Mercurial > repos > galaxyp > probamconvert
changeset 1:37369e255465 draft default tip
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 15 Mar 2017 09:43:14 -0400 |
| parents | 0a77e0c00146 |
| children | |
| files | probamconvert.xml test-data/test.mzid test-data/test.pep.xml |
| diffstat | 3 files changed, 806040 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/probamconvert.xml Tue Mar 14 17:06:41 2017 -0400 +++ b/probamconvert.xml Wed Mar 15 09:43:14 2017 -0400 @@ -7,9 +7,9 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - #set $psm_file = input.${input.datatype.file_ext} + #set $psm_file = 'input.'+str($input.datatype.file_ext) ln -s "$input" $psm_file; - proBAM.py --name="converted" --file=$psm_file + proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode --database=$refsrc.database #if str($refsrc.database) == 'ENSEMBL': --species=$refsrc.species @@ -17,15 +17,14 @@ --version=$refsrc.version #end if #end if - #if str($optional.decoy_annotation) != 'None': + #if str($optional.decoy_annotation) != '': --decoy_annotation='$optional.decoy_annotation' #end if - --pre_picked_annotation=$pre_picked_annotation + --pre_picked_annotation=$optional.pre_picked_annotation --mismatches=$optional.mismatches $optional.rm_duplicates $optional.three_frame_translation $optional.include_unmapped - --directory=outputs ]]></command> <inputs> <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/> @@ -87,21 +86,21 @@ </section> </inputs> <outputs> - <data name="output_bam" format="pro.bam" label="" from_work_dir="outputs/converted.sorted.bam"> + <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam"> <filter>conversion_mode != 'proBED'</filter> </data> - <data name="output_bed" format="pro.bed" label="" from_work_dir="outputs/converted.pro.bed"> + <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed"> <filter>conversion_mode == 'proBED'</filter> </data> </outputs> <tests> <test> <param name="input" ftype="mzid" value="test.mzid"/> - <param name="conversion_mode" value="proBAM_psm"/> + <param name="conversion_mode" value="proBED"/> <param name="database" value="ENSEMBL"/> <param name="species" value="homo_sapiens"/> <param name="version" value="87"/> - <output name="output_bam"> + <output name="output_bed"> <assert_contents> <has_text text="Q7Z6Z7_0" /> </assert_contents>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.mzid Wed Mar 15 09:43:14 2017 -0400 @@ -0,0 +1,679888 @@ +<?xml version="1.0" encoding="UTF-8"?> +<MzIdentML id="PeptideShaker v1.15.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" version="1.1.0" creationDate="2017-03-14T14:00:05"> + <cvList> + <cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/> + <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/> + <cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/> + <cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/> + </cvList> + <AnalysisSoftwareList> + <AnalysisSoftware name="PeptideShaker" version="1.15.1" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html"> + <ContactRole contact_ref="PS_DEV"> + <Role> + <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/> + </Role> + </ContactRole> + <SoftwareName> + <cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/> + </SoftwareName> + <Customizations>No customisations</Customizations> + </AnalysisSoftware> + </AnalysisSoftwareList> + <Provider id="PROVIDER"> + <ContactRole contact_ref="PROVIDER"> + <Role> + <cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/> + </Role> + </ContactRole> + </Provider> + <AuditCollection> + <Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER"> + <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="galaxyp@umn.edu"/> + <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/> + <Affiliation organization_ref="ORG_DOC_OWNER"/> + </Person> + <Organization name="University of Minnesota" id="ORG_DOC_OWNER"> + <cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="University of Minnesota"/> + <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Minneapolis, MN 55455, Vereinigte Staaten"/> + <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/> + </Organization> + <Organization name="PeptideShaker developers" id="PS_DEV"> + <cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="PeptideShaker developers"/> + <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"/> + <cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="http://compomics.github.io/projects/peptide-shaker.html"/> + <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="peptide-shaker@googlegroups.com"/> + </Organization> + </AuditCollection> + <SequenceCollection> + <DBSequence id="Q8IYD1" accession="Q8IYD1" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="ERF3B_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3B OS=Homo sapiens GN=GSPT2 PE=1 SV=2"/> + </DBSequence> + <DBSequence id="Q8IYD1_REVERSED" accession="Q8IYD1_REVERSED" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="ERF3B_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3B OS=Homo sapiens GN=GSPT2 PE=1 SV=2-REVERSED"/> + </DBSequence> + <DBSequence id="Q7Z6Z7" accession="Q7Z6Z7" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3"/> + </DBSequence> + <DBSequence id="Q7Z6Z7_REVERSED" accession="Q7Z6Z7_REVERSED" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3-REVERSED"/> + </DBSequence> + <DBSequence id="Q5JU85" accession="Q5JU85" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="IQEC2_HUMAN IQ motif and SEC7 domain-containing protein 2 OS=Homo sapiens GN=IQSEC2 PE=1 SV=1"/> + </DBSequence> + <DBSequence id="Q5JU85_REVERSED" accession="Q5JU85_REVERSED" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="IQEC2_HUMAN IQ motif and SEC7 domain-containing protein 2 OS=Homo sapiens GN=IQSEC2 PE=1 SV=1-REVERSED"/> + </DBSequence> + <DBSequence id="Q96JG8" accession="Q96JG8" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="MAGD4_HUMAN Melanoma-associated antigen D4 OS=Homo sapiens GN=MAGED4 PE=1 SV=3"/> + </DBSequence> + <DBSequence id="Q96JG8_REVERSED" accession="Q96JG8_REVERSED" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="MAGD4_HUMAN Melanoma-associated antigen D4 OS=Homo sapiens GN=MAGED4 PE=1 SV=3-REVERSED"/> + </DBSequence> + <DBSequence id="O60828" accession="O60828" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="PQBP1_HUMAN Polyglutamine-binding protein 1 OS=Homo sapiens GN=PQBP1 PE=1 SV=1"/> + </DBSequence> + <DBSequence id="O60828_REVERSED" accession="O60828_REVERSED" searchDatabase_ref="SearchDB_1" > + <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="PQBP1_HUMAN Polyglutamine-binding protein 1 OS=Homo sapiens GN=PQBP1 PE=1 SV=1-REVERSED"/> + </DBSequence> + <Peptide id="SGFISSPQNVIRSITE"> + <PeptideSequence>SGFLSSPQNVIRSLTE</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="S" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="KIATMIIDCVRYVTD_15.99491461956-ATAA-5"> + <PeptideSequence>KIATMILDCVRYVTD</PeptideSequence> + <Modification monoisotopicMassDelta="57.021464" residues="C" location="9" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="1" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="15.994915" residues="M" location="5" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/> + 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name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="RTDDRIQIIVQIVRIFFKQTSTK"> + <PeptideSequence>RTDDRLQIIVQLVRLFFKQTSTK</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="18" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="23" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="R" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="RGQPPPETSPIR"> + <PeptideSequence>RGQPPPETSPLR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="R" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="EVIYDMINAIAAYH_-18.010564683699997"> + 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</Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="24" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="Q" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="PMIFDERK"> + <PeptideSequence>PMLFDERK</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="8" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="P" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="GAGRRPARGPR"> + <PeptideSequence>GAGRRPARGPR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="G" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" 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</Peptide> + <Peptide id="GISRQMIGEFIGNR"> + <PeptideSequence>GLSRQMIGEFLGNR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="G" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="VVRSAATSGAGSTTSGVVSGSI"> + <PeptideSequence>VVRSAATSGAGSTTSGVVSGSL</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="V" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="SFMNDFEIIIDDERDFR_15.99491461956-ATAA-3"> + <PeptideSequence>SFMNDFEIILDDERDFR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="S" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="15.994915" residues="M" location="3" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/> + </Modification> + </Peptide> + <Peptide id="TQHNGMNNIIR_15.99491461956-ATAA-6"> + <PeptideSequence>TQHNGMNNIIR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="T" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="15.994915" residues="M" location="6" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/> + </Modification> + </Peptide> + <Peptide id="RIDGIFPHR"> + <PeptideSequence>RLDGLFPHR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="R" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="GPGTQPVGSAASPGETAAEQAPAPRKPR"> + <PeptideSequence>GPGTQPVGSAASPGETAAEQAPAPRKPR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="26" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification 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<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="REMFNPMYAIFRTSPGDR_15.99491461956"> + <PeptideSequence>REMFNPMYALFRTSPGDR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="R" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="15.994915" residues="M" location="3" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/> + </Modification> + </Peptide> + <Peptide id="QSSDFDTQSGFSINSQ"> + <PeptideSequence>QSSDFDTQSGFSINSQ</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="Q" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="MINAIAAYHAPEEADKSD_15.99491461956-ATAA-1"> + <PeptideSequence>MLNALAAYHAPEEADKSD</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" 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</Modification> + </Peptide> + <Peptide id="GKIKTTQPQ"> + <PeptideSequence>GKLKTTQPQ</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="2" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="4" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="G" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="APEEADKSD"> + <PeptideSequence>APEEADKSD</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="7" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="A" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" 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<PeptideSequence>YHQYILNSNRANR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="Y" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="ACVSMIGVPVD"> + <PeptideSequence>ACVSMLGVPVD</PeptideSequence> + <Modification monoisotopicMassDelta="57.021464" residues="C" location="2" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="A" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="HIISNAEYYGP"> + <PeptideSequence>HIISNAEYYGP</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="H" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="QEEEEAKCIEK"> + <PeptideSequence>QEEEEAKCLEK</PeptideSequence> + 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id="IIIPPNPQR"> + <PeptideSequence>LILPPNPQR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="L" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="NQNQAIFRIVR"> + <PeptideSequence>NQNQAIFRLVR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="N" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="DQISPANFII"> + <PeptideSequence>DQLSPANFII</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="D" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="IIPIEPPREEKEK"> + <PeptideSequence>LLPLEPPREEKEK</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="11" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + 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residues="P" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="SSNQISWISVSMDAAIGC"> + <PeptideSequence>SSNQLSWLSVSMDAALGC</PeptideSequence> + <Modification monoisotopicMassDelta="57.021464" residues="C" location="18" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="S" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="NGRERDSECNTEK"> + <PeptideSequence>NGRERDSECNTEK</PeptideSequence> + <Modification monoisotopicMassDelta="57.021464" residues="C" location="9" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="13" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification 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<Modification monoisotopicMassDelta="144.102062" residues="K" location="9" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="22" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="T" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="PSGSNVDTIIRIR"> + <PeptideSequence>PSGSNVDTLLRLR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="P" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="FSFQMRMNSIIIRR_15.99491461956-ATAA-5_15.99491461956-ATAA-7"> + <PeptideSequence>FSFQMRMNSLIIRR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="F" location="0" > + <cvParam 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</Peptide> + <Peptide id="KIRSSNADA"> + <PeptideSequence>KLRSSNADA</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="1" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="SSASIIPK"> + <PeptideSequence>SSASLLPK</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="8" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="S" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="IGDSFAPDQIAK"> + <PeptideSequence>IGDSFAPDQIAK</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" 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location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="KEAGYSAAVGVGPRPPR"> + <PeptideSequence>KEAGYSAAVGVGPRPPR</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="1" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + <Modification monoisotopicMassDelta="144.102062" residues="K" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="DREEQNTDIAWSIYWTERN"> + <PeptideSequence>DREEQNTDLAWSLYWTERN</PeptideSequence> + <Modification monoisotopicMassDelta="144.102062" residues="D" location="0" > + <cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/> + </Modification> + </Peptide> + <Peptide id="ESIAEVQEMEK_-18.010564683699997"> + <PeptideSequence>ESIAEVQEMEK</PeptideSequence> + <Modification monoisotopicMassDelta="-18.010565" residues="E" location="0" > 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