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view test-data/bsa.mzid @ 0:a84952540969 draft

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author iracooke
date Mon, 03 Mar 2014 19:05:35 -0500
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<?xml version="1.0" encoding="UTF-8"?>
<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" 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" creationDate="2013-06-05T16:52:19" >
<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>
    <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
    <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>
</cvList>
<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <AnalysisSoftware version="Beta (v9517)" name="MS-GF+" id="ID_software">
        <SoftwareName>
            <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>
        </SoftwareName>
    </AnalysisSoftware>
</AnalysisSoftwareList>
<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <DBSequence accession="sp|ALBU_BOVIN|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq1">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="sp|ALBU_BOVIN|" name="protein description"/>
    </DBSequence>
    <Peptide id="Pep1">
        <PeptideSequence>YICDNQDTISSK</PeptideSequence>
        <Modification monoisotopicMassDelta="57.021463735" location="3">
            <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
        </Modification>
    </Peptide>
    <PeptideEvidence isDecoy="false" post="L" pre="K" end="297" start="286" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_286_1_286"/>
</SequenceCollection>
<AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
        <InputSpectra spectraData_ref="SID_1"/>
        <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
    </SpectrumIdentification>
</AnalysisCollection>
<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <SpectrumIdentificationProtocol analysisSoftware_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"/>
            <userParam value="false" name="TargetDecoyApproach"/>
            <userParam value="0" name="MinIsotopeError"/>
            <userParam value="1" name="MaxIsotopeError"/>
            <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/>
            <userParam value="LowRes" name="Instrument"/>
            <userParam value="NoProtocol" name="Protocol"/>
            <userParam value="2" name="NumTolerableTermini"/>
            <userParam value="1" name="NumMatchesPerSpec"/>
            <userParam value="6" name="MinPepLength"/>
            <userParam value="40" name="MaxPepLength"/>
            <userParam value="2" name="MinCharge"/>
            <userParam value="3" name="MaxCharge"/>
        </AdditionalSearchParams>
        <ModificationParams>
            <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
                <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
            </SearchModification>
        </ModificationParams>
        <Enzymes>
            <Enzyme missedCleavages="1000" semiSpecific="false" id="Tryp">
                <EnzymeName>
                    <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
                </EnzymeName>
            </Enzyme>
        </Enzymes>
        <ParentTolerance>
            <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance plus value"/>
            <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance minus value"/>
        </ParentTolerance>
        <Threshold>
            <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
        </Threshold>
    </SpectrumIdentificationProtocol>
</AnalysisProtocolCollection>
<DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <Inputs>
        <SearchDatabase numDatabaseSequences="2" location="/Users/iracooke/Sources/protk-wk/bsa.fasta" id="SearchDB_1">
            <FileFormat>
                <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
            </FileFormat>
            <DatabaseName>
                <userParam name="bsa.fasta"/>
            </DatabaseName>
        </SearchDatabase>
        <SpectraData location="/Users/iracooke/Sources/protk-wk/bsa.mzML" name="bsa.mzML" id="SID_1">
            <FileFormat>
                <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
            </FileFormat>
            <SpectrumIDFormat>
                <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/>
            </SpectrumIDFormat>
        </SpectraData>
    </Inputs>
    <AnalysisData>
        <SpectrumIdentificationList id="SI_LIST_1">
            <FragmentationTable>
                <Measure id="Measure_MZ">
                    <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
                </Measure>
            </FragmentationTable>
            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="index=0" id="SIR_1">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="722.3251953125" experimentalMassToCharge="722.3522338867188" chargeState="2" id="SII_1_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_286_1_286"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="21" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="71" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="2.0246382E-9" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="2.2635456E-6" name="MS-GF:EValue"/>
                    <userParam value="0" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                    <userParam value="0.5818614" name="ExplainedIonCurrentRatio"/>
                    <userParam value="0.12558742" name="NTermIonCurrentRatio"/>
                    <userParam value="0.45627397" name="CTermIonCurrentRatio"/>
                    <userParam value="18513.0" name="MS2IonCurrent"/>
                    <userParam value="61.02686" name="MeanErrorAll"/>
                    <userParam value="64.35494" name="StdevErrorAll"/>
                    <userParam value="88.56576" name="MeanErrorTop7"/>
                    <userParam value="86.03032" name="StdevErrorTop7"/>
                </SpectrumIdentificationItem>
            </SpectrumIdentificationResult>
        </SpectrumIdentificationList>
    </AnalysisData>
</DataCollection>
</MzIdentML>