<?xml version="1.0" encoding="UTF-8"?>
<MzIdentML xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" id="a1specoms" version="1.2.0" creationDate="2024-06-04T17:11:24" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.2 https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0-candidate.xsd">
    <cvList>
        <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="PSI-MOD" uri="http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo" fullName="Proteomics Standards Initiative Protein Modifications Vocabularies" version="1.2"/>
        <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>
    </cvList>
    <AnalysisSoftwareList>
        <AnalysisSoftware version="0.0.23" name="SpecOMS" id="as1">
            <SoftwareName>
                <userParam name="SpecOMS:name" value="SpecOMS"/>
                <userParam name="SpecOMS:version" value="0.0.23"/>
            </SoftwareName>
        </AnalysisSoftware>
    </AnalysisSoftwareList>
    <SequenceCollection/>
    <AnalysisCollection>
        <SpectrumIdentification spectrumIdentificationList_ref="sil1" spectrumIdentificationProtocol_ref="sip1" id="si1">
            <InputSpectra spectraData_ref="sidmsrun"/>
            <SearchDatabaseRef searchDatabase_ref="SearchDB1"/>
        </SpectrumIdentification>
    </AnalysisCollection>
    <AnalysisProtocolCollection>
        <SpectrumIdentificationProtocol analysisSoftware_ref="as1" id="sip1">
            <SearchType>
                <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
            </SearchType>
            <AdditionalSearchParams>
                <!--Protein digestion parameters-->
                <userParam name="specoms:enzymePattern" value="([KR])([^P])"/>
                <userParam name="specoms:minimumPeptideLength" value="7"/>
                <userParam name="specoms:maximumPeptideLength" value="25"/>
                <userParam name="specoms:decoyBase" value="true"/>
                <userParam name="specoms:fixedModifications" value="MOD:00397@C"/>
                <userParam name="specoms:variableModifications" value=""/>
                <userParam name="specoms:nbMissCleavage" value="1"/>
                <userParam name="specoms:missDB" value="false"/>
                <!--SpecOms-->
                <userParam name="specoms:threshold" value="5"/>
                <userParam name="specoms:minimumScore" value="9"/>
                <userParam name="specoms:minimalMassDelta" value="-500"/>
                <userParam name="specoms:numberOfDecimals" value="2"/>
                <userParam name="specoms:decimalValue" value="2"/>
                <!--Parent ion selection-->
                <userParam name="specoms:minimumPeptideCharge" value="1"/>
                <userParam name="specoms:maximumPeptideCharge" value="3"/>
                <userParam name="specoms:parentIonMassToleranceUnit" value="ppm"/>
                <userParam name="specoms:parentIonMassTolerance" value="10"/>
                <!--Spectrum processing-->
                <userParam name="specoms:removeIsotope" value="false"/>
                <userParam name="specoms:spectrumLowerMzLimit" value="0"/>
                <userParam name="specoms:spectrumUpperMzLimit" value="2000"/>
                <userParam name="specoms:spectrumMinimumNumberOfPeaks" value="10"/>
                <userParam name="specoms:spectrumDynamicRange" value="0"/>
                <userParam name="specoms:maxMassesCount" value="60"/>
                <userParam name="specoms:modeledIons" value="y b"/>
                <userParam name="specoms:complementIonEnhancer" value="false"/>
                <userParam name="specoms:windowFilterWidth" value="0"/>
                <userParam name="specoms:windowFilterMax" value="0"/>
                <userParam name="specoms:spectrumFilterChargeDeconvolution" value="false"/>
                <!--PSM scoring-->
                <userParam name="specoms:msmsToleranceUnit" value="dalton"/>
                <userParam name="specoms:msmsTolerance" value="0.02"/>
            </AdditionalSearchParams>
            <ParentTolerance/>
            <Threshold>
                <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
            </Threshold>
        </SpectrumIdentificationProtocol>
    </AnalysisProtocolCollection>
    <DataCollection>
        <Inputs>
            <SearchDatabase location="/home/langella/developpement/git/specoms/tests/data/fasta_59678.fasta" id="SearchDB1">
                <FileFormat>
                    <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
                </FileFormat>
                <DatabaseName>
                    <userParam name="/home/langella/developpement/git/specoms/tests/data/fasta_59678.fasta"/>
                </DatabaseName>
            </SearchDatabase>
            <SpectraData location="../tests/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59678.mgf" name="01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59678" id="sidmsrun">
                <FileFormat>
                    <cvParam accession="MS:1000058" 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="sil1"/>
        </AnalysisData>
    </DataCollection>
</MzIdentML>
