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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
author galaxyp
date Tue, 08 May 2018 14:16:45 -0400
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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="2014-01-17T14:17:27" >
<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 (v9881)" 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="gi|24373345|ref|NP_717388.1|" searchDatabase_ref="SearchDB_1" length="735" id="DBSeq1">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373345|ref|NP_717388.1| extracelllular iron oxide respiratory system surface decaheme cytochrome c component OmcA [Shewanella oneidensis MR-1]" name="protein description"/>
    </DBSequence>
    <DBSequence accession="gi|24371739|ref|NP_715781.1|" searchDatabase_ref="SearchDB_1" length="178" id="DBSeq737">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371739|ref|NP_715781.1| ferritin Ftn [Shewanella oneidensis MR-1]" name="protein description"/>
    </DBSequence>
    <DBSequence accession="gi|24371954|ref|NP_715996.1|" searchDatabase_ref="SearchDB_1" length="400" id="DBSeq1994">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371954|ref|NP_715996.1| ISSod4 transposase TnpA_ISSod4 [Shewanella oneidensis MR-1]" name="protein description"/>
    </DBSequence>
    <DBSequence accession="gi|24373023|ref|NP_717065.1|" searchDatabase_ref="SearchDB_1" length="188" id="DBSeq1805">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373023|ref|NP_717065.1| site-specific recombinase phage integrase family [Shewanella oneidensis MR-1]" name="protein description"/>
    </DBSequence>
    <Peptide id="Pep1">
        <PeptideSequence>FKWNGTDTNSAAEK</PeptideSequence>
    </Peptide>
    <Peptide id="Pep2">
        <PeptideSequence>GGESIMNAQSQPQA</PeptideSequence>
    </Peptide>
    <Peptide id="Pep3">
        <PeptideSequence>VIYTTNAVEAVHRQFRKLTK</PeptideSequence>
    </Peptide>
    <Peptide id="Pep4">
        <PeptideSequence>VMRMLR</PeptideSequence>
    </Peptide>
    <PeptideEvidence isDecoy="false" post="R" pre="R" end="556" start="543" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_543_1_543"/>
    <PeptideEvidence isDecoy="false" post="-" pre="K" end="178" start="165" peptide_ref="Pep2" dBSequence_ref="DBSeq737" id="PepEv_901_2_165"/>
    <PeptideEvidence isDecoy="false" post="T" pre="K" end="346" start="327" peptide_ref="Pep3" dBSequence_ref="DBSeq1994" id="PepEv_2320_3_327"/>
    <PeptideEvidence isDecoy="false" post="H" pre="R" end="161" start="156" peptide_ref="Pep4" dBSequence_ref="DBSeq1805" id="PepEv_1960_4_156"/>
</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="true" name="TargetDecoyApproach"/>
            <userParam value="-1" name="MinIsotopeError"/>
            <userParam value="2" 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="1" 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="true" 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="20.0" name="search tolerance plus value"/>
            <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" 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="10" location="C:\cygwin\home\kims336\Data\SkylineDemo\Abbreviated.fasta" id="SearchDB_1">
            <FileFormat>
                <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
            </FileFormat>
            <DatabaseName>
                <userParam name="Abbreviated.fasta"/>
            </DatabaseName>
            <cvParam accession="MS:1001197" cvRef="PSI-MS" name="DB composition target+decoy"/>
            <cvParam accession="MS:1001283" cvRef="PSI-MS" value="^XXX" name="decoy DB accession regexp"/>
            <cvParam accession="MS:1001195" cvRef="PSI-MS" name="decoy DB type reverse"/>
        </SearchDatabase>
        <SpectraData location="msgf-test.mzML" name="msgf-test.mzML" id="SID_1">
            <FileFormat>
                <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
            </FileFormat>
            <SpectrumIDFormat>
                <cvParam accession="MS:1000768" cvRef="PSI-MS" name="Thermo 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="controllerType=0 controllerNumber=1 scan=10073" id="SIR_3">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="784.87060546875" experimentalMassToCharge="784.8652954101562" chargeState="2" id="SII_3_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="173" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="228" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="3.3660747E-14" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="1.6083104E-10" name="MS-GF:EValue"/>
                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
                    <userParam value="0" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                </SpectrumIdentificationItem>
                <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10073" name="scan number(s)"/>
            </SpectrumIdentificationResult>
            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10075" id="SIR_5">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="523.5828247070312" experimentalMassToCharge="523.5802001953125" chargeState="3" id="SII_5_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="81" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="104" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.2290536E-12" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="5.8724186E-9" name="MS-GF:EValue"/>
                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
                    <userParam value="0" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                </SpectrumIdentificationItem>
                <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10075" name="scan number(s)"/>
            </SpectrumIdentificationResult>
            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10071" id="SIR_1">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep2" calculatedMassToCharge="709.3224487304688" experimentalMassToCharge="709.3134765625" chargeState="2" id="SII_1_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_901_2_165"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="50" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="114" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="9.0045643E-10" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="4.3023806E-6" name="MS-GF:EValue"/>
                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
                    <userParam value="0" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                </SpectrumIdentificationItem>
                <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10071" name="scan number(s)"/>
            </SpectrumIdentificationResult>
            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10074" id="SIR_4">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep3" calculatedMassToCharge="792.1166381835938" experimentalMassToCharge="792.4600219726562" chargeState="3" id="SII_4_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2320_3_327"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="25" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="123" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="4.4064498E-7" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0021054016" name="MS-GF:EValue"/>
                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
                    <userParam value="1" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                </SpectrumIdentificationItem>
                <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10074" name="scan number(s)"/>
            </SpectrumIdentificationResult>
            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10072" id="SIR_2">
                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep4" calculatedMassToCharge="403.2303771972656" experimentalMassToCharge="403.7300109863281" chargeState="2" id="SII_2_1">
                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_1960_4_156"/>
                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="27" name="MS-GF:RawScore"/>
                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="50" name="MS-GF:DeNovoScore"/>
                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.4847345E-6" name="MS-GF:SpecEValue"/>
                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0070940615" name="MS-GF:EValue"/>
                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
                    <userParam value="1" name="IsotopeError"/>
                    <userParam value="CID" name="AssumedDissociationMethod"/>
                </SpectrumIdentificationItem>
                <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10072" name="scan number(s)"/>
            </SpectrumIdentificationResult>
        </SpectrumIdentificationList>
    </AnalysisData>
</DataCollection>
</MzIdentML>