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comparison test-data/bsa.mzid @ 5:233ce0ebad08 draft

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author iracooke
date Wed, 05 Mar 2014 01:16:36 -0500
parents a84952540969
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4:106286243378 5:233ce0ebad08
1 <?xml version="1.0" encoding="UTF-8"?>
2 <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" >
3 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
4 <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"/>
5 <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
6 <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>
7 </cvList>
8 <AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
9 <AnalysisSoftware version="Beta (v9517)" name="MS-GF+" id="ID_software">
10 <SoftwareName>
11 <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>
12 </SoftwareName>
13 </AnalysisSoftware>
14 </AnalysisSoftwareList>
15 <SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
16 <DBSequence accession="sp|ALBU_BOVIN|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq1">
17 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="sp|ALBU_BOVIN|" name="protein description"/>
18 </DBSequence>
19 <Peptide id="Pep1">
20 <PeptideSequence>YICDNQDTISSK</PeptideSequence>
21 <Modification monoisotopicMassDelta="57.021463735" location="3">
22 <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
23 </Modification>
24 </Peptide>
25 <PeptideEvidence isDecoy="false" post="L" pre="K" end="297" start="286" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_286_1_286"/>
26 </SequenceCollection>
27 <AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
28 <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
29 <InputSpectra spectraData_ref="SID_1"/>
30 <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
31 </SpectrumIdentification>
32 </AnalysisCollection>
33 <AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
34 <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
35 <SearchType>
36 <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
37 </SearchType>
38 <AdditionalSearchParams>
39 <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
40 <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>
41 <userParam value="false" name="TargetDecoyApproach"/>
42 <userParam value="0" name="MinIsotopeError"/>
43 <userParam value="1" name="MaxIsotopeError"/>
44 <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/>
45 <userParam value="LowRes" name="Instrument"/>
46 <userParam value="NoProtocol" name="Protocol"/>
47 <userParam value="2" name="NumTolerableTermini"/>
48 <userParam value="1" name="NumMatchesPerSpec"/>
49 <userParam value="6" name="MinPepLength"/>
50 <userParam value="40" name="MaxPepLength"/>
51 <userParam value="2" name="MinCharge"/>
52 <userParam value="3" name="MaxCharge"/>
53 </AdditionalSearchParams>
54 <ModificationParams>
55 <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
56 <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
57 </SearchModification>
58 </ModificationParams>
59 <Enzymes>
60 <Enzyme missedCleavages="1000" semiSpecific="false" id="Tryp">
61 <EnzymeName>
62 <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
63 </EnzymeName>
64 </Enzyme>
65 </Enzymes>
66 <ParentTolerance>
67 <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance plus value"/>
68 <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance minus value"/>
69 </ParentTolerance>
70 <Threshold>
71 <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
72 </Threshold>
73 </SpectrumIdentificationProtocol>
74 </AnalysisProtocolCollection>
75 <DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
76 <Inputs>
77 <SearchDatabase numDatabaseSequences="2" location="/Users/iracooke/Sources/protk-wk/bsa.fasta" id="SearchDB_1">
78 <FileFormat>
79 <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
80 </FileFormat>
81 <DatabaseName>
82 <userParam name="bsa.fasta"/>
83 </DatabaseName>
84 </SearchDatabase>
85 <SpectraData location="/Users/iracooke/Sources/protk-wk/bsa.mzML" name="bsa.mzML" id="SID_1">
86 <FileFormat>
87 <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
88 </FileFormat>
89 <SpectrumIDFormat>
90 <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/>
91 </SpectrumIDFormat>
92 </SpectraData>
93 </Inputs>
94 <AnalysisData>
95 <SpectrumIdentificationList id="SI_LIST_1">
96 <FragmentationTable>
97 <Measure id="Measure_MZ">
98 <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
99 </Measure>
100 </FragmentationTable>
101 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="index=0" id="SIR_1">
102 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="722.3251953125" experimentalMassToCharge="722.3522338867188" chargeState="2" id="SII_1_1">
103 <PeptideEvidenceRef peptideEvidence_ref="PepEv_286_1_286"/>
104 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="21" name="MS-GF:RawScore"/>
105 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="71" name="MS-GF:DeNovoScore"/>
106 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="2.0246382E-9" name="MS-GF:SpecEValue"/>
107 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="2.2635456E-6" name="MS-GF:EValue"/>
108 <userParam value="0" name="IsotopeError"/>
109 <userParam value="CID" name="AssumedDissociationMethod"/>
110 <userParam value="0.5818614" name="ExplainedIonCurrentRatio"/>
111 <userParam value="0.12558742" name="NTermIonCurrentRatio"/>
112 <userParam value="0.45627397" name="CTermIonCurrentRatio"/>
113 <userParam value="18513.0" name="MS2IonCurrent"/>
114 <userParam value="61.02686" name="MeanErrorAll"/>
115 <userParam value="64.35494" name="StdevErrorAll"/>
116 <userParam value="88.56576" name="MeanErrorTop7"/>
117 <userParam value="86.03032" name="StdevErrorTop7"/>
118 </SpectrumIdentificationItem>
119 </SpectrumIdentificationResult>
120 </SpectrumIdentificationList>
121 </AnalysisData>
122 </DataCollection>
123 </MzIdentML>