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