin (S) [Unimod] +GlyGly (T) [Unimod] +GlyGly (S) [Unimod] +GlyGly (C) [Unimod] +GlyGly (K) [Unimod] +Formyl (N-term) [Unimod] +Formyl (T) [Unimod] +Formyl (K) [Unimod] +Formyl (N-term) [Unimod] +Formyl (S) [Unimod] +Cation:K (C-term) [Unimod] +Cation:K (E) [Unimod] +Cation:K (D) [Unimod] +Thioacyl (N-term) [Unimod] +Thioacyl (K) [Unimod] +Fluoro (W) [Unimod] +Fluoro (F) [Unimod] +Fluoro (Y) [Unimod] +Fluorescein (C) [Unimod] +Iodo (H) [Unimod] +Iodo (Y) [Unimod] +Diiodo (Y) [Unimod] +Triiodo (Y) [Unimod] +Myristoleyl (G) [Unimod] +Pro->Pyrrolidinone (P) [Unimod] +Myristoyl+Delta:H(-4) (G) [Unimod] +Benzoyl (N-term) [Unimod] +Benzoyl (K) [Unimod] +Dansyl (N-term) [Unimod] +Dansyl (K) [Unimod] +a-type-ion (C-term) [Unimod] +Amidine (N-term) [Unimod] +Amidine (K) [Unimod] +NBS:13C(6) (W) [Unimod] +Methyl:2H(3)13C(1) (R) [Unimod] +Dimethyl:2H(6)13C(2) (R) [Unimod] +NBS (W) [Unimod] +Delta:H(1)O(-1)18O(1) (N) [Unimod] +QAT (C) [Unimod] +BHT (H) [Unimod] +BHT (K) [Unimod] +BHT (C) [Unimod] +Delta:H(4)C(2)O(-1)S(1) (S) [Unimod] +DAET (T) [Unimod] +DAET (S) [Unimod] +Pro->Pyrrolidone (P) [Unimod] +Label:13C(9) (Y) [Unimod] +Label:13C(9) (F) [Unimod] +Label:13C(9)+Phospho (Y) [Unimod] +Label:13C(6) (I) [Unimod] +Label:13C(6) (L) [Unimod] +Label:13C(6) (K) [Unimod] +Label:13C(6) (R) [Unimod] +HPG (R) [Unimod] +2HPG (R) [Unimod] +QAT:2H(3) (C) [Unimod] +Label:18O(2) (C-term) [Unimod] +AccQTag (N-term) [Unimod] +AccQTag (K) [Unimod] +Dimethyl:2H(4) (N-term) [Unimod] +Dimethyl:2H(4) (N-term) [Unimod] +Dimethyl:2H(4) (K) [Unimod] +EQAT (C) [Unimod] +EQAT:2H(5) (C) [Unimod] +Ethanedithiol (T) [Unimod] +Ethanedithiol (S) [Unimod] +NEIAA:2H(5) (Y) [Unimod] +NEIAA:2H(5) (C) [Unimod] +Delta:H(6)C(6)O(1) (K) [Unimod] +Delta:H(4)C(3)O(1) (K) [Unimod] +Delta:H(4)C(3)O(1) (H) [Unimod] +Delta:H(4)C(3)O(1) (C) [Unimod] +Delta:H(2)C(3) (K) [Unimod] +Delta:H(4)C(6) (K) [Unimod] +Delta:H(8)C(6)O(2) (K) [Unimod] +ADP-Ribosyl (E) [Unimod] +ADP-Ribosyl (S) [Unimod] +ADP-Ribosyl (N) [Unimod] +ADP-Ribosyl (C) [Unimod] +ADP-Ribosyl (R) [Unimod] +NEIAA (Y) [Unimod] +NEIAA (C) [Unimod] +iTRAQ4plex (Y) [Unimod] +iTRAQ4plex (N-term) [Unimod] +iTRAQ4plex (K) [Unimod] +Crotonaldehyde (K) [Unimod] +Crotonaldehyde (H) [Unimod] +Crotonaldehyde (C) [Unimod] +Amino (Y) [Unimod] +Argbiotinhydrazide (R) [Unimod] +Label:18O(1) (Y) [Unimod] +Label:18O(1) (T) [Unimod] +Label:18O(1) (S) [Unimod] +Label:18O(1) (C-term) [Unimod] +Label:13C(6)15N(2) (K) [Unimod] +Thiophospho (Y) [Unimod] +Thiophospho (T) [Unimod] +Thiophospho (S) [Unimod] +SPITC (K) [Unimod] +SPITC (N-term) [Unimod] +Cytopiloyne (Y) [Unimod] +Cytopiloyne (S) [Unimod] +Cytopiloyne (R) [Unimod] +Cytopiloyne (P) [Unimod] +Cytopiloyne (N-term) [Unimod] +Cytopiloyne (K) [Unimod] +Cytopiloyne (C) [Unimod] +Cytopiloyne+water (Y) [Unimod] +Cytopiloyne+water (T) [Unimod] +Cytopiloyne+water (S) [Unimod] +Cytopiloyne+water (R) [Unimod] +Cytopiloyne+water (N-term) [Unimod] +Cytopiloyne+water (K) [Unimod] +Cytopiloyne+water (C) [Unimod] +Label:13C(6)15N(4) (R) [Unimod] +Label:13C(9)15N(1) (F) [Unimod] +Label:2H(3) (L) [Unimod] +Label:13C(5)15N(1) (V) [Unimod] +PET (T) [Unimod] +PET (S) [Unimod] +CAF (N-term) [Unimod] +Xlink:SSD (K) [Unimod] +Nitrosyl (C) [Unimod] +AEBS (Y) [Unimod] +AEBS (S) [Unimod] +AEBS (N-term) [Unimod] +AEBS (K) [Unimod] +AEBS (H) [Unimod] +Ethanolyl (C) [Unimod] +HMVK (C) [Unimod] +Ethyl (N-term) [Unimod] +Ethyl (K) [Unimod] +Ethyl (E) [Unimod] +Ethyl (N-term) [Unimod] +CoenzymeA (C) [Unimod] +Methyl+Deamidated (Q) [Unimod] +Methyl+Deamidated (N) [Unimod] +Delta:H(5)C(2) (P) [Unimod] +Methyl:2H(2) (K) [Unimod] +SulfanilicAcid (E) [Unimod] +SulfanilicAcid (D) [Unimod] +SulfanilicAcid (C-term) [Unimod] +SulfanilicAcid:13C(6) (E) [Unimod] +SulfanilicAcid:13C(6) (D) [Unimod] +SulfanilicAcid:13C(6) (C-term) [Unimod] +Biotin-PEO-Amine (D) [Unimod] +Biotin-PEO-Amine (C-term) [Unimod] +Biotin-PEO-Amine (E) [Unimod] +Trp->Oxolactone (W) [Unimod] +Biotin-HPDP (C) [Unimod] +IodoU-AMP (Y) [Unimod] +IodoU-AMP (W) [Unimod] +IodoU-AMP (F) [Unimod] +CAMthiopropanoyl (N-term) [Unimod] +CAMthiopropanoyl (K) [Unimod] +IED-Biotin (C) [Unimod] +Methyl:2H(3) (E) [Unimod] +Methyl:2H(3) (D) [Unimod] +Methyl:2H(3) (C-term) [Unimod] +Carboxy (E) [Unimod] +Carboxy (D) [Unimod] +Carboxy (K) [Unimod] +Carboxy (W) [Unimod] +Carboxy (M) [Unimod] +Bromobimane (C) [Unimod] +Menadione (K) [Unimod] +Menadione (C) [Unimod] +DeStreak (C) [Unimod] +Cysteinyl (C) [Unimod] +Lys-loss (K) [Unimod] +Nmethylmaleimide (K) [Unimod] +Nmethylmaleimide (C) [Unimod] +CyDye-Cy3 (C) [Unimod] +DimethylpyrroleAdduct (K) [Unimod] +Delta:H(2)C(5) (K) [Unimod] +Delta:H(2)C(3)O(1) (K) [Unimod] +Delta:H(2)C(3)O(1) (R) [Unimod] +Nethylmaleimide+water (K) [Unimod] +Nethylmaleimide+water (C) [Unimod] +Methyl+Acetyl:2H(3) (K) [Unimod] +Xlink:B10621 (C) [Unimod] +DTBP (N-term) [Unimod] +DTBP (K) [Unimod] +DTBP (R) [Unimod] +DTBP (Q) [Unimod] +DTBP (N) [Unimod] +FP-Biotin (T) [Unimod] +FP-Biotin (Y) [Unimod] +FP-Biotin (S) [Unimod] +Thiophos-S-S-biotin (Y) [Unimod] +Thiophos-S-S-biotin (T) [Unimod] +Thiophos-S-S-biotin (S) [Unimod] +Can-FP-biotin (T) [Unimod] +Can-FP-biotin (Y) [Unimod] +Can-FP-biotin (S) [Unimod] +HNE+Delta:H(2) (K) [Unimod] +HNE+Delta:H(2) (H) [Unimod] +HNE+Delta:H(2) (C) [Unimod] +Thrbiotinhydrazide (T) [Unimod] +Methylamine (T) [Unimod] +Methylamine (S) [Unimod] +Diisopropylphosphate (Y) [Unimod] +Diisopropylphosphate (T) [Unimod] +Diisopropylphosphate (S) [Unimod] +Isopropylphospho (Y) [Unimod] +Isopropylphospho (T) [Unimod] +Isopropylphospho (S) [Unimod] +ICPL:13C(6) (N-term) [Unimod] +ICPL:13C(6) (N-term) [Unimod] +ICPL:13C(6) (K) [Unimod] +ICPL (N-term) [Unimod] +ICPL (K) [Unimod] +ICPL (N-term) [Unimod] +Deamidated:18O(1) (Q) [Unimod] +Deamidated:18O(1) (N) [Unimod] +Arg->Orn (R) [Unimod] +Dehydro (C) [Unimod] +Diphthamide (H) [Unimod] +Hydroxyfarnesyl (C) [Unimod] +Diacylglycerol (C) [Unimod] +Carboxyethyl (K) [Unimod] +Hypusine (K) [Unimod] +Retinylidene (K) [Unimod] +Lys->AminoadipicAcid (K) [Unimod] +Cys->PyruvicAcid (C) [Unimod] +Ammonia-loss (C) [Unimod] +Ammonia-loss (S) [Unimod] +Ammonia-loss (T) [Unimod] +Ammonia-loss (N) [Unimod] +Phycocyanobilin (C) [Unimod] +Phycoerythrobilin (C) [Unimod] +Phytochromobilin (C) [Unimod] +Quinone (W) [Unimod] +Quinone (Y) [Unimod] +GPIanchor (C-term) [Unimod] +PhosphoribosyldephosphoCoA (S) [Unimod] +GlycerylPE (E) [Unimod] +Triiodothyronine (Y) [Unimod] +Thyroxine (Y) [Unimod] +Tyr->Dha (Y) [Unimod] +Didehydro (S) [Unimod] +Didehydro (Y) [Unimod] +Didehydro (T) [Unimod] +Didehydro (K) [Unimod] +Cys->Oxoalanine (C) [Unimod] +Ser->LacticAcid (S) [Unimod] +GluGlu (E) [Unimod] +GluGlu (C-term) [Unimod] +Phosphoadenosine (H) [Unimod] +Phosphoadenosine (T) [Unimod] +Phosphoadenosine (K) [Unimod] +Phosphoadenosine (Y) [Unimod] +Glu (E) [Unimod] +Glu (C-term) [Unimod] +Hydroxycinnamyl (C) [Unimod] +Glycosyl (P) [Unimod] +FMNH (H) [Unimod] +FMNH (C) [Unimod] +Archaeol (C) [Unimod] +Phenylisocyanate (N-term) [Unimod] +Phenylisocyanate:2H(5) (N-term) [Unimod] +Phosphoguanosine (H) [Unimod] +Phosphoguanosine (K) [Unimod] +Hydroxymethyl (N) [Unimod] +Dipyrrolylmethanemethyl (C) [Unimod] +PhosphoUridine (H) [Unimod] +PhosphoUridine (Y) [Unimod] +Glycerophospho (S) [Unimod] +Carboxy->Thiocarboxy (G) [Unimod] +Sulfide (C) [Unimod] +PyruvicAcidIminyl (K) [Unimod] +PyruvicAcidIminyl (V) [Unimod] +PyruvicAcidIminyl (C) [Unimod] +Dioxidation (Y) [Unimod] +Dioxidation (W) [Unimod] +Dioxidation (F) [Unimod] +Dioxidation (M) [Unimod] +Dioxidation (R) [Unimod] +Dioxidation (K) [Unimod] +Dioxidation (P) [Unimod] +Dioxidation (C) [Unimod] +Octanoyl (T) [Unimod] +Octanoyl (S) [Unimod] +Palmitoleyl (C) [Unimod] +Cholesterol (C-term) [Unimod] +Didehydroretinylidene (K) [Unimod] +CHDH (D) [Unimod] +Methylpyrroline (K) [Unimod] +MicrocinC7 (C-term) [Unimod] +Cyano (C) [Unimod] +Amidino (C) [Unimod] +FMN (S) [Unimod] +FMN (T) [Unimod] +FMNC (C) [Unimod] +Hydroxytrimethyl (K) [Unimod] +Deoxy (T) [Unimod] +Deoxy (D) [Unimod] +Deoxy (S) [Unimod] +Microcin (C-term) [Unimod] +Decanoyl (T) [Unimod] +Decanoyl (S) [Unimod] +GluGluGlu (C-term) [Unimod] +GluGluGlu (E) [Unimod] +GluGluGluGlu (C-term) [Unimod] +GluGluGluGlu (E) [Unimod] +HexN (W) [Unimod] +HexN (T) [Unimod] +HexN (N) [Unimod] +HexN (K) [Unimod] +Xlink:DMP-s (N-term) [Unimod] +Xlink:DMP-s (K) [Unimod] +Xlink:DMP (N-term) [Unimod] +Xlink:DMP (K) [Unimod] +NDA (N-term) [Unimod] +NDA (K) [Unimod] +SPITC:13C(6) (N-term) [Unimod] +SPITC:13C(6) (K) [Unimod] +TMAB:2H(9) (N-term) [Unimod] +TMAB:2H(9) (K) [Unimod] +TMAB (N-term) [Unimod] +TMAB (K) [Unimod] +FTC (S) [Unimod] +FTC (R) [Unimod] +FTC (P) [Unimod] +FTC (K) [Unimod] +FTC (C) [Unimod] +AEC-MAEC (T) [Unimod] +AEC-MAEC (S) [Unimod] +BADGE (C) [Unimod] +Label:2H(4) (K) [Unimod] +CyDye-Cy5 (C) [Unimod] +DHP (C) [Unimod] +BHTOH (H) [Unimod] +BHTOH (C) [Unimod] +BHTOH (K) [Unimod] +Nmethylmaleimide+water (C) [Unimod] +PyMIC (N-term) [Unimod] +LG-lactam-K (N-term) [Unimod] +LG-lactam-K (K) [Unimod] +BisANS (K) [Unimod] +Piperidine (N-term) [Unimod] +Piperidine (K) [Unimod] +Diethyl (N-term) [Unimod] +Diethyl (K) [Unimod] +LG-Hlactam-K (N-term) [Unimod] +LG-Hlactam-K (K) [Unimod] +Dimethyl:2H(4)13C(2) (N-term) [Unimod] +Dimethyl:2H(4)13C(2) (K) [Unimod] +C8-QAT (N-term) [Unimod] +C8-QAT (K) [Unimod] +LG-lactam-R (R) [Unimod] +CLIP_TRAQ_1 (N-term) [Unimod] +CLIP_TRAQ_1 (K) [Unimod] +CLIP_TRAQ_1 (Y) [Unimod] +CLIP_TRAQ_2 (N-term) [Unimod] +CLIP_TRAQ_2 (K) [Unimod] +CLIP_TRAQ_2 (Y) [Unimod] +LG-Hlactam-R (R) [Unimod] +Maleimide-PEO2-Biotin (C) [Unimod] +Sulfo-NHS-LC-LC-Biotin (N-term) [Unimod] +Sulfo-NHS-LC-LC-Biotin (K) [Unimod] +FNEM (C) [Unimod] +PropylNAGthiazoline (C) [Unimod] +Dethiomethyl (M) [Unimod] +iTRAQ4plex114 (Y) [Unimod] +iTRAQ4plex114 (N-term) [Unimod] +iTRAQ4plex114 (K) [Unimod] +iTRAQ4plex115 (Y) [Unimod] +iTRAQ4plex115 (N-term) [Unimod] +iTRAQ4plex115 (K) [Unimod] +LeuArgGlyGly (K) [Unimod] +CLIP_TRAQ_3 (Y) [Unimod] +CLIP_TRAQ_3 (N-term) [Unimod] +CLIP_TRAQ_3 (K) [Unimod] +CLIP_TRAQ_4 (N-term) [Unimod] +CLIP_TRAQ_4 (K) [Unimod] +CLIP_TRAQ_4 (Y) [Unimod] +15dB-biotin (C) [Unimod] +PGA1-biotin (C) [Unimod] +Ala->Ser (A) [Unimod] +Ala->Thr (A) [Unimod] +Ala->Asp (A) [Unimod] +Ala->Pro (A) [Unimod] +Ala->Gly (A) [Unimod] +Ala->Glu (A) [Unimod] +Ala->Val (A) [Unimod] +Cys->Phe (C) [Unimod] +Cys->Ser (C) [Unimod] +Cys->Trp (C) [Unimod] +Cys->Tyr (C) [Unimod] +Cys->Arg (C) [Unimod] +Cys->Gly (C) [Unimod] +Asp->Ala (D) [Unimod] +Asp->His (D) [Unimod] +Asp->Asn (D) [Unimod] +Asp->Gly (D) [Unimod] +Asp->Tyr (D) [Unimod] +Asp->Glu (D) [Unimod] +Asp->Val (D) [Unimod] +Glu->Ala (E) [Unimod] +Glu->Gln (E) [Unimod] +Glu->Asp (E) [Unimod] +Glu->Lys (E) [Unimod] +Glu->Gly (E) [Unimod] +Glu->Val (E) [Unimod] +Phe->Ser (F) [Unimod] +Phe->Cys (F) [Unimod] +Phe->Ile (F) [Unimod] +Phe->Tyr (F) [Unimod] +Phe->Val (F) [Unimod] +Gly->Ala (G) [Unimod] +Gly->Ser (G) [Unimod] +Gly->Trp (G) [Unimod] +Gly->Glu (G) [Unimod] +Gly->Val (G) [Unimod] +Gly->Asp (G) [Unimod] +Gly->Cys (G) [Unimod] +Gly->Arg (G) [Unimod] +dNIC (N-term) [Unimod] +His->Pro (H) [Unimod] +His->Tyr (H) [Unimod] +His->Gln (H) [Unimod] +NIC (N-term) [Unimod] +His->Arg (H) [Unimod] +His->Leu (H) [Unimod] +Ile->Phe (I) [Unimod] +Ile->Ser (I) [Unimod] +Ile->Thr (I) [Unimod] +Ile->Asn (I) [Unimod] +Ile->Lys (I) [Unimod] +Ile->Val (I) [Unimod] +Ile->Met (I) [Unimod] +Ile->Arg (I) [Unimod] +Lys->Thr (K) [Unimod] +Lys->Asn (K) [Unimod] +Lys->Glu (K) [Unimod] +Lys->Gln (K) [Unimod] +Lys->Met (K) [Unimod] +Lys->Arg (K) [Unimod] +Lys->Ile (K) [Unimod] +Leu->Ser (L) [Unimod] +Leu->Phe (L) [Unimod] +Leu->Trp (L) [Unimod] +Leu->Pro (L) [Unimod] +Leu->Val (L) [Unimod] +Leu->His (L) [Unimod] +Leu->Gln (L) [Unimod] +Leu->Met (L) [Unimod] +Leu->Arg (L) [Unimod] +Met->Thr (M) [Unimod] +Met->Arg (M) [Unimod] +Met->Ile (M) [Unimod] +Met->Lys (M) [Unimod] +Met->Leu (M) [Unimod] +Met->Val (M) [Unimod] +Asn->Ser (N) [Unimod] +Asn->Thr (N) [Unimod] +Asn->Lys (N) [Unimod] +Asn->Tyr (N) [Unimod] +Asn->His (N) [Unimod] +Asn->Asp (N) [Unimod] +Asn->Ile (N) [Unimod] +Pro->Ser (P) [Unimod] +Pro->Ala (P) [Unimod] +Pro->His (P) [Unimod] +Pro->Gln (P) [Unimod] +Pro->Thr (P) [Unimod] +Pro->Arg (P) [Unimod] +Pro->Leu (P) [Unimod] +Gln->Pro (Q) [Unimod] +Gln->Lys (Q) [Unimod] +Gln->Glu (Q) [Unimod] +Gln->His (Q) [Unimod] +Gln->Arg (Q) [Unimod] +Gln->Leu (Q) [Unimod] +Arg->Ser (R) [Unimod] +Arg->Trp (R) [Unimod] +Arg->Thr (R) [Unimod] +Arg->Pro (R) [Unimod] +Arg->Lys (R) [Unimod] +Arg->His (R) [Unimod] +Arg->Gln (R) [Unimod] +Arg->Met (R) [Unimod] +Arg->Cys (R) [Unimod] +Arg->Ile (R) [Unimod] +Arg->Gly (R) [Unimod] +Ser->Phe (S) [Unimod] +Ser->Ala (S) [Unimod] +Ser->Trp (S) [Unimod] +Ser->Thr (S) [Unimod] +Ser->Asn (S) [Unimod] +Ser->Pro (S) [Unimod] +Ser->Tyr (S) [Unimod] +Ser->Cys (S) [Unimod] +Ser->Arg (S) [Unimod] +Ser->Ile (S) [Unimod] +Ser->Gly (S) [Unimod] +Thr->Ser (T) [Unimod] +Thr->Ala (T) [Unimod] +Thr->Asn (T) [Unimod] +Thr->Lys (T) [Unimod] +Thr->Pro (T) [Unimod] +Thr->Met (T) [Unimod] +Thr->Ile (T) [Unimod] +Thr->Arg (T) [Unimod] +Val->Phe (V) [Unimod] +Val->Ala (V) [Unimod] +Val->Glu (V) [Unimod] +Val->Met (V) [Unimod] +Val->Asp (V) [Unimod] +Val->Ile (V) [Unimod] +Val->Gly (V) [Unimod] +Trp->Ser (W) [Unimod] +Trp->Cys (W) [Unimod] +Trp->Arg (W) [Unimod] +Trp->Gly (W) [Unimod] +Trp->Leu (W) [Unimod] +Tyr->Phe (Y) [Unimod] +Tyr->Ser (Y) [Unimod] +Tyr->Asn (Y) [Unimod] +Tyr->His (Y) [Unimod] +Tyr->Asp (Y) [Unimod] +Tyr->Cys (Y) [Unimod] +NA-LNO2 (C) [Unimod] +NA-LNO2 (H) [Unimod] +NA-OA-NO2 (C) [Unimod] +NA-OA-NO2 (H) [Unimod] +ICPL:2H(4) (N-term) [Unimod] +ICPL:2H(4) (N-term) [Unimod] +ICPL:2H(4) (K) [Unimod] +iTRAQ8plex (Y) [Unimod] +iTRAQ8plex (N-term) [Unimod] +iTRAQ8plex (K) [Unimod] +Label:13C(6)15N(1) (I) [Unimod] +Label:13C(6)15N(1) (L) [Unimod] +Label:2H(9)13C(6)15N(2) (K) [Unimod] +HNE-Delta:H(2)O (K) [Unimod] +HNE-Delta:H(2)O (H) [Unimod] +HNE-Delta:H(2)O (C) [Unimod] +4-ONE (K) [Unimod] +4-ONE (H) [Unimod] +4-ONE (C) [Unimod] +O-Dimethylphosphate (Y) [Unimod] +O-Dimethylphosphate (T) [Unimod] +O-Dimethylphosphate (S) [Unimod] +O-Methylphosphate (Y) [Unimod] +O-Methylphosphate (T) [Unimod] +O-Methylphosphate (S) [Unimod] +O-Diethylphosphate (Y) [Unimod] +O-Diethylphosphate (T) [Unimod] +O-Diethylphosphate (S) [Unimod] +O-Ethylphosphate (Y) [Unimod] +O-Ethylphosphate (T) [Unimod] +O-Ethylphosphate (S) [Unimod] +O-pinacolylmethylphosphonate (Y) [Unimod] +O-pinacolylmethylphosphonate (T) [Unimod] +O-pinacolylmethylphosphonate (S) [Unimod] +Methylphosphonate (Y) [Unimod] +Methylphosphonate (T) [Unimod] +Methylphosphonate (S) [Unimod] +O-Isopropylmethylphosphonate (Y) [Unimod] +O-Isopropylmethylphosphonate (T) [Unimod] +O-Isopropylmethylphosphonate (S) [Unimod] +iTRAQ8plex:13C(6)15N(2) (Y) [Unimod] +iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod] +iTRAQ8plex:13C(6)15N(2) (K) [Unimod] +DTT_ST (S) [Unimod] +DTT_ST (T) [Unimod] +Ethanolamine (D) [Unimod] +Ethanolamine (C-term) [Unimod] +Ethanolamine (E) [Unimod] +TMT6plex (K) [Unimod] +TMT6plex (N-term) [Unimod] +DTT_C (C) [Unimod] +TMT2plex (N-term) [Unimod] +TMT2plex (K) [Unimod] +TMT (N-term) [Unimod] +TMT (K) [Unimod] +ExacTagThiol (C) [Unimod] +ExacTagAmine (K) [Unimod] +NO_SMX_SEMD (C) [Unimod] +4-ONE+Delta:H(-2)O(-1) (K) [Unimod] +4-ONE+Delta:H(-2)O(-1) (H) [Unimod] +4-ONE+Delta:H(-2)O(-1) (C) [Unimod] +NO_SMX_SMCT (C) [Unimod] +NO_SMX_SIMD (C) [Unimod] +Malonyl (C) [Unimod] +Malonyl (S) [Unimod] +3sulfo (N-term) [Unimod] +trifluoro (L) [Unimod] +TNBS (N-term) [Unimod] +TNBS (K) [Unimod] +Biotin-phenacyl (C) [Unimod] +Biotin-phenacyl (H) [Unimod] +Biotin-phenacyl (S) [Unimod] +DTT_C:2H(6) (C) [Unimod] +lapachenole (C) [Unimod] +Label:13C(5) (P) [Unimod] +maleimide (K) [Unimod] +maleimide (C) [Unimod] +DTT_ST:2H(6) (T) [Unimod] +DTT_ST:2H(6) (S) [Unimod] +Met-loss (M) [Unimod] +Met-loss+Acetyl (M) [Unimod] +Menadione-HQ (K) [Unimod] +Menadione-HQ (C) [Unimod] +Carboxymethyl:13C(2) (C) [Unimod] +NEM:2H(5) (C) [Unimod] +Gly-loss+Amide (G) [Unimod] +TMPP-Ac (N-term) [Unimod] +Label:13C(6)+GlyGly (K) [Unimod] +Arg->Npo (R) [Unimod] +Label:2H(4)+Acetyl (K) [Unimod] +Pentylamine (Q) [Unimod] +PentylamineBiotin (Q) [Unimod] +Dihydroxyimidazolidine (R) [Unimod] +DFDNB (Q) [Unimod] +DFDNB (N) [Unimod] +DFDNB (R) [Unimod] +DFDNB (K) [Unimod] +Cy3b-maleimide (C) [Unimod] +AEC-MAEC:2H(4) (S) [Unimod] +AEC-MAEC:2H(4) (T) [Unimod] +BMOE (C) [Unimod] +Biotin-PEO4-hydrazide (C-term) [Unimod] +Label:13C(6)+Acetyl (K) [Unimod] +Label:13C(6)15N(2)+Acetyl (K) [Unimod] +EQIGG (K) [Unimod] +cGMP (C) [Unimod] +cGMP+RMP-loss (C) [Unimod] +Arg2PG (R) [Unimod] +Label:2H(4)+GlyGly (K) [Unimod] +Label:13C(8)15N(2) (R) [Unimod] +Label:13C(1)2H(3) (M) [Unimod] +ZGB (K) [Unimod] +ZGB (N-term) [Unimod] +MG-H1 (R) [Unimod] +G-H1 (R) [Unimod] +Label:13C(6)15N(2)+GlyGly (K) [Unimod] +ICPL:13C(6)2H(4) (N-term) [Unimod] +ICPL:13C(6)2H(4) (K) [Unimod] +ICPL:13C(6)2H(4) (N-term) [Unimod] +QQQTGG (K) [Unimod] +QEQTGG (K) [Unimod] +Bodipy (C) [Unimod] diff -r 000000000000 -r d4b6c9eae635 maxquant_proteases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_proteases.loc Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,27 @@ +Trypsin +Arg-C +Asp-N +Asp-N_ambic +Chymotrypsin +CNBr +CNBr+Trypsin +Formic_acid +Lys-C +Lys-C/P +PepsinA +Tryp-CNBr +TrypChymo +Trypsin/P +Trypsin/P+DP +V8-DE +V8-E +semiTrypsin +LysC+AspN +Lys-C/P+DP +Trypsin/P + Asp-N +Asp-C +Trypsin/P+Asp-C +SemiLys +SemiGluC +LysC/P+AspC +GluC diff -r 000000000000 -r d4b6c9eae635 maxquant_proteases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_proteases.loc.sample Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,27 @@ +Trypsin +Arg-C +Asp-N +Asp-N_ambic +Chymotrypsin +CNBr +CNBr+Trypsin +Formic_acid +Lys-C +Lys-C/P +PepsinA +Tryp-CNBr +TrypChymo +Trypsin/P +Trypsin/P+DP +V8-DE +V8-E +semiTrypsin +LysC+AspN +Lys-C/P+DP +Trypsin/P + Asp-N +Asp-C +Trypsin/P+Asp-C +SemiLys +SemiGluC +LysC/P+AspC +GluC diff -r 000000000000 -r d4b6c9eae635 maxquant_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_wrapper.py Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,787 @@ +#!/usr/bin/env python +import optparse +import os +import shutil +import sys +import tempfile +import subprocess +import logging +from string import Template +from xml.sax.saxutils import escape +import xml.etree.ElementTree as ET + +log = logging.getLogger(__name__) + +DEBUG = True + +working_directory = os.getcwd() +tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name +tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name + + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit() + + +def read_stderr(): + stderr = '' + if(os.path.exists(tmp_stderr_name)): + with open(tmp_stderr_name, 'rb') as tmp_stderr: + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read(buffsize) + if not stderr or len(stderr) % buffsize != 0: + break + except OverflowError: + pass + return stderr + + +def execute(command, stdin=None): + try: + with open(tmp_stderr_name, 'wb') as tmp_stderr: + with open(tmp_stdout_name, 'wb') as tmp_stdout: + proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) + returncode = proc.wait() + if returncode != 0: + raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) + finally: + print open(tmp_stderr_name, "r").read(64000) + print open(tmp_stdout_name, "r").read(64000) + + +def delete_file(path): + if os.path.exists(path): + try: + os.remove(path) + except: + pass + + +def delete_directory(directory): + if os.path.exists(directory): + try: + shutil.rmtree(directory) + except: + pass + + +def symlink(source, link_name): + import platform + if platform.system() == 'Windows': + try: + import win32file + win32file.CreateSymbolicLink(source, link_name, 1) + except: + shutil.copy(source, link_name) + else: + os.symlink(source, link_name) + + +def copy_to_working_directory(data_file, relative_path): + if os.path.abspath(data_file) != os.path.abspath(relative_path): + shutil.copy(data_file, relative_path) + return relative_path + + +def __main__(): + run_script() + + +## Lock File Stuff +## http://www.evanfosmark.com/2009/01/cross-platform-file-locking-support-in-python/ +import os +import time +import errno + + +class FileLockException(Exception): + pass + + +class FileLock(object): + """ A file locking mechanism that has context-manager support so + you can use it in a with statement. This should be relatively cross + compatible as it doesn't rely on msvcrt or fcntl for the locking. + """ + + def __init__(self, file_name, timeout=10, delay=.05): + """ Prepare the file locker. Specify the file to lock and optionally + the maximum timeout and the delay between each attempt to lock. + """ + self.is_locked = False + self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name) + self.file_name = file_name + self.timeout = timeout + self.delay = delay + + def acquire(self): + """ Acquire the lock, if possible. If the lock is in use, it check again + every `wait` seconds. It does this until it either gets the lock or + exceeds `timeout` number of seconds, in which case it throws + an exception. + """ + start_time = time.time() + while True: + try: + self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR) + break + except OSError as e: + if e.errno != errno.EEXIST: + raise + if (time.time() - start_time) >= self.timeout: + raise FileLockException("Timeout occured.") + time.sleep(self.delay) + self.is_locked = True + + def release(self): + """ Get rid of the lock by deleting the lockfile. + When working in a `with` statement, this gets automatically + called at the end. + """ + if self.is_locked: + os.close(self.fd) + os.unlink(self.lockfile) + self.is_locked = False + + def __enter__(self): + """ Activated when used in the with statement. + Should automatically acquire a lock to be used in the with block. + """ + if not self.is_locked: + self.acquire() + return self + + def __exit__(self, type, value, traceback): + """ Activated at the end of the with statement. + It automatically releases the lock if it isn't locked. + """ + if self.is_locked: + self.release() + + def __del__(self): + """ Make sure that the FileLock instance doesn't leave a lockfile + lying around. + """ + self.release() + +TEMPLATE = """ + + $raw_file_info + + $slice_peaks + + $num_cores + false + 1 + false + NaN + NaN + $calc_peak_properties + $use_original_precursor_mz + $fixed_mods + $multi_modification_search + $database + + + $advanced_ratios + $rt_shift + $fast_lfq + $randomize + $special_aas + $include_contamiants + $equal_il + 100 + $max_peptide_mass + $reporter_pif + $reporter_fraction + $reporter_base_peak_ratio + $score_threshold + $filter_aacounts + $second_peptide + $match_between_runs + $match_between_runs_fdr + $re_quantify + $dependent_peptides + $dependent_peptide_fdr + $dependent_peptide_mass_bin + $label_free + $lfq_min_edges_per_node + $lfq_av_edges_per_node + $hybrid_quantification + $msms_connection + $ibaq + $msms_recalibration + $ibaq_log_fit + $razor_protein_fdr + $calc_sequence_tags + $de_novo_var_mods + $mass_difference_search + $min_pep_len + $peptide_fdr + $peptide_pep + $protein_fdr + $site_fdr + $min_peptide_length_for_unspecific_search + $max_peptide_length_for_unspecific_search + $use_norm_ratios_for_occupancy + $min_peptides + $min_razor_peptides + $min_unique_peptides + $use_counterparts + $min_ratio_count + $lfq_min_ratio_count + $restrict_protein_quantification + $restrict_mods + $matching_time_window + $number_of_candidates_multiplexed_msms + $number_of_candidates_msms + $separate_aas_for_site_fdr + + + + + $group_params + + + + + + + $ftms_fragment_settings + $itms_fragment_settings + $tof_fragment_settings + $unknown_fragment_settings + + $keep_low_scores_mode + $msms_centroid_mode + $quant_mode + $site_quant_mode + + + $group_params + + + +""" + +GROUP_TEMPLATE = """ + $max_charge + $lcms_run_type + $ms_instrument + $group_index + $max_labeled_aa + $max_n_mods + $max_missed_cleavages + $multiplicity + $protease + $protease + false + false + $variable_mods + $isobaric_labels + + Oxidation (M) + Acetyl (Protein N-term) + + false + + + + + + + $do_mass_filtering + $first_search_tol + $main_search_tol + $labels +""" + +# +# +# Arg10; Lys8 +# + +fragment_settings = { + "FTMS": {"InPpm": "true", "Deisotope": "true", "Topx": "10", "HigherCharges": "true", + "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true", + "tolerance_value": "20", "tolerance_unit": "Ppm", "name": "FTMS"}, + "ITMS": {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true", + "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true", + "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "ITMS"}, + "TOF": {"InPpm": "false", "Deisotope": "true", "Topx": "10", "HigherCharges": "true", + "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true", + "tolerance_value": "0.1", "tolerance_unit": "Dalton", "name": "TOF"}, + "Unknown": {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true", + "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true", + "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "Unknown"}, +} + + +def build_isobaric_labels(reporter_type): + if not reporter_type: + return "" + if reporter_type == "itraq_4plex": + prefix = "iTRAQ4plex" + mzs = [114, 115, 116, 117] + elif reporter_type == "itraq_8plex": + prefix = "iTRAQ8plex" + mzs = [113, 114, 115, 116, 117, 118, 119, 121] + elif reporter_type == "tmt_2plex": + prefix = "TMT2plex" + mzs = [126, 127] + elif reporter_type == "tmt_6plex": + prefix = "TMT6plex" + mzs = [126, 127, 128, 129, 130, 131] + else: + raise Exception("Unknown reporter type - %s" % reporter_type) + labels = ["%s-%s%d" % (prefix, term, mz) for term in ["Nter", "Lys"] for mz in mzs] + return wrap(map(xml_string, labels), "isobaricLabels") + + +def parse_groups(inputs_file, group_parts=["num"], input_parts=["name", "path"]): + inputs_lines = [line.strip() for line in open(inputs_file, "r").readlines()] + inputs_lines = [line for line in inputs_lines if line and not line.startswith("#")] + cur_group = None + i = 0 + group_prefixes = ["%s:" % group_part for group_part in group_parts] + input_prefixes = ["%s:" % input_part for input_part in input_parts] + groups = {} + while i < len(inputs_lines): + line = inputs_lines[i] + if line.startswith(group_prefixes[0]): + # Start new group + cur_group = line[len(group_prefixes[0]):] + group_data = {} + for j, group_prefix in enumerate(group_prefixes): + group_line = inputs_lines[i + j] + group_data[group_parts[j]] = group_line[len(group_prefix):] + i += len(group_prefixes) + elif line.startswith(input_prefixes[0]): + input = [] + for j, input_prefix in enumerate(input_prefixes): + part_line = inputs_lines[i + j] + part = part_line[len(input_prefixes[j]):] + input.append(part) + if cur_group not in groups: + groups[cur_group] = {"group_data": group_data, "inputs": []} + groups[cur_group]["inputs"].append(input) + i += len(input_prefixes) + else: + # Skip empty line + i += 1 + return groups + + +def add_fragment_options(parser): + for name, options in fragment_settings.iteritems(): + for key, value in options.iteritems(): + option_key = ("%s_%s" % (name, key)).lower() + parser.add_option("--%s" % option_key, default=value) + + +def update_fragment_settings(arg_options): + for name, options in fragment_settings.iteritems(): + for key, value in options.iteritems(): + arg_option_key = ("%s_%s" % (name, key)).lower() + options[key] = getattr(arg_options, arg_option_key) + + +def to_fragment_settings(name, values): + """ + """ + + fragment_settings_template = """ + + + $tolerance_value + $tolerance_unit + + + """ + safe_values = dict(values) + for key, value in safe_values.iteritems(): + safe_values[key] = escape(value) + return Template(fragment_settings_template).substitute(safe_values) + + +def get_file_paths(files): + return wrap([xml_string(name) for name in files], "filePaths") + + +def get_file_names(file_names): + return wrap([xml_string(name) for name in file_names], "fileNames") + + +def get_file_groups(file_groups): + return wrap([xml_int(file_group) for file_group in file_groups], "paramGroups") + + +def wrap(values, tag): + return "<%s>%s" % (tag, "".join(values), tag) + + +def xml_string(str): + if str: + return "%s" % escape(str) + else: + return "" + + +def xml_int(value): + return "%d" % int(value) + + +def get_properties(options): + direct_properties = ["lcms_run_type", + "max_missed_cleavages", + "protease", + "first_search_tol", + "main_search_tol", + "max_n_mods", + "max_charge", + "max_labeled_aa", + "do_mass_filtering", + "calc_peak_properties", + "use_original_precursor_mz", + "multi_modification_search", + "keep_low_scores_mode", + "msms_centroid_mode", + "quant_mode", + "site_quant_mode", + "advanced_ratios", + "rt_shift", + "fast_lfq", + "randomize", + "aif_sil_weight", + "aif_iso_weight", + "aif_topx", + "aif_correlation", + "aif_correlation_first_pass", + "aif_min_mass", + "aif_msms_tol", + "aif_second_pass", + "aif_iterative", + "aif_threhold_fdr", + "restrict_protein_quantification", + "matching_time_window", + "number_of_candidates_multiplexed_msms", + "number_of_candidates_msms", + "separate_aas_for_site_fdr", + "special_aas", + "include_contamiants", + "equal_il", + "topx_window", + "max_peptide_mass", + "reporter_pif", + "reporter_fraction", + "reporter_base_peak_ratio", + "score_threshold", + "filter_aacounts", + "second_peptide", + "match_between_runs", + "match_between_runs_fdr", + "re_quantify", + "dependent_peptides", + "dependent_peptide_fdr", + "dependent_peptide_mass_bin", + "label_free", + "lfq_min_edges_per_node", + "lfq_av_edges_per_node", + "hybrid_quantification", + "msms_connection", + "ibaq", + "msms_recalibration", + "ibaq_log_fit", + "razor_protein_fdr", + "calc_sequence_tags", + "de_novo_var_mods", + "mass_difference_search", + "min_pep_len", + "peptide_fdr", + "peptide_pep", + "protein_fdr", + "site_fdr", + "min_peptide_length_for_unspecific_search", + "max_peptide_length_for_unspecific_search", + "use_norm_ratios_for_occupancy", + "min_peptides", + "min_razor_peptides", + "min_unique_peptides", + "use_counterparts", + "min_ratio_count", + "lfq_min_ratio_count", + ] + + props = { + "slice_peaks": "true", + "num_cores": str(options.num_cores), + "database": xml_string(setup_database(options)), + "process_folder": os.path.join(os.getcwd(), "process"), + } + for prop in direct_properties: + props[prop] = str(getattr(options, prop)) + + for name, fragment_options in fragment_settings.iteritems(): + key = "%s_fragment_settings" % name.lower() + props[key] = to_fragment_settings(name, fragment_options) + + restrict_mods_string = wrap(map(xml_string, options.restrict_mods), "restrictMods") + props["restrict_mods"] = restrict_mods_string + fixed_mods_string = wrap(map(xml_string, options.fixed_mods), "fixedModifications") + props["fixed_mods"] = fixed_mods_string + variable_mods_string = wrap(map(xml_string, options.variable_mods), "variableModifications") + props["variable_mods"] = variable_mods_string + return props + + +# http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python +def which(program): + import os + + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + + +def get_unique_path(base, extension): + """ + """ + return "%s_%d%s" % (base, int(time.time() * 1000), extension) + + +def get_env_property(name, default): + if name in os.environ: + return os.environ[name] + else: + return default + + +def setup_database(options): + database_path = options.database + database_name = options.database_name + database_name = database_name.replace(" ", "_") + (database_basename, extension) = os.path.splitext(database_name) + database_destination = get_unique_path(database_basename, ".fasta") + assert database_destination == os.path.basename(database_destination) + symlink(database_path, database_destination) + + database_conf = get_env_property("MAXQUANT_DATABASE_CONF", None) + if not database_conf: + exe_path = which("MaxQuantCmd.exe") + database_conf = os.path.join(os.path.dirname(exe_path), "conf", "databases.xml") + with FileLock(database_conf + ".galaxy_lock"): + tree = ET.parse(database_conf) + root = tree.getroot() + databases_node = root.find("Databases") + database_node = ET.SubElement(databases_node, 'databases') + database_node.attrib["search_expression"] = ">([^ ]*)" + database_node.attrib["replacement_expression"] = "%1" + database_node.attrib["filename"] = database_destination + tree.write(database_conf) + return os.path.abspath(database_destination) + + +def setup_inputs(input_groups_path): + parsed_groups = parse_groups(input_groups_path) + paths = [] + names = [] + group_nums = [] + for group, group_info in parsed_groups.iteritems(): + files = group_info["inputs"] + group_num = group_info["group_data"]["num"] + for (name, path) in files: + name = os.path.basename(name) + if not name.lower().endswith(".raw"): + name = "%s.%s" % (name, ".RAW") + symlink(path, name) + paths.append(os.path.abspath(name)) + names.append(os.path.splitext(name)[0]) + group_nums.append(group_num) + file_data = (get_file_paths(paths), get_file_names(names), get_file_groups(group_nums)) + return "%s%s%s " % file_data + + +def set_group_params(properties, options): + labels = [""] + if options.labels: + labels = options.labels + labels_string = wrap([xml_string(label.replace(",", "; ")) for label in labels], "labels") + group_properties = dict(properties) + group_properties["labels"] = labels_string + group_properties["multiplicity"] = len(labels) + group_properties["group_index"] = "1" + group_properties["ms_instrument"] = "0" + group_params = Template(GROUP_TEMPLATE).substitute(group_properties) + properties["group_params"] = group_params + + +def split_mods(mods_string): + return [mod for mod in mods_string.split(",") if mod] if mods_string else [] + + +def run_script(): + parser = optparse.OptionParser() + parser.add_option("--input_groups") + parser.add_option("--database") + parser.add_option("--database_name") + parser.add_option("--num_cores", type="int", default=4) + parser.add_option("--max_missed_cleavages", type="int", default=2) + parser.add_option("--protease", default="Trypsin/P") + parser.add_option("--first_search_tol", default="20") + parser.add_option("--main_search_tol", default="6") + parser.add_option("--max_n_mods", type="int", default=5) + parser.add_option("--max_charge", type="int", default=7) + parser.add_option("--do_mass_filtering", default="true") + parser.add_option("--labels", action="append", default=[]) + parser.add_option("--max_labeled_aa", type="int", default=3) + parser.add_option("--keep_low_scores_mode", type="int", default=0) + parser.add_option("--msms_centroid_mode", type="int", default=1) + # 0 = all peptides, 1 = Use razor and unique peptides, 2 = use unique peptides + parser.add_option("--quant_mode", type="int", default=1) + parser.add_option("--site_quant_mode", type="int", default=0) + parser.add_option("--aif_sil_weight", type="int", default=4) + parser.add_option("--aif_iso_weight", type="int", default=2) + parser.add_option("--aif_topx", type="int", default=50) + parser.add_option("--aif_correlation", type="float", default=0.8) + parser.add_option("--aif_correlation_first_pass", type="float", default=0.8) + parser.add_option("--aif_min_mass", type="float", default=0) + parser.add_option("--aif_msms_tol", type="float", default=10) + parser.add_option("--aif_second_pass", default="false") + parser.add_option("--aif_iterative", default="false") + parser.add_option("--aif_threhold_fdr", default="0.01") + parser.add_option("--restrict_protein_quantification", default="true") + parser.add_option("--matching_time_window", default="2") + parser.add_option("--number_of_candidates_multiplexed_msms", default="50") + parser.add_option("--number_of_candidates_msms", default="15") + parser.add_option("--separate_aas_for_site_fdr", default="true") + parser.add_option("--advanced_ratios", default="false") + parser.add_option("--rt_shift", default="false") + parser.add_option("--fast_lfq", default="true") + parser.add_option("--randomize", default="false") + parser.add_option("--special_aas", default="KR") + parser.add_option("--include_contamiants", default="false") + parser.add_option("--equal_il", default="false") + parser.add_option("--topx_window", default="100") + parser.add_option("--max_peptide_mass", default="5000") + parser.add_option("--reporter_pif", default="0.75") + parser.add_option("--reporter_fraction", default="0") + parser.add_option("--reporter_base_peak_ratio", default="0") + parser.add_option("--score_threshold", default="0") + parser.add_option("--filter_aacounts", default="true") + parser.add_option("--second_peptide", default="true") + parser.add_option("--match_between_runs", default="false") + parser.add_option("--match_between_runs_fdr", default="false") + parser.add_option("--re_quantify", default="true") + parser.add_option("--dependent_peptides", default="false") + parser.add_option("--dependent_peptide_fdr", default="0.01") + parser.add_option("--dependent_peptide_mass_bin", default="0.0055") + parser.add_option("--label_free", default="false") + parser.add_option("--lfq_min_edges_per_node", default="3") + parser.add_option("--lfq_av_edges_per_node", default="6") + parser.add_option("--hybrid_quantification", default="false") + parser.add_option("--msms_connection", default="false") + parser.add_option("--ibaq", default="false") + parser.add_option("--msms_recalibration", default="false") + parser.add_option("--ibaq_log_fit", default="true") + parser.add_option("--razor_protein_fdr", default="true") + parser.add_option("--calc_sequence_tags", default="false") + parser.add_option("--de_novo_var_mods", default="true") + parser.add_option("--mass_difference_search", default="false") + parser.add_option("--min_pep_len", default="7") + parser.add_option("--peptide_fdr", default="0.01") + parser.add_option("--peptide_pep", default="1") + parser.add_option("--protein_fdr", default="0.01") + parser.add_option("--site_fdr", default="0.01") + parser.add_option("--min_peptide_length_for_unspecific_search", default="8") + parser.add_option("--max_peptide_length_for_unspecific_search", default="25") + parser.add_option("--use_norm_ratios_for_occupancy", default="true") + parser.add_option("--min_peptides", default="1") + parser.add_option("--min_razor_peptides", default="1") + parser.add_option("--min_unique_peptides", default="0") + parser.add_option("--use_counterparts", default="false") + parser.add_option("--min_ratio_count", default="2") + parser.add_option("--lfq_min_ratio_count", default="2") + parser.add_option("--calc_peak_properties", default="false") + parser.add_option("--use_original_precursor_mz", default="false") + parser.add_option("--multi_modification_search", default="false") + parser.add_option("--lcms_run_type", default="0") + parser.add_option("--reporter_type", default=None) + parser.add_option("--output_mqpar", default=None) + text_outputs = { + "aif_msms": "aifMsms", + "all_peptides": "allPeptides", + "evidence": "evidence", + "modification_specific_peptides": "modificationSpecificPeptides", + "msms": "msms", + "msms_scans": "msmsScans", + "mz_range": "mzRange", + "parameters": "parameters", + "peptides": "peptides", + "protein_groups": "proteinGroups", + "sim_peptides": "simPeptides", + "sim_scans": "simScans", + "summary": "summary" + } + for output in text_outputs.keys(): + parser.add_option("--output_%s" % output, default=None) + + parser.add_option("--variable_mods", default="Oxidation (M),Acetyl (Protein N-term)") + parser.add_option("--restrict_mods", default="Oxidation (M),Acetyl (Protein N-term)") + parser.add_option("--fixed_mods", default="Carbamidomethyl (C)") + + add_fragment_options(parser) + + (options, args) = parser.parse_args() + options.restrict_mods = split_mods(options.restrict_mods) + options.fixed_mods = split_mods(options.fixed_mods) + options.variable_mods = split_mods(options.variable_mods) + + update_fragment_settings(options) + + raw_file_info = setup_inputs(options.input_groups) + properties = get_properties(options) + properties["raw_file_info"] = raw_file_info + properties["isobaric_labels"] = build_isobaric_labels(options.reporter_type) + set_group_params(properties, options) + driver_contents = Template(TEMPLATE).substitute(properties) + open("mqpar.xml", "w").write(driver_contents) + print driver_contents + execute("MaxQuantCmd.exe mqpar.xml %d" % options.num_cores) + for key, basename in text_outputs.iteritems(): + attribute = "output_%s" % key + destination = getattr(options, attribute, None) + if destination: + source = os.path.join("combined", "txt", "%s.txt" % basename) + shutil.copy(source, destination) + output_mqpar = options.output_mqpar + if output_mqpar: + shutil.copy("mqpar.xml", output_mqpar) + +if __name__ == '__main__': + __main__() diff -r 000000000000 -r d4b6c9eae635 modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/modifications.xml Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,2580 @@ + + + + notCterm + + + + + + + standard + + + proteinNterm + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + + + + + + + + + + + + + + + standard + + + anywhere + + label + + + anywhere + + label + + + anywhere + + label + + + anywhere + + label + + + anywhere + + label + + + anywhere + + standard + + + anywhere + + + standard + + + 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anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + standard + + + anywhere + + + standard + + + anywhere + + label + + + anywhere + + label + + \ No newline at end of file diff -r 000000000000 -r d4b6c9eae635 proteases.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteases.xml Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,1 @@ + \ No newline at end of file diff -r 000000000000 -r d4b6c9eae635 unimod.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unimod.xml Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,15140 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + N-(4-trimethylammoniumbutanoxy)-NHS + + 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 + Journal + + + + 11857757 + PubMed PMID + + + + + + + + + + + + + + + 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 + Journal + + + + 11857757 + PubMed PMID + + + + + + + + + + + + + + + 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 + Journal + + + + 11857757 + PubMed PMID + + + + + + + + + + + + + + + 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 + Journal + + + + 11857757 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316. + Journal + + + + 9252331 + PubMed PMID + + + + + + + + + + + + + Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316. + Journal + + + + 9252331 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AA0021 + RESID + + + + 10825024 + PubMed PMID + + + + 8758896 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AA0211 + RESID + + + + 15799070 + PubMed PMID + + + + AA0021 + RESID + + + + FORM + FindMod + + + + AA0384 + RESID + + + + AA0057 + RESID + + + + AA0384 + RESID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Decarboxylation of C-terminus as reaction inside the mass spectrometer + + 14588022 + PubMed PMID + + + + D. Suckau, A. Resemann, Anal. Chem., 75(21):5817-24 (2003) + Journal + + + 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Butylated Hydroxytoluene + + 9448752 + PubMed PMID + + + BHT metabolism has been studied in rats and mice in relation to tumor promotion. + + + + + + + + + + + + + + + + + + + + heavy phosphotyrosine + + 12716131 + PubMed PMID + + + + Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181 + Journal + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + + + + + + + + + + + Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181 + Journal + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + H2 18O Alkaline Phosphatase + + 11467524 + PubMed PMID + + + + + + + + + + + + heavy lysine + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12771378 + PubMed PMID + + + + + + + + + + Trideuteration + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + + + + + + + + + + 12771378 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + Anal Biochem. 2004 Oct 1;333(1):174-81 + Journal + + + + 15351294 + PubMed PMID + + + 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Introduction to Protein Labeling + Misc. URL + http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB + + EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5\' phosphate groups + + + + + + + + + + + + + + + + + + + UV induced cross-link product of Iodo-U-amp with WFY + + 6540775 + PubMed PMID + + + + 11112526 + PubMed PMID + + + + 11567090 + PubMed PMID + + + 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). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MDA54 + + 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 + Journal + + + + + + + + + + + + + + + + + + + + + + + + + + Thiophos-biotin disulfide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AA0153 + RESID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dimethyl pimelimidate + + Imidoester Cross-linkers + Misc. URL + http://www.piercenet.com/files/0668ss5.pdf + + + Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514. + Journal + + + + 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. + Journal + + + + + + + + + + + + + + + + + + + J. Mass Spectrom. 2005; 40: 238-249 + Journal + + + + + + + + + + + + + + J. Mass Spectrom. 2005; 40: 238-249 + Journal + + + + + + + + + + + + + + + + beta-methylaminoethylcysteine + + Z. A. Knight et al, Nature Biotech., 21(9) 1047-1054 (2003) + Journal + + + Modification procedure used for phosphopeptide mapping + + + + + + + + + + Berger U, Oehme M, Girardin L., Fresenius J Anal Chem. 2001 Jan 2;369(2):115-23. + Journal + + + Found in canned food products + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lac + + ANALYTICAL BIOCHEMISTRY 259, 152-161 (1998) + Journal + + + + BIOCHIMECAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 236, 413-417 (1997) + Journal + + + Lactosylation of bovine Beta-Lactoglobulin + + + + + + + + + + + + + + + + + + + + + + fluorescein-NEM + + 9325338 + PubMed PMID + + + + 11665566 + PubMed PMID + + + + Thiol-Reactive Probes + Misc. URL + http://probes.invitrogen.com/media/pis/mp00003.pdf + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + heavy D9 lysine + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + CDNLM-6810 + Misc. URL + http://www.isotope.com/cil/products/displayproduct.cfm?prod_id=8635 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + threo-1,4-dimercaptobutane-2,3-diol + Cleland's reagent + + Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW. + PubMed PMID + 17116471 + + + 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. + PubMed PMID + 12438562 + + + 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. + PubMed PMID + 15648052 + + Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Biochemistry 2005 vol 44 pp 1833-1845 + Journal + http://dx.doi.org/10.1021/bi048228c + + + + + + + + + + Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181 + Journal + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Acetyl_K4 + For SILAC experiments, + PTM + + + + + + + + + + + + + + + + + + + + + + + + + + + + Pierce product page + Misc. URL + http://www.piercenet.com/products/browse.cfm?fldID=C4FE82D4-DD06-493C-8EC4-9C1D7F83211B + + + + + + + + + + + + Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181 + Journal + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + + Acetyl_heavy lysine + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + 12716131 + PubMed PMID + + + + + + + + + + + + + + + + + + PMID 11698400rnLigand-selective modulation of the permeability transition pore by arginine modification. Opposing effects of p-hydroxyphenylglyoxal and phenylglyoxal. + PubMed PMID + http://www.ncbi.nlm.nih.gov/pubmed/11698400?ordinalpos=39&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum + + + PMID 5723461rnThe reaction of phenylglyoxal with arginine residues in proteins. + PubMed PMID + http://www.ncbi.nlm.nih.gov/pubmed/5723461?ordinalpos=517&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum + + + PMID 11945751rnReaction of arginine residues in basic pancreatic trypsin inhibitor with phenylglyoxal. + PubMed PMID + http://www.ncbi.nlm.nih.gov/pubmed/11945751?ordinalpos=514&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum + + + + + + + + + + + + + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + + + + + + + + + + + + + + + + heavy glygly lysine + + 12716131 + PubMed PMID + + + + Silac introduction + Misc. URL + http://www.pil.sdu.dk/silac_intro.htm + + + + + + + + + + + + + + GlnGlnGlnThrGlyGly + + + + + + + + + + GlnGluGlnThrGlyGly + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r d4b6c9eae635 update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi