Mercurial > repos > galaxyp > peptideshaker
changeset 0:a9e90cdcb97a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,78 @@ +GalaxyP - PeptideShaker +======================= + +- Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +- Tool ID: `peptideshaker`, `search_gui` + + +Description +----------- + +Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker. + +Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. + + +Configuration +------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: + + export _JAVA_OPTIONS='-Xmx1500M' + +On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: + + export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. + +Note: + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for GalaxyP_ and other information can be found at: + +<https://github.com/galaxyproteomics> + +.. _GalaxyP: https://github.com/galaxyproteomics/ + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Bjoern Gruening <bjoern.gruening@gmail.com> +* Ira Cooke +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_mods_loc.py Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,12 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +with open("searchgui_mods.loc.sample", "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())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_species.py Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,10 @@ +#!/usr/bin/env python + +import sys + +for line in open( sys.argv[1] ): + line = line.strip() + if line and not line.startswith('>'): + name, id = line.split('\t') + line = '<option value="%s">%s</option>' % (name, name) + print line
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_mods.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,3021 @@ +<?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->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->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->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->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->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->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->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->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->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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_usermods.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,455 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/species Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,252 @@ +>Fungi +Ashbya gossypii agossypii_eg_gene +Aspergillus clavatus aclavatus_eg_gene +Aspergillus flavus aflavus_eg_gene +Aspergillus fumigatus afumigatus_eg_gene +Aspergillus fumigatusa1163 afumigatusa1163_eg_gene +Aspergillus nidulans anidulans_eg_gene +Aspergillus niger aniger_eg_gene +Aspergillus oryzae aoryzae_eg_gene +Aspergillus terreus aterreus_eg_gene +Blumeria graminis bgraminis_eg_gene +Botrytis cinerea bcinerea_eg_gene +Colletotrichum gloeosporioides cgloeosporioides_eg_gene +Colletotrichum higginsianum chigginsianum_eg_gene +Colletotrichum orbiculare corbiculare_eg_gene +Cryptococcus neoformans cneoformans_eg_gene +Dothistroma septosporum dseptosporum_eg_gene +Fusarium fujikuroi ffujikuroi_eg_gene +Fusarium graminearum fgraminearum_eg_gene +Fusarium oxysporum foxysporum_eg_gene +Fusarium pseudograminearum fpseudograminearum_eg_gene +Fusarium solani fsolani_eg_gene +Fusarium verticillioides fverticillioides_eg_gene +Gaeumannomyces graminis ggraminis_eg_gene +Colletotrichum graminicola cgraminicola_eg_gene +Komagataella pastoris kpastoris_eg_gene +Leptosphaeria maculans lmaculans_eg_gene +Magnaporthe oryzae moryzae_eg_gene +Magnaporthe poae mpoae_eg_gene +Melampsora larici-populina mlaricipopulina_eg_gene +Neosartorya fischeri nfischeri_eg_gene +Neurospora crassa ncrassa_eg_gene +Phaeosphaeria nodorum pnodorum_eg_gene +Puccinia graminis pgraminis_eg_gene +Puccinia graminis Ug99 pgraminisug99_eg_gene +Puccinia triticina ptriticina_eg_gene +Pyrenophora teres pteres_eg_gene +Pyrenophora tritici-repentis ptriticirepentis_eg_gene +Saccharomyces cerevisiae scerevisiae_eg_gene +Schizosaccharomyces cryophilus scryophilus_eg_gene +Schizosaccharomyces japonicus japonicus_eg_gene +Schizosaccharomyces octosporus octosporus_eg_gene +Schizosaccharomyces pombe spombe_eg_gene +Sclerotinia sclerotiorum ssclerotiorum_eg_gene +Sporisorium reilianum sreilianum_eg_gene +Trichoderma reesei treesei_eg_gene +Trichoderma virens tvirens_eg_gene +Tuber melanosporum tmelanosporum_eg_gene +Ustilago maydis umaydis_eg_gene +Verticillium dahliae JR2 vdahliaejr2_eg_gene +Verticillium dahliae dahliae_eg_gene +Yarrowia lipolytica ylipolytica_eg_gene +Zymoseptoria tritici ztritici_eg_gene + +>Metazoa +Acyrthosiphon pisum apisum_eg_gene +Aedes aegypti (Yellow fever mosquito) aaegypti_eg_gene +Amphimedon queenslandica aqueenslandica_eg_gene +Anopheles darlingi adarlingi_eg_gene +Anopheles gambiae (African malaria mosquito) agambiae_eg_gene +Apis mellifera amellifera_eg_gene +Atta cephalotes acephalotes_eg_gene +Bombyx mori bmori_eg_gene +Brugia malayi bmalayi_eg_gene +Caenorhabditis brenneri cbrenneri_eg_gene +Caenorhabditis briggsae cbriggsae_eg_gene +Caenorhabditis elegans celegans_eg_gene +Caenorhabditis japonica cjaponica_eg_gene +Caenorhabditis remanei cremanei_eg_gene +Culex quinquefasciatus (Southern house mosquito) cquinquefasciatus_eg_gene +Danaus plexippus dplexippus_eg_gene +Daphnia pulex dpulex_eg_gene +Dendroctonus ponderosae ponderosae_eg_gene +Drosophila ananassae dananassae_eg_gene +Drosophila erecta derecta_eg_gene +Drosophila grimshawi dgrimshawi_eg_gene +Drosophila melanogaster (Fruit fly) dmelanogaster_eg_gene +Drosophila mojavensis dmojavensis_eg_gene +Drosophila persimilis dpersimilis_eg_gene +Drosophila pseudoobscura dpseudoobscura_eg_gene +Drosophila sechellia dsechellia_eg_gene +Drosophila simulans dsimulans_eg_gene +Drosophila virilis dvirilis_eg_gene +Drosophila willistoni dwillistoni_eg_gene +Drosophila yakuba dyakuba_eg_gene +Heliconius melpomene hmelpomene_eg_gene +Helobdella robusta robusta_eg_gene +Ixodes scapularis (Black-legged tick) iscapularis_eg_gene +Loa loa lloa_eg_gene +Lottia gigantea lgigantea_eg_gene +Megaselia scalaris mscalaris_eg_gene +Melitaea cinxia mcinxia_eg_gene +Mnemiopsis leidyi mleidyi_eg_gene +Nasonia vitripennis nvitripennis_eg_gene +Nematostella vectensis nvectensis_eg_gene +Onchocerca volvulus ovolvulus_eg_gene +Pediculus humanus (Human louse) phumanus_eg_gene +Pristionchus pacificus ppacificus_eg_gene +Rhodnius prolixus rprolixus_eg_gene +Schistosoma mansoni smansoni_eg_gene +Solenopsis invicta (Red fire ant) sinvicta_eg_gene +Strigamia maritima smaritima_eg_gene +Strongylocentrotus purpuratus spurpuratus_eg_gene +Tetranychus urticae turticae_eg_gene +Tribolium castaneum (red flour beetle) tcastaneum_eg_gene +Trichinella spiralis tspiralis_eg_gene +Trichoplax adhaerens tadhaerens_eg_gene +Zootermopsis nevadensis znevadensis_eg_gene + +>Plants +Amborella (Amborella trichopoda) atrichopoda_eg_gene +Arabidopsis lyrata (Lyrate rockcress) alyrata_eg_gene +Arabidopsis thaliana (Thale-cress) athaliana_eg_gene +Brachypodium distachyon (False brome) bdistachyon_eg_gene +Brassica oleracea boleracea_eg_gene +Brassica rapa genes (Field mustard) brapa_eg_gene +Chlamydomonas reinhardtii (Green algae) creinhardtii_eg_gene +Cyanidioschyzon merolae (Red algae) cmerolae_eg_gene +Glycine max (Soybean) gmax_eg_gene +Hordeum vulgare (Barley) hvulgare_eg_gene +Leersia perrieri (Leersia) lperrieri_eg_gene +Medicago truncatula (Barrel medic) mtruncatula_eg_gene +Musa acuminata (Banana) macuminata_eg_gene +Oryza brachyantha obrachyantha_eg_gene +Oryza glumaepatula oglumaepatula_eg_gene +Oryza meridionalis omeridionalis_eg_gene +Oryza nivara onivara_eg_gene +Oryza punctata opunctata_eg_gene +Oryza rufipogon (Common wild rice) orufipogon_eg_gene +Oryza sativa (Indica rice) osativa_eg_gene +Oryza sativa Indica Group oindica_eg_gene +Oryza sativa Japonica (Japonica rice) osativa_eg_gene +Ostreococcus lucimarinus (Green algae) olucimarinus_eg_gene +Physcomitrella patens ppatens_eg_gene +Physcomitrella patens (Moss) ppatens_eg_gene +Populus trichocarpa ptrichocarpa_eg_gene +Populus trichocarpa (Western balsam poplar) ptrichocarpa_eg_gene +Prunus persica (Peach) ppersica_eg_gene +Selaginella moellendorffii (Spike moss) smoellendorffii_eg_gene +Setaria italica (Foxtail millet) sitalica_eg_gene +Solanum lycopersicum (Tomato) slycopersicum_eg_gene +Solanum tuberosum (Potato) stuberosum_eg_gene +Sorghum bicolor (Sorghum) sbicolor_eg_gene +Theobroma cacao (Cocoa) tcacao_eg_gene +Triticum aestivum (Bread wheat) taestivum_eg_gene +Triticum urartu (Einkorn) turartu_eg_gene +Vitis vinifera (Wine grape) vvinifera_eg_gene +Zea mays (Maize) zmays_eg_gene + +>Protists +Albugo laibachii alaibachii_eg_gene +Bigelowiella natans bnatans_eg_gene +Dictyostelium discoideum ddiscoideum_eg_gene +Emiliania huxleyi ehuxleyi_eg_gene +Entamoeba histolytica ehistolytica_eg_gene +Giardia lamblia glamblia_eg_gene +Guillardia theta CCMP2712 gtheta_eg_gene +Hyaloperonospora arabidopsidis harabidopsidis_eg_gene +Leishmania major lmajor_eg_gene +Paramecium tetraurelia ptetraurelia_eg_gene +Phaeodactylum tricornutum ptricornutum_eg_gene +Phytophthora infestans pinfestans_eg_gene +Phytophthora kernoviae pkernoviae_eg_gene +Phytophthora lateralis plateralis_eg_ge +Phytophthora parasitica pparasitica_eg_gene +Phytophthora ramorum pramorum_eg_gene +Phytophthora sojae psojae_eg_gene +Plasmodium berghei pberghei_eg_gene +Plasmodium chabaudi pchabaudi_eg_gene +Plasmodium falciparum pfalciparum_eg_gene +Plasmodium knowlesi pknowlesi_eg_gene +Plasmodium vivax pvivax_eg_gene +Pythium aphanidermatum paphanidermatum_eg_gene +Pythium arrhenomanes parrhenomanes_eg_gene +Pythium irregulare pirregulare_eg_gene +Pythium iwayamai piwayamai_eg_gene +Pythium ultimum pultimum_eg_gene +Pythium vexans pvexans_eg_gene +Tetrahymena thermophila tthermophila_eg_gene +Thalassiosira pseudonana tpseudonana_eg_gene +Toxoplasma gondii tgondii_eg_gene +Trypanosoma brucei tbrucei_eg_gene + +>Vertebrates +Alpaca (Vicugna pacos) vpacos_gene_ensembl +Amazon molly (Poecilia formosa) pformosa_gene_ensembl +Anole lizard (Anolis carolinensis) acarolinensis_gene_ensembl +Armadillo (Dasypus novemcinctus) dnovemcinctus_gene_ensembl +Bushbaby (Otolemur garnettii) ogarnettii_gene_ensembl +C. elegans (Caenorhabditis elegans) celegans_gene_ensembl +C.intestinalis (Ciona intestinalis) cintestinalis_gene_ensembl +C.savignyi (Ciona savignyi) csavignyi_gene_ensembl +Cat (Felis catus) fcatus_gene_ensembl +Cave fish (Astyanax mexicanus) amexicanus_gene_ensembl +Chicken (Gallus gallus) ggallus_gene_ensembl +Chimpanzee (Pan troglodytes) ptroglodytes_gene_ensembl +Chinese softshell turtle (Pelodiscus sinensis) psinensis_gene_ensembl +Cod (Gadus morhua) gmorhua_gene_ensembl +Coelacanth (Latimeria chalumnae) lchalumnae_gene_ensembl +Cow (Bos taurus) btaurus_gene_ensembl +Dog (Canis lupus familiaris) cfamiliaris_gene_ensembl +Dolphin (Tursiops truncatus) ttruncatus_gene_ensembl +Duck (Anas platyrhynchos) aplatyrhynchos_gene_ensembl +Elephant (Loxodonta africana) lafricana_gene_ensembl +Ferret (Mustela putorius furo) mfuro_gene_ensembl +Flycatcher (Ficedula albicollis) falbicollis_gene_ensembl +Fruitfly (Drosophila melanogaster) dmelanogaster_gene_ensembl +Fugu (Takifugu rubripes) trubripes_gene_ensembl +Gibbon (Nomascus leucogenys) nleucogenys_gene_ensembl +Gorilla (Gorilla gorilla gorilla) ggorilla_gene_ensembl +Guinea Pig (Cavia porcellus) cporcellus_gene_ensembl +Hedgehog (Erinaceus europaeus) eeuropaeus_gene_ensembl +Horse (Equus caballus) ecaballus_gene_ensembl +Human (Homo sapiens) hsapiens_gene_ensembl +Hyrax (Procavia capensis) pcapensis_gene_ensembl +Kangaroo rat (Dipodomys ordii) dordii_gene_ensembl +Lamprey (Petromyzon marinus) pmarinus_gene_ensembl +Lesser hedgehog tenrec (Echinops telfairi) etelfairi_gene_ensembl +Macaque (Macaca mulatta) mmulatta_gene_ensembl +Marmoset (Callithrix jacchus) cjacchus_gene_ensembl +Medaka (Oryzias latipes) olatipes_gene_ensembl +Megabat (Pteropus vampyrus) pvampyrus_gene_ensembl +Microbat (Myotis lucifugus) mlucifugus_gene_ensembl +Mouse (Mus musculus) mmusculus_gene_ensembl +Mouse Lemur (Microcebus murinus) mmurinus_gene_ensembl +Opossum (Monodelphis domestica) mdomestica_gene_ensembl +Orangutan (Pongo abelii) pabelii_gene_ensembl +Panda (Ailuropoda melanoleuca) amelanoleuca_gene_ensembl +Pig (Sus scrofa) sscrofa_gene_ensembl +Pika (Ochotona princeps) oprinceps_gene_ensembl +Platyfish (Xiphophorus maculatus) xmaculatus_gene_ensembl +Platypus (Ornithorhynchus anatinus) oanatinus_gene_ensembl +Rabbit (Oryctolagus cuniculus) ocuniculus_gene_ensembl +Rat (Rattus norvegicus) rnorvegicus_gene_ensembl +S. cerevisiae (Saccharomyces cerevisiae) scerevisiae_gene_ensembl +Sheep (Ovis aries) oaries_gene_ensembl +Shrew (Sorex araneus) saraneus_gene_ensembl +Sloth (Choloepus hoffmanni) choffmanni_gene_ensembl +Spotted gar (Lepisosteus oculatus) loculatus_gene_ensembl +Squirrel (Ictidomys tridecemlineatus) itridecemlineatus_gene_ensembl +Stickleback (Gasterosteus aculeatus) gaculeatus_gene_ensembl +Tarsier (Tarsius syrichta) tsyrichta_gene_ensembl +Tasmanian devil (Sarcophilus harrisii) sharrisii_gene_ensembl +Tetraodon (Tetraodon nigroviridis) tnigroviridis_gene_ensembl +Tilapia (Oreochromis niloticus) oniloticus_gene_ensembl +Tree Shrew (Tupaia belangeri) tbelangeri_gene_ensembl +Turkey (Meleagris gallopavo) mgallopavo_gene_ensembl +Vervet-AGM (Chlorocebus sabaeus) csabaeus_gene_ensembl +Wallaby (Macropus eugenii) meugenii_gene_ensembl +Xenopus (Xenopus tropicalis) xtropicalis_gene_ensembl +Zebra Finch (Taeniopygia guttata) tguttata_gene_ensembl +Zebrafish (Danio rerio) drerio_gene_ensembl \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,105 @@ +<macros> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + <regex match="java.*Exception" level="fatal" description="Java Exception"/> + <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> + </stdio> + </xml> + <token name="@GENERAL_PARAMETERS@"> + -frag_tol "${fragment_tol}" + -prec_tol "${precursor_ion_tol}" + -prec_ppm "${precursor_ion_tol_units}" + -enzyme "${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 + -min_charge $min_charge + -max_charge $max_charge + -mc $missed_cleavages + -fi $forward_ion + -ri $reverse_ion + </token> + + <xml name="general_options"> + <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="2">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."/> + <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> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1471-2105-12-70</citation> + <citation type="doi">10.1002/pmic.201000595</citation> + <citation type="doi">doi:10.1038/nbt.3109</citation> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,743 @@ +<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0"> + <description> + Perform protein identification using various search engines based on results from SearchGUI + </description> + <requirements> + <requirement type="package" version="0.38">peptide_shaker</requirement> + </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command> +<![CDATA[ + #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") + #set $temp_stderr = "peptideshaker_stderr" + + mkdir output_reports; + cwd=`pwd`; + + ln -s '$searchgui_input' searchgui_input.zip && + ###################### + ## PeptideShakerCLI ## + ###################### + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + -temp_folder \$cwd/PeptideShakerCLI + -experiment '$exp_str' + -sample '$samp_str' + -replicate 1 + -identification_files \$cwd/searchgui_input.zip + -out \$cwd/peptideshaker_output.cps + -zip \$cwd/peptideshaker_output.zip + + -threads "\${GALAXY_SLOTS:-12}" + + ##Optional gene annotation parameter + #if $species_type.species_type_selector != 'no_species_type': + -species_type "${species_type.species_type_selector}" + -species "${species_type.species}" + -species_update 1 + #end if + + ##Optional processing parameters: + #if $processing_options.processing_options_selector == "yes" + -protein_FDR "${processing_options.protein_fdr}" + -peptide_FDR "${processing_options.peptide_fdr}" + -psm_FDR "${processing_options.psm_fdr}" + -ptm_score "${processing_options.ptm_score.ptm_score_selector}" + #if $processing_options.ptm_score.ptm_score_selector == 1 + -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" + #if str($processing_options.ptm_score.ptm_threshold) != '' + -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" + #end if + #end if + -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" + #end if + + ##Optional filtering parameters: + #if $filtering_options.filtering_options_selector == "yes": + -min_peptide_length "${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 "${filtering_options.max_omssa_e}" + ##-max_mascot_e "${filtering_options.max_mascot_e}" + -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" + #end if + + 2>> $temp_stderr) + + && + + echo "Running Reports"; + + ################################## + ## PeptideShaker Report options ## + ################################## + + #if 'mzidentML' in str($outputs).split(','): + echo "Generating mzIdentML"; + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI + -in \$cwd/peptideshaker_output.zip + -output_file output.mzid + -contact_first_name "Proteomics" + -contact_last_name "Galaxy" + -contact_email "galaxyp@umn.edu" + -contact_address "galaxyp@umn.edu" + -organization_name "University of Minnesota" + -organization_email "galaxyp@umn.edu" + -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" + 2>> $temp_stderr) + && + #end if + + ## Generate Reports if the user has selected one of the 8 additional reports + ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker + ## and will not be passed to the command line + #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): + + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI + -temp_folder \$cwd/ReportCLI + -in \$cwd/peptideshaker_output.zip + -out_reports \$cwd/output_reports + #set $cleaned_list = str($outputs).split(',') + #if 'cps' in $cleaned_list: + #silent $cleaned_list.remove('cps') + #end if + #if 'mzidentML' in $cleaned_list: + #silent $cleaned_list.remove('mzidentML') + #end if + #if 'zip' in $cleaned_list: + #silent $cleaned_list.remove('zip') + #end if + ## Only numbers are left over. These corresponds to different reports. + -reports #echo ','.join($cleaned_list)# + + 2>> $temp_stderr) + && + #end if + + + #if '0' in str($outputs).split(','): + find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; + ; + #end if + #if '1' in str($outputs).split(','): + find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; + ; + #end if + #if '2' in str($outputs).split(','): + find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; + ; + #end if + #if '3' in str($outputs).split(','): + find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; + ; + #end if + #if '4' in str($outputs).split(','): + find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \; + ; + #end if + #if '5' in str($outputs).split(','): + find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; + ; + #end if + #if '6' in str($outputs).split(','): + find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \; + ; + #end if + #if '7' in str($outputs).split(','): + find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; + ; + #end if + + exit_code_for_galaxy=\$?; + cat $temp_stderr 2>&1; + (exit \$exit_code_for_galaxy) + +]]> + </command> + <inputs> + <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results" + help="SearchGUI Results from History"/> + + <conditional name="species_type"> + <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" + help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> + <option value="Fungi">Fungi</option> + <option value="Plants">Plants</option> + <option value="Metazoa">Metazoa</option> + <option value="Vertebrates">Vertebrates</option> + <option value="Protists">Protists</option> + <option value="no_species_type" selected="true">No species restriction</option> + </param> + <when value="Protists"> + <param name="species" type="select" label="The species to use for the gene annotation" + help=""> + <option value="Albugo laibachii">Albugo laibachii</option> + <option value="Bigelowiella natans">Bigelowiella natans</option> + <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> + <option value="Emiliania huxleyi">Emiliania huxleyi</option> + <option value="Entamoeba histolytica">Entamoeba histolytica</option> + <option value="Giardia lamblia">Giardia lamblia</option> + <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option> + <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option> + <option value="Leishmania major">Leishmania major</option> + <option value="Paramecium tetraurelia">Paramecium tetraurelia</option> + <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> + <option value="Phytophthora infestans">Phytophthora infestans</option> + <option value="Phytophthora kernoviae">Phytophthora kernoviae</option> + <option value="Phytophthora lateralis">Phytophthora lateralis</option> + <option value="Phytophthora parasitica">Phytophthora parasitica</option> + <option value="Phytophthora ramorum">Phytophthora ramorum</option> + <option value="Phytophthora sojae">Phytophthora sojae</option> + <option value="Plasmodium berghei">Plasmodium berghei</option> + <option value="Plasmodium chabaudi">Plasmodium chabaudi</option> + <option value="Plasmodium falciparum">Plasmodium falciparum</option> + <option value="Plasmodium knowlesi">Plasmodium knowlesi</option> + <option value="Plasmodium vivax">Plasmodium vivax</option> + <option value="Pythium aphanidermatum">Pythium aphanidermatum</option> + <option value="Pythium arrhenomanes">Pythium arrhenomanes</option> + <option value="Pythium irregulare">Pythium irregulare</option> + <option value="Pythium iwayamai">Pythium iwayamai</option> + <option value="Pythium ultimum">Pythium ultimum</option> + <option value="Pythium vexans">Pythium vexans</option> + <option value="Tetrahymena thermophila">Tetrahymena thermophila</option> + <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option> + <option value="Toxoplasma gondii">Toxoplasma gondii</option> + <option value="Trypanosoma brucei">Trypanosoma brucei</option> + </param> + </when> + <when value="Plants"> + <param name="species" type="select" label="The species to use for the gene annotation" + help=""> + <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option> + <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option> + <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option> + <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option> + <option value="Brassica oleracea">Brassica oleracea</option> + <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option> + <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option> + <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option> + <option value="Glycine max (Soybean)">Glycine max (Soybean)</option> + <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option> + <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option> + <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option> + <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option> + <option value="Oryza brachyantha">Oryza brachyantha</option> + <option value="Oryza glumaepatula">Oryza glumaepatula</option> + <option value="Oryza meridionalis">Oryza meridionalis</option> + <option value="Oryza nivara">Oryza nivara</option> + <option value="Oryza punctata">Oryza punctata</option> + <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option> + <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option> + <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> + <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option> + <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option> + <option value="Physcomitrella patens">Physcomitrella patens</option> + <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option> + <option value="Populus trichocarpa">Populus trichocarpa</option> + <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option> + <option value="Prunus persica (Peach)">Prunus persica (Peach)</option> + <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option> + <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option> + <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option> + <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option> + <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option> + <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option> + <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option> + <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option> + <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option> + <option value="Zea mays (Maize)">Zea mays (Maize)</option> + </param> + </when> + <when value="Metazoa"> + <param name="species" type="select" label="The species to use for the gene annotation" + help=""> + <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option> + <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option> + <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> + <option value="Anopheles darlingi">Anopheles darlingi</option> + <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option> + <option value="Apis mellifera ">Apis mellifera </option> + <option value="Atta cephalotes ">Atta cephalotes </option> + <option value="Bombyx mori ">Bombyx mori </option> + <option value="Brugia malayi ">Brugia malayi </option> + <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option> + <option value="Caenorhabditis briggsae ">Caenorhabditis briggsae </option> + <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option> + <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option> + <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option> + <option value="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option> + <option value="Danaus plexippus ">Danaus plexippus </option> + <option value="Daphnia pulex ">Daphnia pulex </option> + <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option> + <option value="Drosophila ananassae ">Drosophila ananassae </option> + <option value="Drosophila erecta ">Drosophila erecta </option> + <option value="Drosophila grimshawi ">Drosophila grimshawi </option> + <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option> + <option value="Drosophila mojavensis ">Drosophila mojavensis </option> + <option value="Drosophila persimilis ">Drosophila persimilis </option> + <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option> + <option value="Drosophila sechellia ">Drosophila sechellia </option> + <option value="Drosophila simulans ">Drosophila simulans </option> + <option value="Drosophila virilis ">Drosophila virilis </option> + <option value="Drosophila willistoni ">Drosophila willistoni </option> + <option value="Drosophila yakuba ">Drosophila yakuba </option> + <option value="Heliconius melpomene ">Heliconius melpomene </option> + <option value="Helobdella robusta">Helobdella robusta</option> + <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option> + <option value="Loa loa ">Loa loa </option> + <option value="Lottia gigantea">Lottia gigantea</option> + <option value="Megaselia scalaris ">Megaselia scalaris </option> + <option value="Melitaea cinxia">Melitaea cinxia</option> + <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option> + <option value="Nasonia vitripennis ">Nasonia vitripennis </option> + <option value="Nematostella vectensis ">Nematostella vectensis </option> + <option value="Onchocerca volvulus">Onchocerca volvulus</option> + <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option> + <option value="Pristionchus pacificus ">Pristionchus pacificus </option> + <option value="Rhodnius prolixus">Rhodnius prolixus</option> + <option value="Schistosoma mansoni ">Schistosoma mansoni </option> + <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option> + <option value="Strigamia maritima ">Strigamia maritima </option> + <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option> + <option value="Tetranychus urticae">Tetranychus urticae</option> + <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option> + <option value="Trichinella spiralis ">Trichinella spiralis </option> + <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option> + <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option> + </param> + </when> + <when value="Fungi"> + <param name="species" type="select" label="The species to use for the gene annotation" + help=""> + <option value="Ashbya gossypii">Ashbya gossypii</option> + <option value="Aspergillus clavatus">Aspergillus clavatus</option> + <option value="Aspergillus flavus">Aspergillus flavus</option> + <option value="Aspergillus fumigatus">Aspergillus fumigatus</option> + <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option> + <option value="Aspergillus nidulans">Aspergillus nidulans</option> + <option value="Aspergillus niger">Aspergillus niger</option> + <option value="Aspergillus oryzae">Aspergillus oryzae</option> + <option value="Aspergillus terreus">Aspergillus terreus</option> + <option value="Blumeria graminis">Blumeria graminis</option> + <option value="Botrytis cinerea">Botrytis cinerea</option> + <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option> + <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option> + <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option> + <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> + <option value="Dothistroma septosporum">Dothistroma septosporum</option> + <option value="Fusarium fujikuroi">Fusarium fujikuroi</option> + <option value="Fusarium graminearum">Fusarium graminearum</option> + <option value="Fusarium oxysporum">Fusarium oxysporum</option> + <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option> + <option value="Fusarium solani">Fusarium solani</option> + <option value="Fusarium verticillioides">Fusarium verticillioides</option> + <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option> + <option value="Colletotrichum graminicola">Colletotrichum graminicola</option> + <option value="Komagataella pastoris">Komagataella pastoris</option> + <option value="Leptosphaeria maculans">Leptosphaeria maculans</option> + <option value="Magnaporthe oryzae">Magnaporthe oryzae</option> + <option value="Magnaporthe poae">Magnaporthe poae</option> + <option value="Melampsora larici-populina">Melampsora larici-populina</option> + <option value="Neosartorya fischeri">Neosartorya fischeri</option> + <option value="Neurospora crassa">Neurospora crassa</option> + <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option> + <option value="Puccinia graminis">Puccinia graminis</option> + <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option> + <option value="Puccinia triticina">Puccinia triticina</option> + <option value="Pyrenophora teres">Pyrenophora teres</option> + <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option> + <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> + <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option> + <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option> + <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option> + <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option> + <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option> + <option value="Sporisorium reilianum">Sporisorium reilianum</option> + <option value="Trichoderma reesei">Trichoderma reesei</option> + <option value="Trichoderma virens">Trichoderma virens</option> + <option value="Tuber melanosporum">Tuber melanosporum</option> + <option value="Ustilago maydis">Ustilago maydis</option> + <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option> + <option value="Verticillium dahliae">Verticillium dahliae</option> + <option value="Yarrowia lipolytica">Yarrowia lipolytica</option> + <option value="Zymoseptoria tritici">Zymoseptoria tritici</option> + </param> + </when> + <when value="Vertebrates"> + <param name="species" type="select" label="The species to use for the gene annotation" + help=""> + <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option> + <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option> + <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option> + <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option> + <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option> + <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option> + <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option> + <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option> + <option value="Cat (Felis catus)">Cat (Felis catus)</option> + <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option> + <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option> + <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option> + <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option> + <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option> + <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option> + <option value="Cow (Bos taurus)">Cow (Bos taurus)</option> + <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option> + <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option> + <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option> + <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option> + <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option> + <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option> + <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option> + <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option> + <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option> + <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option> + <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option> + <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option> + <option value="Horse (Equus caballus)">Horse (Equus caballus)</option> + <option value="Human (Homo sapiens)">Human (Homo sapiens)</option> + <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option> + <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option> + <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option> + <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option> + <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option> + <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option> + <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option> + <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option> + <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option> + <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option> + <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option> + <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option> + <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option> + <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option> + <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option> + <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option> + <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option> + <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option> + <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option> + <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option> + <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option> + <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option> + <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option> + <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option> + <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option> + <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option> + <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option> + <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option> + <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option> + <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option> + <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option> + <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option> + <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option> + <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option> + <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option> + <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option> + <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option> + <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option> + </param> + </when> + </conditional> + <conditional name="processing_options"> + <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> + <option value="no" selected="True">Default Processing Options</option> + <option value="yes">Advanced Processing Options</option> + </param> + <when value="no" /> + <when value="yes"> + <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="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" + help="default 95%: '95.0'" /> + <conditional name="ptm_score"> + <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> + <option value="0" selected="True">A-score</option> + <option value="1">PhosphoRS</option> + </param> + <when value="0" /> + <when value="1"> + <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> + <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float" + help="Automatic mode will be used if not set" /> + </when> + </conditional> + <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> + </when> + </conditional> + <conditional name="filtering_options"> + <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" + help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"> + <option value="no" selected="True">Default Filtering Options</option> + <option value="yes">Advanced Filtering Options</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> + <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> + <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" + 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="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> + <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </when> + </conditional> + <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> + <option value="zip">Zip File for import to Desktop App</option> + <option value="mzidentML" selected="True">mzidentML File</option> + <option value="3" >PSM Report</option> + <option value="4" >Peptide Phosphorylation Report</option> + <option value="5" >Peptide Report</option> + <option value="6" >Protein Phosphorylation Report</option> + <option value="7" >Protein Report</option> + <option value="2">PSM Phosphorylation Report</option> + <option value="0">Certificate of Analysis</option> + <option value="1">Hierarchical Report</option> + <option value="cps">CPS file</option> + <validator type="no_options" message="Please select at least one output file" /> + </param> + + </inputs> + <outputs> + <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> + <filter>'mzidentML' in outputs</filter> + </data> + <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> + <filter>'cps' in outputs</filter> + </data> + <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> + <filter>'zip' in outputs</filter> + </data> + <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> + <filter>'0' in outputs</filter> + </data> + <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> + <filter>'1' in outputs</filter> + </data> + <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> + <filter>'2' in outputs</filter> + </data> + <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> + <filter>'3' in outputs</filter> + </data> + <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> + <filter>'4' in outputs</filter> + </data> + <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> + <filter>'5' in outputs</filter> + </data> + <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> + <filter>'6' in outputs</filter> + </data> + <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> + <filter>'7' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="species_type_selector" value="no_species_type"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="no"/> + <param name="outputs" value="zip,cps,3"/> + <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> + <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> + <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> + </test> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="species_type_selector" value="no_species_type"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="yes"/> + <param name="min_peptide_length" value="1"/> + <param name="outputs" value="0,1,2,3,4,5,6,7"/> + <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/> + <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> + <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> + <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> + <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> + <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> + <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> + <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> + </test> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="species_type_selector" value="Vertebrates"/> + <param name="species" value="Human (Homo sapiens)"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="yes"/> + <param name="min_peptide_length" value="1"/> + <param name="outputs" value="5"/> + <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" /> + </test> + </tests> + <help> +**What it does** + +Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. + +https://code.google.com/p/peptide-shaker/ + +https://code.google.com/p/searchgui/ + +---- + +Reports +======= + + +PSM Report +---------- + +* Protein(s): Protein(s) to which the peptide can be attached +* Sequence: Sequence of the peptide +* Variable Modifications: The variable modifications +* D-score: D-score for variable PTM localization +* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. +* Localization Confidence: The confidence in variable PTM localization. +* Fixed Modifications: The fixed modifications. +* Spectrum File: The spectrum file. +* Spectrum Title: The title of the spectrum. +* Spectrum Scan Number: The spectrum scan number. +* RT: Retention time +* m/z: Measured m/z +* Measured Charge: The charge as given in the spectrum file. +* Identification Charge: The charge as inferred by the search engine. +* Theoretical Mass: The theoretical mass of the peptide. +* Isotope Number: The isotope number targetted by the instrument. +* Precursor m/z Error: The precursor m/z matching error. +* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). +* Confidence: Confidence in percent associated to the retained PSM. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. + + +Protein Report +-------------- + +* Main Accession: Main accession of the protein group. +* Description: Description of the protein designed by the main accession. +* Gene Name: The gene names of the Ensembl gene ID associated to the main accession. +* Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. +* PI: Protein Inference status of the protein group. +* Secondary Accessions: Other accessions in the protein group (alphabetical order). +* Protein Group: The complete protein group (alphabetical order). +* #Peptides: Total number of peptides. +* #Validated Peptides: Number of validated peptides. +* #Unique: Total number of peptides unique to this protein group. +* #PSMs: Number of PSMs +* #Validated PSMs: Number of validated PSMs +* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. +* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. +* MW (kDa): Molecular Weight. +* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) +* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) +* Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. +* Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. +* Score: Score of the protein group. +* Confidence: Confidence in percent associated to the protein group. +* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. + + +Peptide Report +-------------- + + +* Protein(s): Protein(s) to which this peptide can be attached. +* AAs Before: The amino-acids before the sequence. +* Sequence: Sequence of the peptide. +* AAs After: The amino-acids after the sequence. +* Modified Sequence: The peptide sequence annotated with variable modifications. +* Variable Modifications: The variable modifications. +* Localization Confidence: The confidence in PTMs localization. +* Fixed Modifications: The fixed modifications. +* #Validated PSMs: Number of validated PSMs. +* #PSMs: Number of PSMs. +* Score: Score of the peptide. +* Confidence: Confidence in percent associated to the peptide. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. + + +Hierachical Report +------------------ + +* Main Accession: Main accession of the protein group. +* Description: Description of the protein designed by the main accession. +* PI: Protein Inference status of the protein group. +* Secondary Accessions: Other accessions in the protein group (alphabetical order). +* Protein Group: The complete protein group (alphabetical order). +* #Peptides: Total number of peptides. +* #Validated Peptides: Number of validated peptides. +* #Unique: Total number of peptides unique to this protein group. +* #PSMs: Number of PSMs +* #Validated PSMs: Number of validated PSMs +* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. +* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. +* MW (kDa): Molecular Weight. +* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) +* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) +* Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. +* Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. +* Score: Score of the protein group. +* Confidence: Confidence in percent associated to the protein group. +* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which this peptide can be attached. +* AAs Before: The amino-acids before the sequence. +* Sequence: Sequence of the peptide. +* AAs After: The amino-acids after the sequence. +* Variable Modifications: The variable modifications. +* Localization Confidence: The confidence in PTMs localization. +* Fixed Modifications: The fixed modifications. +* #Validated PSMs: Number of validated PSMs. +* #PSMs: Number of PSMs. +* Score: Score of the peptide. +* Confidence: Confidence in percent associated to the peptide. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which the peptide can be attached. +* Sequence: Sequence of the peptide. +* Modified Sequence: The peptide sequence annotated with variable modifications. +* Variable Modifications: The variable modifications. +* D-score: D-score for variable PTM localization. +* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. +* Localization Confidence: The confidence in variable PTM localization. +* Fixed Modifications: The fixed modifications. +* Spectrum File: The spectrum file. +* Spectrum Title: The title of the spectrum. +* Spectrum Scan Number: The spectrum scan number. +* RT: Retention time +* m/z: Measured m/z +* Measured Charge: The charge as given in the spectrum file. +* Identification Charge: The charge as inferred by the search engine. +* Theoretical Mass: The theoretical mass of the peptide. +* Isotope Number: The isotope number targetted by the instrument. +* Precursor m/z Error: The precursor m/z matching error. +* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). +* Confidence: Confidence in percent associated to the retained PSM. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. + + +------ + +**Citation** + +To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com + +If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="6ab4a0bf67df" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,365 @@ +<tool id="search_gui" name="Search GUI" version="1.27.0"> + <description> + Perform protein identification using various search engines and prepare results for input to Peptide Shaker + </description> + <requirements> + <requirement type="package" version="1.27">searchgui</requirement> + </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command> +<![CDATA[ + #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") + #set $temp_stderr = "searchgui_stderr" + + mkdir output; + mkdir output_reports; + cwd=`pwd`; + #for $mgf in $peak_lists: + #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" + ln -s -f '${mgf}' '${input_name}'; + #end for + ##ln -s "${input_database}" input_database.fasta; + cp "${input_database}" input_database.fasta; + + ########################################### + #### Creating decoy database #### + ########################################### + #if $create_decoy: + echo "Creating decoy database."; + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && + rm input_database.fasta && + cp input_database_concatenated_target_decoy.fasta input_database.fasta && + ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; + #end if + + ##################################################### + ## generate IdentificationParameters for SearchGUI ## + ##################################################### + + (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI + -out SEARCHGUI_IdentificationParameters.parameters + + @GENERAL_PARAMETERS@ + + -db input_database.fasta + + #if $advanced.advanced_type_selector == "advanced": + + #if $advanced.xtandem.xtandem_selector == "yes" + + -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} + + #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" + -xtandem_refine 1 + -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} + #end if + #end if + + #if $advanced.omssa.omssa_selector == "yes" + -omssa_hitlist_length ${advanced.omssa.hitlist_length} + -omssa_remove_prec ${advanced.omssa.remove_precursor} + -omssa_scale_prec ${advanced.omssa.scale_precursor} + -omssa_estimate_charge ${advanced.omssa.estimate_charge} + #end if + + #if $advanced.msgf.msgf_selector == "yes" + -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} + -msgf_termini ${advanced.msgf.msgf_termini} + -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} + #end if + + ##if $advanced.ms_amanda.ms_amanda_selector == "yes" + ##end if + + #end if + + 2> $temp_stderr) + && + + ################ + ## Search CLI ## + ################ + (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + -temp_folder `pwd` + -spectrum_files \$cwd + -output_folder \$cwd/output + -id_params SEARCHGUI_IdentificationParameters.parameters + + -threads "\${GALAXY_SLOTS:-12}" + -correct_titles "${correct_titles}" + $missing_titles + -mgf_splitting "${mgf_splitting}" + -mgf_spectrum_count "${mgf_spectrum_count}" + + ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created + ## the tree is generated afterwards in PeptideShaker + -protein_index 0 + + ##-makeblastdb_folder \$BLAST_ROOT_DIR + + #if $advanced.advanced_type_selector == "advanced": + + #if $advanced.xtandem.xtandem_selector == "yes" + -xtandem 1 + #else + -xtandem 0 + #end if + + #if $advanced.omssa.omssa_selector == "yes" + -omssa 1 + #else + -omssa 0 + #end if + + #if $advanced.msgf.msgf_selector == "yes" + -msgf 1 + #else + -msgf 0 + #end if + + #if $advanced.myrimatch.myrimatch_selector == "yes" + -myrimatch 1 + #else + -myrimatch 0 + #end if + + #if $advanced.comet.comet_selector == "yes" + -comet 1 + #else + -comet 0 + #end if + + #if $advanced.ms_amanda.ms_amanda_selector == "yes" + -ms_amanda 1 + #else + -ms_amanda 0 + #end if + + #if $advanced.tide.tide_selector == "yes" + -tide 1 + #else + -tide 0 + #end if + + #else + -ms_amanda 0 -tide 0 + #end if + + ## single zip file + -output_option 0 + + ## mgf and database in output + -output_data 1 + + 2>> $temp_stderr) + + && + + (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) + + && + + exit_code_for_galaxy=\$?; + cat $temp_stderr 2>&1; + (exit \$exit_code_for_galaxy) +]]> + </command> + <inputs> + <param format="fasta" name="input_database" type="data" label="Protein Database" + help="Select FASTA database from history"/> + + <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" + label="Create a concatenated target/decoy database before running PeptideShaker" + help="Selecting this option will help PeptideShaker calculate FDR values" /> + + <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" + help="Select appropriate MGF dataset(s) from history" /> + + <expand macro="general_options"/> + + <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" + help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> + <option value="0">no correction</option> + <option value="1" selected="True">rename spectra</option> + <option value="2">delete spectra</option> + </param> + + <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" + label="Add missing spectrum titles" help="(-missing_titles)"/> + + <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" + help="Choose a smaller value if you are running on a machine with limited memory"/> + + <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" + help="Choose a smaller value if you are running on a machine with limited memory"/> + + <conditional name="advanced"> + <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <conditional name="xtandem"> + <param name="xtandem_selector" type="select" label="Run X!Tandem search"> + <option value="yes" selected="True">Search with X!Tandem</option> + <option value="no">No X!Tandem search</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="xtandem_npeaks" type="integer" value="50" + label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> + <param name="xtandem_min_peaks" type="integer" value="15" + label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> + <param name="xtandem_min_frag_mz" type="integer" value="200" + label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> + <param name="xtandem_min_prec_mass" type="integer" value="200" + label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" + label="X!Tandem: Noise Suppression" help="Use noise suppression"/> + + <conditional name="xtandem_refine"><!-- -xtandem_refine --> + <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> + <option value="no" selected="True">Don't refine</option> + <option value="yes" >Use refinement</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> + <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> + <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> + </when> + </conditional> + </when> + </conditional> + + <conditional name="omssa"> + <param name="omssa_selector" type="select" label="Run OMSSA search"> + <option value="yes" selected="True">Search with OMSSA</option> + <option value="no">No OMSSA search</option> + </param> + <when value="no" /> + <when value="yes"> + <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> + + <conditional name="msgf"> + <param name="msgf_selector" type="select" label="Run MSGF search"> + <option value="yes" selected="True">Search with MSGF</option> + <option value="no">No MSGF search</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="msgf_min_pep_length" type="integer" value="6" + label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" type="integer" value="30" + label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" type="select" format="text" + label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> + <option value="0">0 (ie non-specific cleavage)</option> + <option value="1">1 (ie semi-tryptic cleavage)</option> + <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> + </param> + <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/> + </when> + </conditional> + + <conditional name="myrimatch"> + <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> + <option value="yes" selected="True">Search with MyriMatch</option> + <option value="no">No MyriMatch search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + <conditional name="comet"> + <param name="comet_selector" type="select" label="Run Comet search"> + <option value="yes" selected="True">Search with Comet</option> + <option value="no">No Comet search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + <conditional name="ms_amanda"> + <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> + <option value="yes">Search with MS Amanda</option> + <option value="no" selected="True">No MS Amanda search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + <conditional name="tide"> + <param name="tide_selector" type="select" label="Run Tide search"> + <option value="yes">Search with Tide</option> + <option value="no" selected="True">No Comet search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + </when> + </conditional> + </inputs> + <outputs> + <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> + <param name="fixed_modifications" value="carbamidomethyl c"/> + <param name="variable_modifications" value="oxidation of m"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> + <param name="advanced_type_selector" value="advanced"/> + <param name="xtandem_selector" value="yes"/> + <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> + <param name="omssa_selector" value="no"/> + <param name="msgf_selector" value="yes"/> + <param name="ms_amanda_selector" value="no"/> + <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> + </test> + </tests> + <help> +**What it does** + +Runs multiple search engines on any number of MGF peak lists using the SearchGUI. + +By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run. + + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,210 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_certificate_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,68 @@ +Project Details1: PeptideShaker Version: 0.37.4-beta +2: Date: Sat Feb 14 20:04:49 CET 2015 +3: Experiment: Galaxy_Experiment_2015021420041423940686 +4: Sample: Sample_2015021420041423940686 +5: Replicate Number: 1 +6: Identification Algorithms: X!Tandem and MS-GF+ +Database Search Parameters + +1: Precursor Accuracy Unit: ppm +2: Precursor Ion m/z Tolerance: 100.0 +3: Fragment Ion m/z Tolerance: 0.5 +4: Enzyme: Trypsin +5: Number of Missed Cleavages: Not implemented +6: Database: input_database.fasta +7: Forward Ion: b +8: Rewind Ion: y +9: Fixed Modifications: carbamidomethyl c +10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q +11: Refinement Variable Modifications: +12: Refinement Fixed Modifications: +Input Filters + +1: Minimal Peptide Length: 1 +2: Maximal Peptide Length: 30 +3: Precursor m/z Tolerance: 10.0 +4: Precursor m/z Tolerance Unit: Yes +5: Unrecognized Modifications Discarded: No +Validation Summary + +1: #Validated Proteins: 0.0 +2: Protein Total: 0.0 +3Protein FDR Limit: 1.0 % +4: Protein FNR Limit: 0.0 % +5: Protein Confidence Limit: -1.0 % +6: Protein PEP Limit: 101.0 % +7: Protein Confidence Accuracy: 0.0 % +8: #Validated Peptides: 0.0 +9: Peptide Total: 0.0 +10: Peptide FDR Limit: 1.0 % +11: Peptide FNR Limit: 0.0 % +12: Peptide Confidence Limit: -1.0 % +13: Peptide PEP Limit: 101.0 % +14: Peptide Confidence Accuracy: 0.0 % +15: #Validated PSM: 0.0 +16: PSM Total: 0.0 +17: PSM FDR Limit: 1.0 % +18: PSM FNR Limit: 0.0 % +19: PSM Confidence Limit: -1.0 % +20: PSM PEP Limit: 101.0 % +21: PSM Confidence Accuracy: 0.0 % +Postranslational Modification Scoring Settings + +1: A-score: No +2: Accounting for Neutral Losses: No +3: False Location Rate: 1.0 +Spectrum Counting Parameters + +1: Method: NSAF +2: Validated Matches Only: Yes +Annotation Settings + +1: Intensity Limit: 0.75 +2: Automatic Annotation: Yes +3: Selected Ions: b, y +4: Neutral Losses: NH3, H2O +5: Neutral Losses Sequence Dependence: Yes +6: Selected Charges: 1, 2 +7: Fragment Ion m/z Tolerance: 0.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_hierarchical_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,78 @@ + Main Accession Description MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful + Protein(s) Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +1.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR LK; LK IN; IN 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.1.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +1.1.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +1.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK AK; AK IS; IS 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.2.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +1.2.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +1.2.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +1.2.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +1.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR VR; VR LK; LK 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.3.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +1.3.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +1.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK AR; AR LI; LI 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.4.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +1.4.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +1.5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR MK; MK SN; SN 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.5.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +1.5.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +1.6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NK; NK LS; LS 3 3 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.6.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +1.6.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +1.6.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +1.7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR AR; AR QS; QS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.7.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +1.7.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +1.8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR QK; QK SV; SV 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.8.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +1.8.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +1.8.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +1.8.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +1.9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR RR; RR AS; AS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.9.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +1.9.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +1.10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NR; NR SE; SE 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.10.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +1.10.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +1.10.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +1.10.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +1.11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK RR; RR NL; NL 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.11.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +1.11.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +1.12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK GR; GR DM; DM 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.12.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +1.12.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +1.13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.13.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +1.13.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +1.14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.14.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +1.14.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +1.14.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +1.14.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +1.15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.15.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +1.15.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful + Protein(s) Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +2.1 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK MR; MR YQ; YQ 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +2.1.1 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +2.1.2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 0 0 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 0 0 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result1.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result2.tabular Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinydb1.fasta Sat May 30 05:25:00 2015 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinyspectra1.mgf Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,6153 @@ +BEGIN IONS +TITLE= Cmpd 636, +MSn(730.3981), 66.9 min +PEPMASS=730.39814 92569 +CHARGE=2+ +156.06738 122 +175.10440 1049 +186.08322 120 +187.12501 241 +188.06515 494 1+ +193.09503 180 +197.12522 208 +199.17309 1374 1+ +204.08687 454 1+ +213.14347 128 +215.11998 747 1+ +227.17167 1524 1+ +229.12416 156 +233.09327 3574 1+ +236.99586 113 +243.14264 571 1+ +244.07481 236 +245.12901 240 +246.12647 275 +256.20038 432 1+ +258.12496 133 +260.19976 423 +261.09190 17853 1+ +270.16206 114 +274.12614 207 +283.15366 136 +284.18559 406 1+ +286.14626 237 +287.10013 105 +301.15759 131 +303.17924 2962 1+ +310.21264 944 1+ +315.13250 122 +316.16696 108 +326.16601 145 +328.21268 874 1+ +335.13393 406 1+ +338.20704 186 +339.16449 110 +342.17857 106 +344.13585 148 +346.17426 809 1+ +356.21762 685 1+ +358.15839 265 +359.26213 106 +362.14671 528 1+ +366.16564 103 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135 +775.43074 138 +779.38031 110 +784.42558 899 1+ +787.90750 114 +788.43303 156 +802.43422 958 1+ +818.92372 110 +819.43952 106 +830.50628 147 +838.45103 121 +855.49252 207 +866.39951 113 +872.50085 6571 1+ +880.44367 148 +886.46997 133 +891.44688 208 +899.47954 151 +912.47926 133 +914.49331 112 +916.46838 134 +924.48363 139 +926.42073 111 +955.52131 165 +956.52827 785 1+ +973.55087 13950 1+ +978.51217 225 +979.51564 116 +980.49756 186 +1008.48933 103 +1044.54839 219 +1068.60979 255 1+ +1086.63071 4224 1+ +1187.60270 135 +1199.72200 1064 1+ +END IONS + +BEGIN IONS +TITLE= Cmpd 67, +MSn(562.2947), 26.3 min +PEPMASS=562.29468 458049 +CHARGE=2+ +173.10446 888 +175.10614 7500 1+ +179.03885 2115 1+ +181.05013 1444 +185.10363 748 +188.09581 546 +189.08230 1123 +191.10888 1205 +193.08988 20362 1+ +197.12012 1004 +198.08421 1715 +199.08156 3683 1+ +201.11270 1482 +202.08307 5961 1+ +204.12828 1144 +207.10914 5879 1+ +212.09747 547 +214.14801 786 +215.13458 1085 +216.09374 15154 1+ +219.10360 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat May 30 05:25:00 2015 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="searchgui" version="1.27"> + <repository changeset_revision="6f6961d6bea5" name="package_searchgui_1_27" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="peptide_shaker" version="0.38"> + <repository changeset_revision="3b8f4f9f93d2" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>