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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 03090c9f45e9be50ed4c5e4df6419d0e8525c52d
author galaxyp
date Tue, 12 Mar 2024 11:46:44 +0000
parents 1320693cbf1e
children
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<?xml version="1.0" encoding="UTF-8"?>
<MzIdentML id="PeptideShaker v1.16.9" 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="2018-01-19T02:00:07">
	<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="1.16.9" 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">
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			<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></SequenceCollection>
	<AnalysisCollection>
		<SpectrumIdentification spectrumIdentificationList_ref="SIL_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 13.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 8.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 7.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 6.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 12.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 14.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 11.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 10.mgf"/>
			<InputSpectra spectraData_ref="Mascot formatted MGF of data 9.mgf"/>
			<SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
		</SpectrumIdentification>
		<ProteinDetection proteinDetectionProtocol_ref="PeptideShaker_1" proteinDetectionList_ref="Protein_groups" id="PD_1">
			<InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>
		</ProteinDetection>
	</AnalysisCollection>
	<AnalysisProtocolCollection>
		<SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
			<SearchType>
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			</SearchType>
			<AdditionalSearchParams>
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				<cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"/>
			</AdditionalSearchParams>
			<ModificationParams>
				<SearchModification residues="C" massDelta="57.021464" fixedMod= "true" >
					<cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
				</SearchModification>
				<SearchModification residues="K" massDelta="144.102062" fixedMod= "true" >
					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
				</SearchModification>
				<SearchModification residues="." massDelta="144.102062" fixedMod= "true" >
					<SpecificityRules>
						<cvParam cvRef="PSI-MS" accession="MS:1001189" name="modification specificity peptide N-term"/>
					</SpecificityRules>
					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
				</SearchModification>
				<SearchModification residues="M" massDelta="15.994915" fixedMod= "false" >
					<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
				</SearchModification>
				<SearchModification residues="Y" massDelta="144.102062" fixedMod= "false" >
					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
				</SearchModification>
			</ModificationParams>
			<Enzymes independent="false">
			<Enzyme missedCleavages="2" semiSpecific="false" id="Enz1" name="Trypsin">
				<EnzymeName>
					<cvParam cvRef="PSI-MS" accession="MS:1001251" name="Trypsin"/>
				</EnzymeName>
			</Enzyme>
		</Enzymes>
		<FragmentTolerance>
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		</ParentTolerance>
		<Threshold>
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			<cvParam cvRef="PSI-MS" accession="MS:1002350" name="PSM-level global FDR" value="1.0"/>
			<cvParam cvRef="PSI-MS" accession="MS:1002567" name="phosphoRS score threshold" value="95.0"/>
			<cvParam cvRef="PSI-MS" accession="MS:1002557" name="D-Score threshold" value="95.0"/>
		</Threshold>
	</SpectrumIdentificationProtocol>
	<ProteinDetectionProtocol analysisSoftware_ref="ID_software" id="PeptideShaker_1">
		<Threshold>
			<cvParam cvRef="PSI-MS" accession="MS:1002369" name="protein group-level global FDR" value="0.01"/>
		</Threshold>
	</ProteinDetectionProtocol>
</AnalysisProtocolCollection>
<DataCollection>
	<Inputs>
		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2010.t.xml" id="SourceFile_1">
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		</SourceFile>
		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2011.t.xml" id="SourceFile_2">
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		<SearchDatabase numDatabaseSequences="50348" location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/input_database.fasta" id="SearchDB_1">
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			<DatabaseName>
				<userParam name="input_database.fasta"/>
			</DatabaseName>
			<cvParam cvRef="PSI-MS" accession="MS:1001073" name="database type amino acid"/>
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		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2013.mgf" id="Mascot formatted MGF of data 13.mgf" name="Mascot formatted MGF of data 13.mgf">
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	<AnalysisData>
		<SpectrumIdentificationList id="SIL_1">
			<FragmentationTable>
				<Measure id="Measure_MZ">
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			</FragmentationTable>
			<SpectrumIdentificationResult spectraData_ref="Mascot formatted MGF of data 13.mgf" spectrumID="index=8003" id="SIR_1">
				<SpectrumIdentificationItem passThreshold="false" rank="1" peptide_ref="YPDSVCTVPSPPK_144.10206242080005-ATAA-1" calculatedMassToCharge="627.004694306842" experimentalMassToCharge="627.01001" chargeState="3" id="SII_1_1">
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						<IonType charge="1" index="0">
							<FragmentArray measure_ref="Measure_MZ" values="115.107475"/>
							<FragmentArray measure_ref="Measure_Int" values="28673.560547"/>
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							<FragmentArray measure_ref="Measure_MZ" values="746.385559"/>
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						<IonType charge="1" index="1 2 4 5 9">
							<FragmentArray measure_ref="Measure_MZ" values="291.216156 388.266693 572.326904 669.367859 1128.594971"/>
							<FragmentArray measure_ref="Measure_Int" values="3281.50415 2398.454346 483.902496 8817.573242 515.554626"/>
							<FragmentArray measure_ref="Measure_Error" values="0.0012894146879034452 -9.374341621537496E-4 -0.025518687282101382 -0.037327536132124806 -0.02537033580233583"/>
							<cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
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						<IonType charge="2" index="2 5 10">
							<FragmentArray measure_ref="Measure_MZ" values="194.601517 335.187775 608.353699"/>
							<FragmentArray measure_ref="Measure_Int" values="449.08316 3051.163086 580.203918"/>
							<FragmentArray measure_ref="Measure_Error" values="-0.03593645048707117 -0.018456501472030595 0.023875896557797205"/>
							<cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
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					<cvParam cvRef="PSI-MS" accession="MS:1002466" name="PeptideShaker PSM score" value="-5.9106"/>
					<cvParam cvRef="PSI-MS" accession="MS:1002467" name="PeptideShaker PSM confidence" value="10.1695"/>
					<cvParam cvRef="PSI-MS" accession="MS:1001330" name="X!Tandem:expect" value="3.9"/>
					<cvParam cvRef="PSI-MS" accession="MS:1001117" name="theoretical mass" value="1877.99225352009" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
					<cvParam cvRef="PSI-MS" accession="MS:1002540" name="PeptideShaker PSM confidence type" value="Not Validated"/>
				</SpectrumIdentificationItem>
				<cvParam cvRef="PSI-MS" accession="MS:1000796" name="spectrum title" value="Mo_Tai_iTRAQ_f8.09495.09495.3"/>
				<cvParam cvRef="PSI-MS" accession="MS:1000894" name="retention time" value="-1.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
			</SpectrumIdentificationResult>
			
			
			
		</SpectrumIdentificationList>
		<ProteinDetectionList id="Protein_groups">
			<ProteinAmbiguityGroup id="PAG_0">
				<ProteinDetectionHypothesis id="PAG_0_1" dBSequence_ref="P27048" passThreshold="true">
					<PeptideHypothesis peptideEvidence_ref="PepEv_5247">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_11948">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_38645">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_64667">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_68343">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>
					</PeptideHypothesis>
					<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>
					<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
					<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.0649"/>
				</ProteinDetectionHypothesis>
				<ProteinDetectionHypothesis id="PAG_0_2" dBSequence_ref="P63163" passThreshold="true">
					<PeptideHypothesis peptideEvidence_ref="PepEv_5248">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_11949">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_38646">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_64668">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>
					</PeptideHypothesis>
					<PeptideHypothesis peptideEvidence_ref="PepEv_68344">
						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>
					</PeptideHypothesis>
					<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
				</ProteinDetectionHypothesis>
				<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="62.4192"/>
				<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="99.9665"/>
				<cvParam cvRef="PSI-MS" accession="MS:1002542" name="PeptideShaker protein confidence type" value="Confident"/>
				<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="true"/>
			</ProteinAmbiguityGroup>
			
			<cvParam cvRef="PSI-MS" accession="MS:1002404" name="count of identified proteins" value="3290"/>
		</ProteinDetectionList>
	</AnalysisData>
</DataCollection>
</MzIdentML>