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< SpectrumIdentificationResult spectraData_ref ="SID_1" spectrumID ="index=145" id="SIR_5&q

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< SpectrumIdentificationResult spectraData_ref ="SID_1" spectrumID ="index=145" id="SIR_5&q

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  1. <SpectrumIdentificationProtocolanalysisSoftware_ref="ID_software" id="SearchProtocol_1"> <SearchType> <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/> </SearchType> <AdditionalSearchParams> <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/> <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" name="peptide-level scoring performed"/> </AdditionalSearchParams> <ModificationParams> <SearchModification residues="C" massDelta="57.021465" fixedMod="true"> <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/> </SearchModification> <SearchModification residues="M" massDelta="15.994915" fixedMod="false"> <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/> </SearchModification> </ModificationParams> <Enzymes independent="false"> <Enzyme missedCleavages="1" semiSpecific="false" cTermGain="OH" nTermGain="H" id="Enz1"> <EnzymeName> <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/> </EnzymeName> </Enzyme> </Enzymes> <FragmentTolerance> <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.8" name="search tolerance plus value"/> <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.8" name="search tolerance minus value"/> </FragmentTolerance> <ParentTolerance> <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="1.5" name="search tolerance plus value"/> <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="1.5" name="search tolerance minus value"/> </ParentTolerance> <Threshold> <cvParam accession="MS:1001868" cvRef="PSI-MS" name="distinct peptide-level q-value" value="0.01"/> <cvParam accession="MS:1002354" cvRef="PSI-MS" name="PSM-level q-value" value="0.01"/> </Threshold> </SpectrumIdentificationProtocol> A B C <SpectrumIdentificationResultspectraData_ref="SID_1" spectrumID="index=145" id="SIR_5"> <SpectrumIdentificationItempassThreshold="false" rank="1" peptide_ref="SSHAPVPHGVRLWK" calculatedMassToCharge="523.284" experimentalMassToCharge="523.194" chargeState="3" id="SII_5_1"> <PeptideEvidenceRefpeptideEvidence_ref="PE5_2_9"/> <cvParam accession="MS:1001328" cvRef="PSI-MS" value="3.05370337630321" name="OMSSA:evalue"/> <cvParam accession="MS:1001329" cvRef="PSI-MS" value="6.82544339808495E-4" name="OMSSA:pvalue"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="SSHAPVPHGVRLWK" name="Group PSMs (distinct peptide sequence, ignore modifications)"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="peptide level score" name="6.82544339808495E-4"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="peptide passes threshold" name="true"/> </SpectrumIdentificationItem> <cvParam accession="MS:1000796" cvRef="PSI-MS" value="55.6021.6024.3.dta" name="spectrum title"/> </SpectrumIdentificationResult> <SpectrumIdentificationResultspectraData_ref="SID_1" spectrumID="index=121" id="SIR_6"> <SpectrumIdentificationItempassThreshold="false" rank="1" peptide_ref="SSHAPVPHGVRLWK" calculatedMassToCharge="523.284" experimentalMassToCharge="523.194" chargeState="3" id="SII_6_1"> <PeptideEvidenceRefpeptideEvidence_ref="PE5_2_9"/> <cvParam accession="MS:1001328" cvRef="PSI-MS" value="4.05370337630321" name="OMSSA:evalue"/> <cvParam accession="MS:1001329" cvRef="PSI-MS" value="7.82544339808495E-4" name="OMSSA:pvalue"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="SSHAPVPHGVRLWK" name="Group PSMs (distinct peptide sequence, ignore modifications)"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="peptide level score" name="6.82544339808495E-4"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="peptide passes threshold" name="true"/> </SpectrumIdentificationItem> <cvParam accession="MS:1000796" cvRef="PSI-MS" value="55.6021.6025.3.dta" name="spectrum title"/> </SpectrumIdentificationResult> D E F D E F

  2. <SpectrumIdentificationProtocolanalysisSoftware_ref="ID_software" id="SearchProtocol_1"> <SearchType> <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/> </SearchType> <AdditionalSearchParams> <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/> <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" name="Modification localization scoring performed"/> </AdditionalSearchParams> .... <Threshold> <cvParam accession="MS:1002354" cvRef="PSI-MS" name="PSM-level q-value" value="0.01"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" name="false localization rate" value="0.05"/> </Threshold> A B <Peptide id="KYYGNVVYYIGER_p@2|3"> <PeptideSequence>KYYGNVVYYIGER</PeptideSequence> <Modification monoisotopicMassDelta="79.966331" location="2" residues="Y"> <cvParam accession="UNIMOD:21" cvRef="UNIMOD" name="Phospho"/> </Modification> </Peptide> <Peptide id="KYYGNVVYYIGER_p@2|3_p@8|9"> <PeptideSequence>KYYGNVVYYIGER</PeptideSequence> <Modification monoisotopicMassDelta="79.966331" location="2" residues="Y"> <cvParam accession="UNIMOD:21" cvRef="UNIMOD" name="Phospho"/> </Modification> <Modification monoisotopicMassDelta="79.966331" location="2" residues="Y"> <cvParam accession="UNIMOD:21" cvRef="UNIMOD" name="Phospho"/> </Modification> </Peptide> C <SpectrumIdentificationResultspectraData_ref="SID_1" spectrumID="index=137" id="SIR_1"> <SpectrumIdentificationItempassThreshold="false" rank="1" peptide_ref="KYYGNVVYYIGER_p@2|3" calculatedMassToCharge="582.954" experimentalMassToCharge="582.931" chargeState="3" id="SII_1_1"> <PeptideEvidenceRefpeptideEvidence_ref="PE1_2_0"/> <cvParam accession="MS:1001328" cvRef="PSI-MS" value="0.0560993822629918" name="OMSSA:evalue"/> <cvParam accession="MS:1001329" cvRef="PSI-MS" value="1.34757103682421E-5" name="OMSSA:pvalue"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" value="1:0.03:2|3:true" name="modification rescored by false localization rate"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" value="1:0.97:8|9:false" name="modification rescored by false localization rate"/> <!-- Example alternative if position 2 had more evidence than position 3: <cvParam accession="MS:1002380" cvRef="PSI-MS" value="1:0.01:2:true" name="modification rescored by false localization rate"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" value="1:0.4:3:true" name="modification rescored by false localization rate"/> --> </SpectrumIdentificationItem> <cvParam accession="MS:1000796" cvRef="PSI-MS" value="55.574.579.3.dta" name="spectrum title"/> </SpectrumIdentificationResult> <SpectrumIdentificationResultspectraData_ref="SID_1" spectrumID="index=136" id="SIR_2"> <SpectrumIdentificationItempassThreshold="false" rank="1" peptide_ref="KYYGNVVYYIGER_p@2|3_p@8|9" calculatedMassToCharge="588.316" experimentalMassToCharge="588.4" chargeState="3" id="SII_2_1"> <PeptideEvidenceRefpeptideEvidence_ref="PE2_2_4"/> <cvParam accession="MS:1001328" cvRef="PSI-MS" value="5.92798649659846" name="OMSSA:evalue"/> <cvParam accession="MS:1001329" cvRef="PSI-MS" value="0.00145794060418064" name="OMSSA:pvalue"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" value="1:0.03:2|3:true" name="modification rescored by false localization rate"/> <cvParam accession="MS:1002380" cvRef="PSI-MS" value="2:0.01:8|9:true" name="modification rescored by false localization rate"/> </SpectrumIdentificationItem> <cvParam accession="MS:1000796" cvRef="PSI-MS" value="55.567.572.3.dta" name="spectrum title"/> </SpectrumIdentificationResult> D E

  3. <AnalysisProtocolCollectionxmlns="http://psidev.info/psi/pi/mzIdentML/1.1"><AnalysisProtocolCollectionxmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> <SpectrumIdentificationProtocolanalysisSoftware_ref="ID_software" id="SearchProtocol_1"> <SearchType> <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/> </SearchType> <AdditionalSearchParams> <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/> <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" name="crosslinking search"/> </AdditionalSearchParams> A <Peptide id="30491856_30492180_2_4_p1"> <PeptideSequence>AAFTKQAADK</PeptideSequence> <Modification monoisotopicMassDelta="142.0931769836" location="5"> <cvParam accession="MOD:100XXX" cvRef="PSI-MOD" name="xlink:dss"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" name="crosslink donor" value="5448"/> </Modification> </Peptide> <Peptide id="30491856_30492180_2_4_p2"> <PeptideSequence>AMYPPKEDR</PeptideSequence> <Modification monoisotopicMassDelta="0.0" location="6"> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" name="crosslink receiver" value="5448"/> </Modification> </Peptide> B C B <SpectrumIdentificationResultspectraData_ref="SID_1" spectrumID="index=2776" id="SIR_1"> <SpectrumIdentificationItempassThreshold="true" rank="1" peptide_ref="30491856_30492180_2_4_p1" experimentalMassToCharge="345.6" chargeState="3" id="SII_1_1"> <PeptideEvidenceRefpeptideEvidence_ref="pepevid_psm121558473_pep30491845_protP02768-A_target_535"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="1" name="Cross-linked Spectrum Identification Item"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="0.001" name="xlsearch:evalue"/> </SpectrumIdentificationItem> <SpectrumIdentificationItempassThreshold="true" rank="1" peptide_ref="30491715_30491845_3_7_p0" experimentalMassToCharge="647.6" chargeState="3" id="SII_1_2"> <PeptideEvidenceRefpeptideEvidence_ref="pepevid_psm121558473_pep30491715_protP02768-A_target_411"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="1" name="Cross-linked Spectrum Identification Item"/> <cvParam accession="MS:100XXXX" cvRef="PSI-MS" value="0.001" name="xlsearch:evalue"/> </SpectrumIdentificationItem> </SpectrumIdentificationResult> D E

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