changeset 17:6cdbfdffb38e draft

Uploaded
author iracooke
date Wed, 25 Jun 2014 11:49:19 -0400
parents 186fdc4b3310
children a5f9b959d5d1
files #env.sh# COPYING LICENSE README.md README_GALAXYP.md README_REPO.md build_mods_loc.py datatypes_conf.xml dbtoolkit-4.2/LICENSE-2.0.txt dbtoolkit-4.2/dbtoolkit-4.2.jar dbtoolkit-4.2/lib/jargs-1.0.jar dbtoolkit-4.2/lib/jargs-1.0.jar~ dbtoolkit-4.2/lib/log4j-1.2.12.jar dbtoolkit-4.2/lib/utilities-3.8.7.jar peptide_shaker.xml peptideshaker.py repository_dependencies.xml reverse.py reverse.xml searchGUI_mods.xml searchGUI_usermods.xml searchgui_mods.loc searchgui_mods.loc.sample test-data/._tinyoutput.cps test-data/tinydb.fasta test-data/tinyoutput.cps test-data/tinyspectra.mgf tool_dependencies.xml update.sh
diffstat 29 files changed, 6298 insertions(+), 4629 deletions(-) [+]
line wrap: on
line diff
--- a/#env.sh#	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-
-export PATH=/path/to/2134123412341/tint_proteomics_scripts/:$PATH
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Wed Jun 25 11:49:19 2014 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
+
+CC0 1.0 Universal
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+limitation commercial, advertising or promotional purposes (the
+"License"). The License shall be deemed effective as of the date CC0 was
+applied by Affirmer to the Work. Should any part of the License for any
+reason be judged legally invalid or ineffective under applicable law, such
+partial invalidity or ineffectiveness shall not invalidate the remainder
+of the License, and in such case Affirmer hereby affirms that he or she
+will not (i) exercise any of his or her remaining Copyright and Related
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+express Statement of Purpose.
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+4. Limitations and Disclaimers.
+
+ a. No trademark or patent rights held by Affirmer are waived, abandoned,
+    surrendered, licensed or otherwise affected by this document.
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--- a/LICENSE	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
---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]
-
--- a/README.md	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
-of mgf files and performs X! Tandem and OMSSA searches on these via
-SearchGUI and merges the results using PeptideShaker.
-
-For Galaxy-P we are installing this tool via CloudBioLinux
-(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
-this fabric script may not be exactly appropriate for your environment
-it may serve as a template for how to install this software. In
-particular these tools require CLI wrappers to be placed for
-PeptideShaker and SearchGUI that can be installed as demostrated in
-these fabric functions.
-
-Note: Also SearchGUI requires a version greater than 1.12.2 which
-contained several bugs preventing this from working on the
-command-line and via Linux.
-
-Also, PeptideShaker may require xvfb to simulate an X environment if
-this is installed on a headless server.
-# 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.
--- a/README_GALAXYP.md	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-# 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.
--- a/README_REPO.md	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
-of mgf files and performs X! Tandem and OMSSA searches on these via
-SearchGUI and merges the results using PeptideShaker.
-
-For Galaxy-P we are installing this tool via CloudBioLinux
-(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
-this fabric script may not be exactly appropriate for your environment
-it may serve as a template for how to install this software. In
-particular these tools require CLI wrappers to be placed for
-PeptideShaker and SearchGUI that can be installed as demostrated in
-these fabric functions.
-
-Note: Also SearchGUI requires a version greater than 1.12.2 which
-contained several bugs preventing this from working on the
-command-line and via Linux.
-
-Also, PeptideShaker may require xvfb to simulate an X environment if
-this is installed on a headless server.
--- a/build_mods_loc.py	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-
-import xml.etree.ElementTree as ET
-from os.path import exists
-
-with open("searchgui_mods.loc", "w") as output:
-    for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]:
-        tree = ET.parse(mods_path)
-        modifications_el = tree.getroot()
-        for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"):
-            name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name")
-            output.write("%s\n" % name_el.text.lower())
--- a/datatypes_conf.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="peptideshaker.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="cps" type="galaxy.datatypes.peptideshaker:Cps" display_in_upload="true" />
-  </registration>
-</datatypes>
--- a/dbtoolkit-4.2/LICENSE-2.0.txt	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-
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-                           Version 2.0, January 2004
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Binary file dbtoolkit-4.2/dbtoolkit-4.2.jar has changed
--- a/dbtoolkit-4.2/lib/jargs-1.0.jar	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="SearchGUI" version="1.13.1">
-        <install version="1.0">
-            <actions>
-              <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action>
-	      <action type="shell_command">tar -xf $DIR_NAME/*.tar</action>
-	      <action type="shell_command">cd $DIR_NAME</action>
-	      <action type="shell_command">chmod -R $DIR_NAME/*resources</action>
-              <action type="move_directory_files">
-                <source_directory>.</source_directory>
-                <destination_directory>$INSTALL_DIR/</destination_directory>
-              </action>
-	      <action type="shell_command">mkdir -p $BIN_DIR</action>
-              <action type="set_environment">
-                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-              </action>                
-            </actions>
-        </install>
-        <readme>
-          This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool.
-          (https://github.com/jmchilton/peptide-shaker).
-
-        </readme>
-    </package>
-    
-    <package name="PeptideShaker" version="0.20.1">
-        <install version="1.0">
-            <actions>
-              <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action>
-	      <action type="shell_command">chmod -R o+w resources</action>
-              <action type="move_directory_files">
-                <source_directory>.</source_directory>
-                <destination_directory>$INSTALL_DIR/</destination_directory>
-              </action>
-              <action type="shell_command">mkdir -p $BIN_DIR</action>
-              <action type="set_environment">
-                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-              </action>                
-            </actions>
-        </install>
-        <readme>
-          This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework.
-          (https://github.com/jmchilton/peptide-shaker).
-
-        </readme>
-    </package>
-</tool_dependency>
Binary file dbtoolkit-4.2/lib/jargs-1.0.jar~ has changed
Binary file dbtoolkit-4.2/lib/log4j-1.2.12.jar has changed
Binary file dbtoolkit-4.2/lib/utilities-3.8.7.jar has changed
--- a/peptide_shaker.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,228 +0,0 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
-  <!-- TODO: Set defaults for weights correctly -->
-  <description>
-    Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
-  </description>
-  <command>
-    #from datetime import datetime
-    #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")              
-    #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
-    mkdir spectra;
-    mkdir output;
-    mkdir output_reports;
-    cwd=`pwd`;
-    #for $mgf in $peak_lists:
-    #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
-    ln -s '$mgf' 'spectra/$input_name';
-    #end for
-    SearchCLI \
-    -spectrum_files \$cwd/spectra \
-    -output_folder \$cwd/output \
-    -ppm $precursor_ion_tol_units \
-    -prec_tol $precursor_ion_tol \
-    -frag_tol $fragment_tol \
-    -enzyme '$enzyme' \
-    #set $fixed_mods_str = $fixed_modifications or ''
-    #set $variable_mods_str = $variable_modifications or ''
-    #if $fixed_mods_str
-    -fixed_mods "$fixed_mods_str" \
-    #end if
-    #if $variable_mods_str
-    -variable_mods "$variable_mods_str" \
-    #end if
-    -mc $missed_cleavages \
-    #if $advanced.specify:
-    -xtandem $advanced.xtandem \
-    #if $advanced.omssa.run_omssa
-    #set $omssa = 1
-    #else 
-    #set $omssa = 0
-    #end if
-    -omssa $omssa \
-    #if $omssa == 1
-    -hitlist_length ${advanced.omssa.hitlist_length} \
-    -remove_prec ${advanced.omssa.remove_precursor} \
-    -scale_prec ${advanced.omssa.scale_precursor} \
-    -estimate_charge ${advanced.omssa.estimate_charge} \
-    #end if
-    #end if
-    -db $input_database;
-    PeptideShakerCLI \
-    -experiment '$exp_str' \
-    -sample '$samp_str' \ 
-    -replicate 1 \
-    -spectrum_files \$cwd/spectra \
-    -identification_files \$cwd/output \ 
-    -search_params \$cwd/output/SearchGUI.parameters \
-    -out_txt_1 \$cwd/output_reports \
-    #if $processing_options.specify
-    -protein_FDR ${processing_options.protein_fdr} \
-    -peptide_FDR ${processing_options.peptide_fdr} \ 
-    -psm_FDR ${processing_options.psm_fdr} \
-    -psm_FLR ${processing_options.psm_flr} \
-    #if str($processing_options.a_score.use) == "1"
-    #set $a_score = 1
-    #else
-    #set $a_score = 0
-    #end if
-    -a_score $a_score \
-    #if str($a_score) == "1"
-    -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
-    #end if
-    #end if
-    #if $filtering_options.specify
-    -min_peptide_length ${filtering_options.min_peptide_length} \
-    -max_peptide_length ${filtering_options.max_peptide_length} \
-    -max_precursor_error ${filtering_options.max_precursor_error}  \
-    -max_precursor_error_type ${filtering_options.max_precursor_error_type}  \
-    -max_xtandem_e ${filtering_options.max_xtandem_e} \
-    -max_omssa_e ${filtering_options.max_omssa_e} \
-    -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
-    #end if
-    -out \$cwd/output.cps ; 
-    mv output_reports/*peptides.txt peptides.txt ;
-    mv output_reports/*psms.txt psms.txt ;
-    mv output_reports/*proteins.txt proteins.txt
-  </command>
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Job Failed" />
-  </stdio>
-  <inputs>
-    <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>
-    <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" />
-    <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
-      <option value="1">Parts per million (ppm)</option>
-      <option value="0">Daltons</option>
-    </param>    
-    <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
-    <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" help="Provide error value for fragment ions, based on instrument used"/>
-    <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
-      <option value="Trypsin">Trypsin</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
-      <option value="Formic Acid">Formic Acid</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="Lys-C, no P rule">Lys-C, no P rule</option>
-      <option value="Pepsin A">Pepsin A</option>
-      <option value="Trypsin + CNBr">Trypsin + CNBr</option>
-      <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
-      <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-      <option value="whole protein">whole protein</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Glu-C">Glu-C</option>
-      <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
-      <option value="Top-Down">Top-Down</option>
-      <option value="Semi-Tryptic">Semi-Tryptic</option>
-      <option value="No enzyme">No enzyme</option>
-      <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
-      <option value="Asp-N (DE)">Asp-N (DE)</option>
-      <option value="Glu-C (DE)">Glu-C (DE)</option>
-      <option value="Lys-N (K)">Lys-N (K)</option>
-      <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
-      <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
-      <option value="Semi-Glu-C">Semi-Glu-C</option>      
-    </param>
-    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/>
-    <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
-      <options from_file="searchgui_mods.loc">
-        <column name="name" index="0" />
-        <column name="value" index="0" />
-      </options>
-    </param>
-    <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
-      <options from_file="searchgui_mods.loc">
-        <column name="name" index="0" />
-        <column name="value" index="0" />
-      </options>
-    </param>        
-    <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
-    <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
-    <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
-      <option value="a">a</option>
-      <option value="b" selected="true">b</option>
-      <option value="c">c</option>
-    </param>
-    <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
-      <option value="x">x</option>
-      <option value="y" selected="true">y</option>
-      <option value="z">z</option>
-    </param>
-    <conditional name="advanced">
-      <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/>
-      <when value="false" />
-      <when value="true">
-        <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-        <conditional name="omssa">
-          <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-          <when value="0" />
-          <when value="1">
-            <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-            <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-            <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-            <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-          </when>
-        </conditional>
-      </when>
-    </conditional>
-    <conditional name="processing_options">
-      <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details
-
- .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />
-      <when value="false" />
-      <when value="true">
-        <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-        <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-        <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-        <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />
-        <conditional name="a_score">
-          <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-          <when value="0" />
-          <when value="1">
-            <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
-          </when>
-        </conditional>
-        <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
-      </when>
-    </conditional>    
-    <conditional name="filtering_options">
-      <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"/>
-      <when value="false" />
-      <when value="true">
-        <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
-        <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
-        <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
-        <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
-          <option value="0">ppm</option>
-          <option value="1">Daltons</option>
-        </param>
-        <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />
-        <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />
-        <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-      </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />
-    <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />
-    <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />
-    <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />
-  </outputs>
-  <requirements>
-    <requirement type="package" version="0.20.1">peptide_shaker</requirement>
-    <requirement type="package" version="1.14.4">searchgui</requirement>
-  </requirements>
-  <help>
-**What it does**
-
-Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `TODO`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
-  </help>
-</tool>
--- a/peptideshaker.py	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-from galaxy.datatypes.binary import Binary
-
-
-class Cps(Binary):
-    """Class describing a PeptideShaker CPS files"""
-    file_ext = "cps"
-
-Binary.register_unsniffable_binary_ext('cps')
--- a/repository_dependencies.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Required proteomics dependencies.">
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_searchgui_1_14_4" owner="galaxyp" changeset_revision="67de51d52907" />
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_peptideshaker_0_20_1" owner="galaxyp" changeset_revision="cfd55b6c4fa2" />
-</repositories>
--- a/reverse.py	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-from os.path import dirname, join, abspath
-import sys
-from optparse import OptionParser
-from ConfigParser import SafeConfigParser
-import subprocess
-
-DEBUG = False
-
-
-def main():
-    (options, args) = _parse_args()
-    format_args = (options.input, options.output)
-    _run_shell("cat '%s' > '%s'" % format_args)
-    _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % \
-                       format_args)
-
-
-def _run_shell(command):
-    if DEBUG:
-        print "Running shell command %s" % command
-    _exec(command)
-
-
-def _run_dbtoolkit(java_class, args):
-    command_prefix = "java -cp %s" % _dbtoolkit_jar_path()
-    _exec("%s %s %s" % (command_prefix, java_class, args))
-
-
-def _dbtoolkit_jar_path():
-    py_path = __file__
-    jar_path = join(dirname(py_path), "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
-    return jar_path
-
-def _exec(command):
-    proc = subprocess.Popen(args=command, shell=True)
-    return_code = proc.wait()
-    if return_code != 0:
-        print "Error executing command [%s], return code is %d" % (command, return_code)
-        sys.exit(return_code)
-
-
-def _parse_args():
-    parser = OptionParser()
-    parser.add_option("-i", "--input")
-    parser.add_option("-o", "--output")
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    main()
--- a/reverse.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<tool id="compomics_reverse" name="Create Target-Decoy Database" version="0.1.0">
-  <description>Creates a target-decoy database for use with Peptide Shaker</description>
-
-  <requirements>
-  </requirements>
-
-  <command interpreter="python">reverse.py --input='$input' --output='$output'</command>
-
-  <inputs>
-    <param format="fasta" name="input" type="data" label="FASTA Input" />
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="output" />
-  </outputs>
-
-  <help>
-**What it does**
-
-Given an input database, this tool will produce a target-decoy
-database in the format required by PeptideShaker using dbtoolkit.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`.
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker .
-
-  </help>
-</tool>
--- a/searchGUI_mods.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3021 +0,0 @@
-<?xml version="1.0"?>
-<MSModSpecSet
-        xmlns="http://www.ncbi.nlm.nih.gov"
-        xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
-        xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"
-        >
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methylk">0</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of K</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="oxym">1</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of M</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carboxymethylc">2</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxymethyl C</MSModSpec_name>
-        <MSModSpec_monomass>58.005479</MSModSpec_monomass>
-        <MSModSpec_averagemass>58.0361</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>6</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carboxymethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamidomethylc">3</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carbamidomethyl C</MSModSpec_name>
-        <MSModSpec_monomass>57.021464</MSModSpec_monomass>
-        <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>4</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="deamidationkq">4</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>deamidation of N and Q</MSModSpec_name>
-        <MSModSpec_monomass>0.984016</MSModSpec_monomass>
-        <MSModSpec_averagemass>0.9848</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-            <MSModSpec_residues_E>Q</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>7</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Deamidated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="propionamidec">5</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>propionamide C</MSModSpec_name>
-        <MSModSpec_monomass>71.037114</MSModSpec_monomass>
-        <MSModSpec_averagemass>71.0779</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>24</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Propionamide</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphorylations">6</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of S</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphorylationt">7</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of T</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphorylationy">8</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of Y</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermmcleave">9</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnaa">2</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>M cleavage from protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>-131.040485</MSModSpec_monomass>
-        <MSModSpec_averagemass>-131.1961</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>765</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Met-loss</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermacetyl">10</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modn">1</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>acetylation of protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>42.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0367</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>1</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Acetyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermmethyl">11</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modn">1</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermtrimethyl">12</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modn">1</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-methylation of protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>42.046950</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0797</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>37</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methythiold">13</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>beta methythiolation of D</MSModSpec_name>
-        <MSModSpec_monomass>45.987721</MSModSpec_monomass>
-        <MSModSpec_averagemass>46.0916</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>39</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methylthio</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methylq">14</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of Q</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Q</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="trimethylk">15</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-methylation of K</MSModSpec_name>
-        <MSModSpec_monomass>42.046950</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0797</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>37</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methyld">16</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of D</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methyle">17</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of E</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpepmethyl">18</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcp">7</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of peptide c-term</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="trideuteromethyld">19</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-deuteromethylation of D</MSModSpec_name>
-        <MSModSpec_monomass>17.034480</MSModSpec_monomass>
-        <MSModSpec_averagemass>17.0451</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>298</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl:2H(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="trideuteromethyle">20</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-deuteromethylation of E</MSModSpec_name>
-        <MSModSpec_monomass>17.034480</MSModSpec_monomass>
-        <MSModSpec_averagemass>17.0451</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>298</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl:2H(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpeptrideuteromethyl">21</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcp">7</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-deuteromethylation of peptide c-term</MSModSpec_name>
-        <MSModSpec_monomass>17.034480</MSModSpec_monomass>
-        <MSModSpec_averagemass>17.0451</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>298</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl:2H(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="nformylmet">22</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modn">1</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>n-formyl met addition</MSModSpec_name>
-        <MSModSpec_monomass>159.035399</MSModSpec_monomass>
-        <MSModSpec_averagemass>159.2062</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>107</MSModSpec_unimod>
-        <MSModSpec_psi-ms>FormylMet</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="twoamino3oxobutanoicacid">23</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>2-amino-3-oxo-butanoic acid T</MSModSpec_name>
-        <MSModSpec_monomass>-2.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>-2.0159</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>401</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Didehydro</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="acetylk">24</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>acetylation of K</MSModSpec_name>
-        <MSModSpec_monomass>42.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0367</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>1</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Acetyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermamide">25</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcp">7</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>amidation of peptide c-term</MSModSpec_name>
-        <MSModSpec_monomass>-0.984016</MSModSpec_monomass>
-        <MSModSpec_averagemass>-0.9848</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>2</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Amidated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="bmethylthiold">26</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>beta-methylthiolation of D (duplicate of 13)</MSModSpec_name>
-        <MSModSpec_monomass>45.987721</MSModSpec_monomass>
-        <MSModSpec_averagemass>46.0916</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>39</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methylthio</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamidomethylk">27</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxyamidomethylation of K</MSModSpec_name>
-        <MSModSpec_monomass>57.021464</MSModSpec_monomass>
-        <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>4</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamidometylh">28</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxyamidomethylation of H</MSModSpec_name>
-        <MSModSpec_monomass>57.021464</MSModSpec_monomass>
-        <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>4</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamidomethyld">29</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxyamidomethylation of D</MSModSpec_name>
-        <MSModSpec_monomass>57.021464</MSModSpec_monomass>
-        <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>4</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamidomethyle">30</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxyamidomethylation of E</MSModSpec_name>
-        <MSModSpec_monomass>57.021464</MSModSpec_monomass>
-        <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>4</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carbamylk">31</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carbamylation of K</MSModSpec_name>
-        <MSModSpec_monomass>43.005814</MSModSpec_monomass>
-        <MSModSpec_averagemass>43.0247</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>5</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermcarbamyl">32</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carbamylation of n-term peptide</MSModSpec_name>
-        <MSModSpec_monomass>43.005814</MSModSpec_monomass>
-        <MSModSpec_averagemass>43.0247</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>X</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>5</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carbamyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="citrullinationr">33</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>citrullination of R</MSModSpec_name>
-        <MSModSpec_monomass>0.984016</MSModSpec_monomass>
-        <MSModSpec_averagemass>0.9848</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>7</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Deamidated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="cysteicacidc">34</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of C to cysteic acid</MSModSpec_name>
-        <MSModSpec_monomass>47.984744</MSModSpec_monomass>
-        <MSModSpec_averagemass>47.9982</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>345</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trioxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="diiodinationy">35</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>di-iodination of Y</MSModSpec_name>
-        <MSModSpec_monomass>251.793296</MSModSpec_monomass>
-        <MSModSpec_averagemass>251.7931</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>130</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Diiodo</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="dimethylk">36</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>di-methylation of K</MSModSpec_name>
-        <MSModSpec_monomass>28.031300</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0532</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>36</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="dimethylr">37</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>di-methylation of R</MSModSpec_name>
-        <MSModSpec_monomass>28.031300</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0532</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>36</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepdimethyl">38</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>di-methylation of peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>28.031300</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0532</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>36</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="dihydroxyf">39</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of F to dihydroxyphenylalanine</MSModSpec_name>
-        <MSModSpec_monomass>31.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>31.9988</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>F</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>425</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dioxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="thioacetylk">40</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>gammathiopropionylation of K</MSModSpec_name>
-        <MSModSpec_monomass>87.998285</MSModSpec_monomass>
-        <MSModSpec_averagemass>88.1283</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>126</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Thioacyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeptioacetyl">41</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>gammathiopropionylation of peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>87.998285</MSModSpec_monomass>
-        <MSModSpec_averagemass>88.1283</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>126</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Thioacyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="farnesylationc">42</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>farnesylation of C</MSModSpec_name>
-        <MSModSpec_monomass>204.187801</MSModSpec_monomass>
-        <MSModSpec_averagemass>204.3511</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>44</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Farnesyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="formylk">43</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>formylation of K</MSModSpec_name>
-        <MSModSpec_monomass>27.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0101</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>122</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Formyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepformyl">44</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>formylation of peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>27.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0101</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>122</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Formyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="formylkynureninw">45</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of W to formylkynurenin</MSModSpec_name>
-        <MSModSpec_monomass>31.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>31.9988</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>425</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dioxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phef">46</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>fluorophenylalanine</MSModSpec_name>
-        <MSModSpec_monomass>17.990578</MSModSpec_monomass>
-        <MSModSpec_averagemass>17.9905</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>F</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>127</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Fluoro</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="gammacarboxyld">47</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>beta-carboxylation of D</MSModSpec_name>
-        <MSModSpec_monomass>43.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>44.0095</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>299</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carboxy</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="gammacarboxyle">48</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>gamma-carboxylation of E</MSModSpec_name>
-        <MSModSpec_monomass>43.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>44.0095</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>299</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Carboxy</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="geranylgeranylc">49</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>geranyl-geranyl</MSModSpec_name>
-        <MSModSpec_monomass>272.250401</MSModSpec_monomass>
-        <MSModSpec_averagemass>272.4681</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>48</MSModSpec_unimod>
-        <MSModSpec_psi-ms>GeranylGeranyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepglucuronylg">50</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnaa">2</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>glucuronylation of protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>176.032088</MSModSpec_monomass>
-        <MSModSpec_averagemass>176.1241</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>G</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>54</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Glucuronyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="glutathionec">51</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>glutathione disulfide</MSModSpec_name>
-        <MSModSpec_monomass>305.068156</MSModSpec_monomass>
-        <MSModSpec_averagemass>305.3076</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>55</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Glutathione</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="glyglyk">52</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>ubiquitinylation residue</MSModSpec_name>
-        <MSModSpec_monomass>114.042927</MSModSpec_monomass>
-        <MSModSpec_averagemass>114.1026</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>121</MSModSpec_unimod>
-        <MSModSpec_psi-ms>GlyGly</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="guanidinationk">53</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>guanidination of K</MSModSpec_name>
-        <MSModSpec_monomass>42.021798</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0400</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>52</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Guanidinyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="his2asnh">54</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of H to N</MSModSpec_name>
-        <MSModSpec_monomass>-23.015984</MSModSpec_monomass>
-        <MSModSpec_averagemass>-23.0366</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>348</MSModSpec_unimod>
-        <MSModSpec_psi-ms>His-&gt;Asn</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="his2asph">55</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of H to D</MSModSpec_name>
-        <MSModSpec_monomass>-22.031969</MSModSpec_monomass>
-        <MSModSpec_averagemass>-22.0519</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>349</MSModSpec_unimod>
-        <MSModSpec_psi-ms>His-&gt;Asp</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpephsem">56</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcpaa">8</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>homoserine</MSModSpec_name>
-        <MSModSpec_monomass>-29.992806</MSModSpec_monomass>
-        <MSModSpec_averagemass>-30.0922</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>10</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Met-&gt;Hse</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpephselactm">57</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcpaa">8</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>homoserine lactone</MSModSpec_name>
-        <MSModSpec_monomass>-48.003371</MSModSpec_monomass>
-        <MSModSpec_averagemass>-48.1075</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>11</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Met-&gt;Hsl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxykynureninw">58</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of W to hydroxykynurenin</MSModSpec_name>
-        <MSModSpec_monomass>19.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>19.9881</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>350</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trp-&gt;Hydroxykynurenin</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationd">59</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of D</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationk">60</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of K</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationn">61</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of N</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationp">62</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of P</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>P</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationf">63</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of F</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>F</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hydroxylationy">64</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>hydroxylation of Y</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iodinationy">65</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iodination of Y</MSModSpec_name>
-        <MSModSpec_monomass>125.896648</MSModSpec_monomass>
-        <MSModSpec_averagemass>125.8965</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>129</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Iodo</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="kynureninw">66</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of W to kynurenin</MSModSpec_name>
-        <MSModSpec_monomass>3.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>3.9887</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>351</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trp-&gt;Kynurenin</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="lipoylk">67</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>lipoyl K</MSModSpec_name>
-        <MSModSpec_monomass>188.032956</MSModSpec_monomass>
-        <MSModSpec_averagemass>188.3103</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>42</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Lipoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpepmeester">68</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modcp">7</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl ester of peptide c-term (duplicate of 18)</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="meesterd">69</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl ester of D</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="meestere">70</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl ester of E (duplicate of 17)</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="meesters">71</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl ester of S</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="meestery">72</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl ester of Y</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methylc">73</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl C</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methylh">74</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl H</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methyln">75</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl N</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepmethyl">76</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methylation of peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="methylr">77</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>methyl R</MSModSpec_name>
-        <MSModSpec_monomass>14.015650</MSModSpec_monomass>
-        <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>34</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepmyristoyeylationg">78</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnaa">2</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>myristoleylation of G</MSModSpec_name>
-        <MSModSpec_monomass>208.182715</MSModSpec_monomass>
-        <MSModSpec_averagemass>208.3398</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>G</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>134</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Myristoleyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepmyristoyl4hg">79</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnaa">2</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>myristoyl-4H of G</MSModSpec_name>
-        <MSModSpec_monomass>206.167065</MSModSpec_monomass>
-        <MSModSpec_averagemass>206.3239</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>G</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>135</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Myristoyl+Delta:H(-4)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpepmyristoylationg">80</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>myristoylation of peptide n-term G</MSModSpec_name>
-        <MSModSpec_monomass>210.198366</MSModSpec_monomass>
-        <MSModSpec_averagemass>210.3556</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>G</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>45</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Myristoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="myristoylationk">81</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>myristoylation of K</MSModSpec_name>
-        <MSModSpec_monomass>210.198366</MSModSpec_monomass>
-        <MSModSpec_averagemass>210.3556</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>45</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Myristoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermformyl">82</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modn">1</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>formylation of protein n-term</MSModSpec_name>
-        <MSModSpec_monomass>27.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>28.0101</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>122</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Formyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="nemc">83</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>NEM C</MSModSpec_name>
-        <MSModSpec_monomass>125.047679</MSModSpec_monomass>
-        <MSModSpec_averagemass>125.1253</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>108</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Nethylmaleimide</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="nipcam">84</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>NIPCAM</MSModSpec_name>
-        <MSModSpec_monomass>99.068414</MSModSpec_monomass>
-        <MSModSpec_averagemass>99.1311</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>17</MSModSpec_unimod>
-        <MSModSpec_psi-ms>NIPCAM</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="nitrow">85</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of W to nitro</MSModSpec_name>
-        <MSModSpec_monomass>44.985078</MSModSpec_monomass>
-        <MSModSpec_averagemass>44.9976</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>354</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Nitro</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="nitroy">86</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of Y to nitro</MSModSpec_name>
-        <MSModSpec_monomass>44.985078</MSModSpec_monomass>
-        <MSModSpec_averagemass>44.9976</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>354</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Nitro</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpepo18">87</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>O18 on peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>2.004246</MSModSpec_monomass>
-        <MSModSpec_averagemass>1.9998</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>258</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:18O(1)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ctermpepdio18">88</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>di-O18 on peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>4.00849</MSModSpec_monomass>
-        <MSModSpec_averagemass>3.9995</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>193</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:18O(2)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="oxyh">89</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of H</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="oxyw">90</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of W</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ppantetheines">91</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphopantetheine S</MSModSpec_name>
-        <MSModSpec_monomass>340.085794</MSModSpec_monomass>
-        <MSModSpec_averagemass>340.3330</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>49</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phosphopantetheine</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="palmitoylationc">92</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoylation of C</MSModSpec_name>
-        <MSModSpec_monomass>238.229666</MSModSpec_monomass>
-        <MSModSpec_averagemass>238.4088</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>47</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="palmitoylationk">93</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoylation of K</MSModSpec_name>
-        <MSModSpec_monomass>238.229666</MSModSpec_monomass>
-        <MSModSpec_averagemass>238.4088</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>47</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="palmitoylations">94</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoylation of S</MSModSpec_name>
-        <MSModSpec_monomass>238.229666</MSModSpec_monomass>
-        <MSModSpec_averagemass>238.4088</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>47</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="palmitoylationt">95</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoylation of T</MSModSpec_name>
-        <MSModSpec_monomass>238.229666</MSModSpec_monomass>
-        <MSModSpec_averagemass>238.4088</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>47</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phospholosss">96</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of S with prompt loss</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phospholosst">97</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of T with prompt loss</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phospholossy">98</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with prompt loss on Y</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoneutrallossc">99</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with neutral loss on C</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>97.976896</MSMassSet_monomass>
-                <MSMassSet_averagemass>97.9952</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoneutrallossd">100</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with neutral loss on D</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>D</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>97.976896</MSMassSet_monomass>
-                <MSMassSet_averagemass>97.9952</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoneutrallossh">101</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with neutral loss on H</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>97.976896</MSMassSet_monomass>
-                <MSMassSet_averagemass>97.9952</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="propionylk">102</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>propionyl light K</MSModSpec_name>
-        <MSModSpec_monomass>56.026215</MSModSpec_monomass>
-        <MSModSpec_averagemass>56.0633</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>58</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Propionyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppropionyl">103</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>propionyl light on peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>56.026215</MSModSpec_monomass>
-        <MSModSpec_averagemass>56.0633</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>58</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Propionyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="propionylheavyk">104</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>propionyl heavy K</MSModSpec_name>
-        <MSModSpec_monomass>59.036279</MSModSpec_monomass>
-        <MSModSpec_averagemass>59.0412</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>59</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Propionyl:13C(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppropionylheavy">105</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>propionyl heavy peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>59.036279</MSModSpec_monomass>
-        <MSModSpec_averagemass>59.0412</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>59</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Propionyl:13C(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="pyridylk">106</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>pyridyl K</MSModSpec_name>
-        <MSModSpec_monomass>119.037114</MSModSpec_monomass>
-        <MSModSpec_averagemass>119.1207</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>25</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Pyridylacetyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppyridyl">107</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>pyridyl peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>119.037114</MSModSpec_monomass>
-        <MSModSpec_averagemass>119.1207</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>25</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Pyridylacetyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppyrocmc">108</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>pyro-cmC</MSModSpec_name>
-        <MSModSpec_monomass>-17.026549</MSModSpec_monomass>
-        <MSModSpec_averagemass>-17.0305</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>385</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Ammonia-loss</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppyroe">109</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>pyro-glu from n-term E</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>E</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>27</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Glu-&gt;pyro-Glu</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeppyroq">110</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>pyro-glu from n-term Q</MSModSpec_name>
-        <MSModSpec_monomass>-17.026549</MSModSpec_monomass>
-        <MSModSpec_averagemass>-17.0305</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Q</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>385</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Ammonia-loss</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="pyroglutamicp">111</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of P to pyroglutamic acid</MSModSpec_name>
-        <MSModSpec_monomass>13.979265</MSModSpec_monomass>
-        <MSModSpec_averagemass>13.9835</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>P</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>359</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Pro-&gt;pyro-Glu</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="spyridylethylc">112</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>s-pyridylethylation of C</MSModSpec_name>
-        <MSModSpec_monomass>105.057849</MSModSpec_monomass>
-        <MSModSpec_averagemass>105.1372</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>31</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Pyridylethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="semetm">113</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>SeMet</MSModSpec_name>
-        <MSModSpec_monomass>47.944449</MSModSpec_monomass>
-        <MSModSpec_averagemass>46.8950</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>162</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Delta:S(-1)Se(1)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="sulfationy">114</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>sulfation of Y</MSModSpec_name>
-        <MSModSpec_monomass>79.956815</MSModSpec_monomass>
-        <MSModSpec_averagemass>80.0632</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>40</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Sulfo</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="suphonem">115</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>sulphone of M</MSModSpec_name>
-        <MSModSpec_monomass>31.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>31.9988</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>M</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>425</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dioxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="triiodinationy">116</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-iodination of Y</MSModSpec_name>
-        <MSModSpec_monomass>377.689944</MSModSpec_monomass>
-        <MSModSpec_averagemass>377.6896</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>131</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Triiodo</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="trimethylationr">117</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>tri-methylation of R</MSModSpec_name>
-        <MSModSpec_monomass>42.046950</MSModSpec_monomass>
-        <MSModSpec_averagemass>42.0797</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>37</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Trimethyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="ntermpeptripalmitatec">118</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>n-acyl diglyceride cysteine</MSModSpec_name>
-        <MSModSpec_monomass>788.725777</MSModSpec_monomass>
-        <MSModSpec_averagemass>789.3049</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>51</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Tripalmitate</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="icatlight">129</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>ICAT light</MSModSpec_name>
-        <MSModSpec_monomass>227.126991</MSModSpec_monomass>
-        <MSModSpec_averagemass>227.2603</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>105</MSModSpec_unimod>
-        <MSModSpec_psi-ms>ICAT-C</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="icatheavy">130</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>ICAT heavy</MSModSpec_name>
-        <MSModSpec_monomass>236.157185</MSModSpec_monomass>
-        <MSModSpec_averagemass>236.1942</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>106</MSModSpec_unimod>
-        <MSModSpec_psi-ms>ICAT-C:13C(9)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="camthiopropanoylk">131</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>CAMthiopropanoyl K</MSModSpec_name>
-        <MSModSpec_monomass>145.019749</MSModSpec_monomass>
-        <MSModSpec_averagemass>145.1796</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>293</MSModSpec_unimod>
-        <MSModSpec_psi-ms>CAMthiopropanoyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoneutrallosss">132</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with neutral loss on S</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>97.976896</MSMassSet_monomass>
-                <MSMassSet_averagemass>97.9952</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoneutrallosst">133</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation with neutral loss on T</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>97.976896</MSMassSet_monomass>
-                <MSMassSet_averagemass>97.9952</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoetdlosss">134</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of S with ETD loss</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>2.016</MSMassSet_monomass>
-                <MSMassSet_averagemass>2.016</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="phosphoetdlosst">135</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of T with ETD loss</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_neutralloss>
-            <MSMassSet>
-                <MSMassSet_monomass>2.016</MSMassSet_monomass>
-                <MSMassSet_averagemass>2.016</MSMassSet_averagemass>
-                <MSMassSet_n15mass>0</MSMassSet_n15mass>
-            </MSMassSet>
-        </MSModSpec_neutralloss>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="arg-13c6">136</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>heavy arginine-13C6</MSModSpec_name>
-        <MSModSpec_monomass>6.020129</MSModSpec_monomass>
-        <MSModSpec_averagemass>5.9559</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>188</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:13C(6)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="arg-13c6-15n4">137</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>heavy arginine-13C6-15N4</MSModSpec_name>
-        <MSModSpec_monomass>10.008269</MSModSpec_monomass>
-        <MSModSpec_averagemass>9.9296</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>267</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:13C(6)15N(4)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="lys-13c6">138</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>heavy lysine-13C6</MSModSpec_name>
-        <MSModSpec_monomass>6.020129</MSModSpec_monomass>
-        <MSModSpec_averagemass>5.9559</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>188</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:13C(6)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="oxy18">139</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnpaa">6</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>PNGasF in O18 water</MSModSpec_name>
-        <MSModSpec_monomass>2.988261</MSModSpec_monomass>
-        <MSModSpec_averagemass>2.9845</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>366</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Deamidated:18O(1)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="beta-elim-s">140</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>beta elimination of S</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="beta-elim-t">141</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>beta elimination of T</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="sulfinicacid">162</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of C to sulfinic acid</MSModSpec_name>
-        <MSModSpec_monomass>31.989829</MSModSpec_monomass>
-        <MSModSpec_averagemass>31.9988</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>425</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dioxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="arg2orn">163</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>arginine to ornithine</MSModSpec_name>
-        <MSModSpec_monomass>-42.021798</MSModSpec_monomass>
-        <MSModSpec_averagemass>-42.0400</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>R</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>372</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Arg-&gt;Orn</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="dehydro">164</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>dehydro of S and T</MSModSpec_name>
-        <MSModSpec_monomass>-18.010565</MSModSpec_monomass>
-        <MSModSpec_averagemass>-18.0153</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>23</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dehydrated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="carboxykynurenin">165</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxykynurenin of W</MSModSpec_name>
-        <MSModSpec_monomass>47.98474389</MSModSpec_monomass>
-        <MSModSpec_averagemass>47.9979141</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>W</MSModSpec_residues_E>
-        </MSModSpec_residues>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="sumoylation">166</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>sumoylation of K</MSModSpec_name>
-        <MSModSpec_monomass>484.2282</MSModSpec_monomass>
-        <MSModSpec_averagemass>0</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>846</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ114nterm">167</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ114 on nterm</MSModSpec_name>
-        <MSModSpec_monomass>144.105918</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1680</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>532</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex114</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ114K">168</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ114 on K</MSModSpec_name>
-        <MSModSpec_monomass>144.105918</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1680</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>532</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex114</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ114Y">169</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ114 on Y</MSModSpec_name>
-        <MSModSpec_monomass>144.105918</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1680</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>532</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex114</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ115nterm">170</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ115 on nterm</MSModSpec_name>
-        <MSModSpec_monomass>144.099599</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1688</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>533</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex115</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ115K">171</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ115 on K</MSModSpec_name>
-        <MSModSpec_monomass>144.099599</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1688</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>533</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex115</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ115Y">172</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ115 on Y</MSModSpec_name>
-        <MSModSpec_monomass>144.099599</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1688</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>533</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex115</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ116nterm">173</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ116 on nterm</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ116K">174</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ116 on K</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ116Y">175</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ116 on Y</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ117nterm">176</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ117 on nterm</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ117K">177</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ117 on K</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="iTRAQ117Y">178</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ117 on Y</MSModSpec_name>
-        <MSModSpec_monomass>144.102063</MSModSpec_monomass>
-        <MSModSpec_averagemass>144.1544</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>214</MSModSpec_unimod>
-        <MSModSpec_psi-ms>iTRAQ4plex</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mmts">179</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>MMTS on C</MSModSpec_name>
-        <MSModSpec_monomass>45.987721</MSModSpec_monomass>
-        <MSModSpec_averagemass>46.0916</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>39</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Methylthio</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="lys-2H4">180</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>heavy lysine - 2H4</MSModSpec_name>
-        <MSModSpec_monomass>4.025107</MSModSpec_monomass>
-        <MSModSpec_averagemass>4.0246</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>481</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:2H(4)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="lys-13C615N2">181</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>heavy lysine - 13C6 15N2</MSModSpec_name>
-        <MSModSpec_monomass>8.014199</MSModSpec_monomass>
-        <MSModSpec_averagemass>7.9427</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>259</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:13C(6)15N(2)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hexNAcN">182</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Asparagine HexNAc</MSModSpec_name>
-        <MSModSpec_monomass>203.079373</MSModSpec_monomass>
-        <MSModSpec_averagemass>203.1925</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>43</MSModSpec_unimod>
-        <MSModSpec_psi-ms>HexNAc</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="dHexHexNAcN">183</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Asparagine dHexHexNAc</MSModSpec_name>
-        <MSModSpec_monomass>349.137281</MSModSpec_monomass>
-        <MSModSpec_averagemass>349.3337</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>142</MSModSpec_unimod>
-        <MSModSpec_psi-ms>HexNAc(1)dHex(1)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hexNAcS">184</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Serine HexNAc</MSModSpec_name>
-        <MSModSpec_monomass>203.079373</MSModSpec_monomass>
-        <MSModSpec_averagemass>203.1925</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>43</MSModSpec_unimod>
-        <MSModSpec_psi-ms>HexNAc</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="hexNAcT">185</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Threonine HexNAc</MSModSpec_name>
-        <MSModSpec_monomass>203.079373</MSModSpec_monomass>
-        <MSModSpec_averagemass>203.1925</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>43</MSModSpec_unimod>
-        <MSModSpec_psi-ms>HexNAc</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod186">186</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoleyl of S</MSModSpec_name>
-        <MSModSpec_monomass>236.214016</MSModSpec_monomass>
-        <MSModSpec_averagemass>236.3929</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>S</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>431</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoleyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod187">187</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoleyl of C</MSModSpec_name>
-        <MSModSpec_monomass>236.214016</MSModSpec_monomass>
-        <MSModSpec_averagemass>236.3929</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>431</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoleyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod188">188</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>palmitoleyl of T</MSModSpec_name>
-        <MSModSpec_monomass>236.214016</MSModSpec_monomass>
-        <MSModSpec_averagemass>236.3929</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>T</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>431</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Palmitoleyl</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod189">189</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>CHD2-di-methylation of K</MSModSpec_name>
-        <MSModSpec_monomass>32.056407</MSModSpec_monomass>
-        <MSModSpec_averagemass>32.0778</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>199</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dimethyl:2H(4)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod190">190</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>CHD2-di-methylation of peptide n-term</MSModSpec_name>
-        <MSModSpec_monomass>32.056407</MSModSpec_monomass>
-        <MSModSpec_averagemass>32.0778</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>199</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Dimethyl:2H(4)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod191">191</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Maleimide-PEO2-Biotin of C</MSModSpec_name>
-        <MSModSpec_monomass>525.225719</MSModSpec_monomass>
-        <MSModSpec_averagemass>525.6183</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>522</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Maleimide-PEO2-Biotin</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod192">192</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>phosphorylation of H</MSModSpec_name>
-        <MSModSpec_monomass>79.966331</MSModSpec_monomass>
-        <MSModSpec_averagemass>79.9799</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>H</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>21</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Phospho</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod193">193</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of C</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod194">194</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>oxidation of Y (duplicate of 64)</MSModSpec_name>
-        <MSModSpec_monomass>15.994915</MSModSpec_monomass>
-        <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>35</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod195">195</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>Uniblue A on K</MSModSpec_name>
-        <MSModSpec_monomass>484.039891</MSModSpec_monomass>
-        <MSModSpec_averagemass>484.5016</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod196">196</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>deamidation of N</MSModSpec_name>
-        <MSModSpec_monomass>0.984016</MSModSpec_monomass>
-        <MSModSpec_averagemass>0.9848</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>N</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>7</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Deamidated</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod197">197</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>trideuteration of L (SILAC)</MSModSpec_name>
-        <MSModSpec_monomass>3.018830</MSModSpec_monomass>
-        <MSModSpec_averagemass>3.0185</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>L</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>262</MSModSpec_unimod>
-        <MSModSpec_psi-ms>Label:2H(3)</MSModSpec_psi-ms>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod198">198</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>TMT duplex on K</MSModSpec_name>
-        <MSModSpec_monomass>225.155833</MSModSpec_monomass>
-        <MSModSpec_averagemass>225.2921</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>738</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod199">199</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>TMT duplex on n-term peptide</MSModSpec_name>
-        <MSModSpec_monomass>225.155833</MSModSpec_monomass>
-        <MSModSpec_averagemass>225.2921</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>X</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>738</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod198">198</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>TMT 6-plex on K</MSModSpec_name>
-        <MSModSpec_monomass>229.162932</MSModSpec_monomass>
-        <MSModSpec_averagemass>229.2634</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>738</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod199">199</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>TMT 6-plex on n-term peptide</MSModSpec_name>
-        <MSModSpec_monomass>229.162932</MSModSpec_monomass>
-        <MSModSpec_averagemass>229.2634</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>X</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>738</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod200">200</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(7)15N(1) on nterm</MSModSpec_name>
-        <MSModSpec_monomass>304.205360</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3074</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>730</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod201">201</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(7)15N(1) on K</MSModSpec_name>
-        <MSModSpec_monomass>304.205360</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3074</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>730</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod202">202</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(7)15N(1) on Y</MSModSpec_name>
-        <MSModSpec_monomass>304.205360</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3074</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>730</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod203">203</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modnp">5</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on nterm</MSModSpec_name>
-        <MSModSpec_monomass>304.199040</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_unimod>731</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod204">204</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on K</MSModSpec_name>
-        <MSModSpec_monomass>304.199040</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>K</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>731</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod205">205</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on Y</MSModSpec_name>
-        <MSModSpec_monomass>304.199040</MSModSpec_monomass>
-        <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>Y</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>731</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod206">206</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>selenocysteine</MSModSpec_name>
-        <MSModSpec_monomass>47.944449</MSModSpec_monomass>
-        <MSModSpec_averagemass>46.8950</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-        <MSModSpec_unimod>162</MSModSpec_unimod>
-    </MSModSpec>
-    <MSModSpec>
-        <MSModSpec_mod>
-            <MSMod value="mod207">207</MSMod>
-        </MSModSpec_mod>
-        <MSModSpec_type>
-            <MSModType value="modaa">0</MSModType>
-        </MSModSpec_type>
-        <MSModSpec_name>carboxymethylated selenocysteine</MSModSpec_name>
-        <MSModSpec_monomass>105.949928</MSModSpec_monomass>
-        <MSModSpec_averagemass>104.9311</MSModSpec_averagemass>
-        <MSModSpec_n15mass>0</MSModSpec_n15mass>
-        <MSModSpec_residues>
-            <MSModSpec_residues_E>C</MSModSpec_residues_E>
-        </MSModSpec_residues>
-    </MSModSpec>
-</MSModSpecSet>
--- a/searchGUI_usermods.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,455 +0,0 @@
-<?xml version="1.0"?>
-<MSModSpecSet
-xmlns="http://www.ncbi.nlm.nih.gov"
-xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
-xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"
->
-
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod1">119</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modnp">5</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>dimethyl 2d n-terminus</MSModSpec_name>
-		<MSModSpec_monomass>32.0564</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod2">120</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>dimethyl 2d k</MSModSpec_name>
-		<MSModSpec_monomass>32.0564</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>K</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod3">121</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>gtp desthiobiotinc12</MSModSpec_name>
-		<MSModSpec_monomass>196.121178</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>K</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod4">122</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>gtp desthiobiotinc13</MSModSpec_name>
-		<MSModSpec_monomass>202.141307</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>K</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod5">123</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 5</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod6">124</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 6</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod7">125</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 7</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod8">126</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 8</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod9">127</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 9</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod10">128</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 10</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod11">142</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 11</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod12">143</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 12</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod13">144</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 13</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod14">145</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 14</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod15">146</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 15</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod16">147</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 16</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod17">148</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 17</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod18">149</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 18</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod19">150</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 19</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod20">151</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 20</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod21">152</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 21</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod22">153</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 22</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod23">154</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 23</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod24">155</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 24</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod25">156</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 25</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod26">157</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 26</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod27">158</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 27</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod28">159</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 28</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod29">160</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 29</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-	<MSModSpec>
-		<MSModSpec_mod>
-			<MSMod value="usermod30">161</MSMod>
-		</MSModSpec_mod>
-		<MSModSpec_type>
-			<MSModType value="modaa">0</MSModType>
-		</MSModSpec_type>
-		<MSModSpec_name>User modification 30</MSModSpec_name>
-		<MSModSpec_monomass>0</MSModSpec_monomass>
-		<MSModSpec_averagemass>0</MSModSpec_averagemass>
-		<MSModSpec_n15mass>0</MSModSpec_n15mass>
-		<MSModSpec_residues>
-			<MSModSpec_residues_E>X</MSModSpec_residues_E>
-		</MSModSpec_residues>
-	</MSModSpec>
-</MSModSpecSet>
\ No newline at end of file
--- a/searchgui_mods.loc	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-methylation of k
-oxidation of m
-carboxymethyl c
-carbamidomethyl c
-deamidation of n and q
-propionamide c
-phosphorylation of s
-phosphorylation of t
-phosphorylation of y
-m cleavage from protein n-term
-acetylation of protein n-term
-methylation of protein n-term
-tri-methylation of protein n-term
-beta methythiolation of d
-methylation of q
-tri-methylation of k
-methylation of d
-methylation of e
-methylation of peptide c-term
-tri-deuteromethylation of d
-tri-deuteromethylation of e
-tri-deuteromethylation of peptide c-term
-n-formyl met addition
-2-amino-3-oxo-butanoic acid t
-acetylation of k
-amidation of peptide c-term
-beta-methylthiolation of d (duplicate of 13)
-carboxyamidomethylation of k
-carboxyamidomethylation of h
-carboxyamidomethylation of d
-carboxyamidomethylation of e
-carbamylation of k
-carbamylation of n-term peptide
-citrullination of r
-oxidation of c to cysteic acid
-di-iodination of y
-di-methylation of k
-di-methylation of r
-di-methylation of peptide n-term
-oxidation of f to dihydroxyphenylalanine
-gammathiopropionylation of k
-gammathiopropionylation of peptide n-term
-farnesylation of c
-formylation of k
-formylation of peptide n-term
-oxidation of w to formylkynurenin
-fluorophenylalanine
-beta-carboxylation of d
-gamma-carboxylation of e
-geranyl-geranyl
-glucuronylation of protein n-term
-glutathione disulfide
-ubiquitinylation residue
-guanidination of k
-oxidation of h to n
-oxidation of h to d
-homoserine
-homoserine lactone
-oxidation of w to hydroxykynurenin
-hydroxylation of d
-hydroxylation of k
-hydroxylation of n
-hydroxylation of p
-hydroxylation of f
-hydroxylation of y
-iodination of y
-oxidation of w to kynurenin
-lipoyl k
-methyl ester of peptide c-term (duplicate of 18)
-methyl ester of d
-methyl ester of e (duplicate of 17)
-methyl ester of s
-methyl ester of y
-methyl c
-methyl h
-methyl n
-methylation of peptide n-term
-methyl r
-myristoleylation of g
-myristoyl-4h of g
-myristoylation of peptide n-term g
-myristoylation of k
-formylation of protein n-term
-nem c
-nipcam
-oxidation of w to nitro
-oxidation of y to nitro
-o18 on peptide n-term
-di-o18 on peptide n-term
-oxidation of h
-oxidation of w
-phosphopantetheine s
-palmitoylation of c
-palmitoylation of k
-palmitoylation of s
-palmitoylation of t
-phosphorylation of s with prompt loss
-phosphorylation of t with prompt loss
-phosphorylation with prompt loss on y
-phosphorylation with neutral loss on c
-phosphorylation with neutral loss on d
-phosphorylation with neutral loss on h
-propionyl light k
-propionyl light on peptide n-term
-propionyl heavy k
-propionyl heavy peptide n-term
-pyridyl k
-pyridyl peptide n-term
-pyro-cmc
-pyro-glu from n-term e
-pyro-glu from n-term q
-oxidation of p to pyroglutamic acid
-s-pyridylethylation of c
-semet
-sulfation of y
-sulphone of m
-tri-iodination of y
-tri-methylation of r
-n-acyl diglyceride cysteine
-icat light
-icat heavy
-camthiopropanoyl k
-phosphorylation with neutral loss on s
-phosphorylation with neutral loss on t
-phosphorylation of s with etd loss
-phosphorylation of t with etd loss
-heavy arginine-13c6
-heavy arginine-13c6-15n4
-heavy lysine-13c6
-pngasf in o18 water
-beta elimination of s
-beta elimination of t
-oxidation of c to sulfinic acid
-arginine to ornithine
-dehydro of s and t
-carboxykynurenin of w
-sumoylation of k
-itraq114 on nterm
-itraq114 on k
-itraq114 on y
-itraq115 on nterm
-itraq115 on k
-itraq115 on y
-itraq116 on nterm
-itraq116 on k
-itraq116 on y
-itraq117 on nterm
-itraq117 on k
-itraq117 on y
-mmts on c
-heavy lysine - 2h4
-heavy lysine - 13c6 15n2
-asparagine hexnac
-asparagine dhexhexnac
-serine hexnac
-threonine hexnac
-palmitoleyl of s
-palmitoleyl of c
-palmitoleyl of t
-chd2-di-methylation of k
-chd2-di-methylation of peptide n-term
-maleimide-peo2-biotin of c
-phosphorylation of h
-oxidation of c
-oxidation of y (duplicate of 64)
-uniblue a on k
-deamidation of n
-trideuteration of l (silac)
-tmt duplex on k
-tmt duplex on n-term peptide
-tmt 6-plex on k
-tmt 6-plex on n-term peptide
-itraq8plex:13c(7)15n(1) on nterm
-itraq8plex:13c(7)15n(1) on k
-itraq8plex:13c(7)15n(1) on y
-itraq8plex:13c(6)15n(2) on nterm
-itraq8plex:13c(6)15n(2) on k
-itraq8plex:13c(6)15n(2) on y
-selenocysteine
-carboxymethylated selenocysteine
-dimethyl 2d n-terminus
-dimethyl 2d k
-gtp desthiobiotinc12
-gtp desthiobiotinc13
-user modification 5
-user modification 6
-user modification 7
-user modification 8
-user modification 9
-user modification 10
-user modification 11
-user modification 12
-user modification 13
-user modification 14
-user modification 15
-user modification 16
-user modification 17
-user modification 18
-user modification 19
-user modification 20
-user modification 21
-user modification 22
-user modification 23
-user modification 24
-user modification 25
-user modification 26
-user modification 27
-user modification 28
-user modification 29
-user modification 30
--- a/searchgui_mods.loc.sample	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-methylation of k
-oxidation of m
-carboxymethyl c
-carbamidomethyl c
-deamidation of n and q
-propionamide c
-phosphorylation of s
-phosphorylation of t
-phosphorylation of y
-m cleavage from protein n-term
-acetylation of protein n-term
-methylation of protein n-term
-tri-methylation of protein n-term
-beta methythiolation of d
-methylation of q
-tri-methylation of k
-methylation of d
-methylation of e
-methylation of peptide c-term
-tri-deuteromethylation of d
-tri-deuteromethylation of e
-tri-deuteromethylation of peptide c-term
-n-formyl met addition
-2-amino-3-oxo-butanoic acid t
-acetylation of k
-amidation of peptide c-term
-beta-methylthiolation of d (duplicate of 13)
-carboxyamidomethylation of k
-carboxyamidomethylation of h
-carboxyamidomethylation of d
-carboxyamidomethylation of e
-carbamylation of k
-carbamylation of n-term peptide
-citrullination of r
-oxidation of c to cysteic acid
-di-iodination of y
-di-methylation of k
-di-methylation of r
-di-methylation of peptide n-term
-oxidation of f to dihydroxyphenylalanine
-gammathiopropionylation of k
-gammathiopropionylation of peptide n-term
-farnesylation of c
-formylation of k
-formylation of peptide n-term
-oxidation of w to formylkynurenin
-fluorophenylalanine
-beta-carboxylation of d
-gamma-carboxylation of e
-geranyl-geranyl
-glucuronylation of protein n-term
-glutathione disulfide
-ubiquitinylation residue
-guanidination of k
-oxidation of h to n
-oxidation of h to d
-homoserine
-homoserine lactone
-oxidation of w to hydroxykynurenin
-hydroxylation of d
-hydroxylation of k
-hydroxylation of n
-hydroxylation of p
-hydroxylation of f
-hydroxylation of y
-iodination of y
-oxidation of w to kynurenin
-lipoyl k
-methyl ester of peptide c-term (duplicate of 18)
-methyl ester of d
-methyl ester of e (duplicate of 17)
-methyl ester of s
-methyl ester of y
-methyl c
-methyl h
-methyl n
-methylation of peptide n-term
-methyl r
-myristoleylation of g
-myristoyl-4h of g
-myristoylation of peptide n-term g
-myristoylation of k
-formylation of protein n-term
-nem c
-nipcam
-oxidation of w to nitro
-oxidation of y to nitro
-o18 on peptide n-term
-di-o18 on peptide n-term
-oxidation of h
-oxidation of w
-phosphopantetheine s
-palmitoylation of c
-palmitoylation of k
-palmitoylation of s
-palmitoylation of t
-phosphorylation of s with prompt loss
-phosphorylation of t with prompt loss
-phosphorylation with prompt loss on y
-phosphorylation with neutral loss on c
-phosphorylation with neutral loss on d
-phosphorylation with neutral loss on h
-propionyl light k
-propionyl light on peptide n-term
-propionyl heavy k
-propionyl heavy peptide n-term
-pyridyl k
-pyridyl peptide n-term
-pyro-cmc
-pyro-glu from n-term e
-pyro-glu from n-term q
-oxidation of p to pyroglutamic acid
-s-pyridylethylation of c
-semet
-sulfation of y
-sulphone of m
-tri-iodination of y
-tri-methylation of r
-n-acyl diglyceride cysteine
-icat light
-icat heavy
-camthiopropanoyl k
-phosphorylation with neutral loss on s
-phosphorylation with neutral loss on t
-phosphorylation of s with etd loss
-phosphorylation of t with etd loss
-heavy arginine-13c6
-heavy arginine-13c6-15n4
-heavy lysine-13c6
-pngasf in o18 water
-beta elimination of s
-beta elimination of t
-oxidation of c to sulfinic acid
-arginine to ornithine
-dehydro of s and t
-carboxykynurenin of w
-sumoylation of k
-itraq114 on nterm
-itraq114 on k
-itraq114 on y
-itraq115 on nterm
-itraq115 on k
-itraq115 on y
-itraq116 on nterm
-itraq116 on k
-itraq116 on y
-itraq117 on nterm
-itraq117 on k
-itraq117 on y
-mmts on c
-heavy lysine - 2h4
-heavy lysine - 13c6 15n2
-asparagine hexnac
-asparagine dhexhexnac
-serine hexnac
-threonine hexnac
-palmitoleyl of s
-palmitoleyl of c
-palmitoleyl of t
-chd2-di-methylation of k
-chd2-di-methylation of peptide n-term
-maleimide-peo2-biotin of c
-phosphorylation of h
-oxidation of c
-oxidation of y (duplicate of 64)
-uniblue a on k
-deamidation of n
-trideuteration of l (silac)
-tmt duplex on k
-tmt duplex on n-term peptide
-tmt 6-plex on k
-tmt 6-plex on n-term peptide
-itraq8plex:13c(7)15n(1) on nterm
-itraq8plex:13c(7)15n(1) on k
-itraq8plex:13c(7)15n(1) on y
-itraq8plex:13c(6)15n(2) on nterm
-itraq8plex:13c(6)15n(2) on k
-itraq8plex:13c(6)15n(2) on y
-selenocysteine
-carboxymethylated selenocysteine
-dimethyl 2d n-terminus
-dimethyl 2d k
-gtp desthiobiotinc12
-gtp desthiobiotinc13
-user modification 5
-user modification 6
-user modification 7
-user modification 8
-user modification 9
-user modification 10
-user modification 11
-user modification 12
-user modification 13
-user modification 14
-user modification 15
-user modification 16
-user modification 17
-user modification 18
-user modification 19
-user modification 20
-user modification 21
-user modification 22
-user modification 23
-user modification 24
-user modification 25
-user modification 26
-user modification 27
-user modification 28
-user modification 29
-user modification 30
Binary file test-data/._tinyoutput.cps has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tinydb.fasta	Wed Jun 25 11:49:19 2014 -0400
@@ -0,0 +1,24 @@
+>cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68
+LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV
+>cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14
+DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ
+>cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32
+KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR
+>cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10
+SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20
+YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL
+>cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0
+MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ
+>cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87
+MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN
+>cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16
+FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
Binary file test-data/tinyoutput.cps has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tinyspectra.mgf	Wed Jun 25 11:49:19 2014 -0400
@@ -0,0 +1,6153 @@
+BEGIN IONS
+TITLE= Cmpd 636, +MSn(730.3981), 66.9 min
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+END IONS
+
+BEGIN IONS
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+BEGIN IONS
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+END IONS
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+BEGIN IONS
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+BEGIN IONS
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+BEGIN IONS
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+END IONS
+
+BEGIN IONS
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+END IONS
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+BEGIN IONS
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+END IONS
+
+BEGIN IONS
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+END IONS
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+BEGIN IONS
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+BEGIN IONS
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+BEGIN IONS
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+BEGIN IONS
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+BEGIN IONS
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+BEGIN IONS
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+END IONS
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+BEGIN IONS
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+END IONS
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+BEGIN IONS
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+979.48197	4959	1+
+989.53004	584	
+1006.54607	892	
+1007.53391	495	
+END IONS
+
+BEGIN IONS
+TITLE= Cmpd 204, +MSn(524.2825), 35.5 min
+PEPMASS=524.28252	121118
+CHARGE=3+
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+1117.55479	637	
+1118.57910	362	
+END IONS
+
--- a/tool_dependencies.xml	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="searchgui" version="1.14.1">
-      <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_searchgui_1_14_4" owner="galaxyp" changeset_revision="67de51d52907" />
-    </package>
-    <package name="peptide_shaker" version="0.20.1">
-      <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_peptideshaker_0_20_1" owner="galaxyp" changeset_revision="cfd55b6c4fa2" />
-    </package>
-</tool_dependency>
--- a/update.sh	Mon Sep 16 17:32:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/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