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comparison test-data/msgf-test.mzid @ 0:5a4801b7d106 draft default tip

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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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-1:000000000000 0:5a4801b7d106
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="2014-01-17T14:17:27" >
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 (v9881)" 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="gi|24373345|ref|NP_717388.1|" searchDatabase_ref="SearchDB_1" length="735" id="DBSeq1">
17 <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"/>
18 </DBSequence>
19 <DBSequence accession="gi|24371739|ref|NP_715781.1|" searchDatabase_ref="SearchDB_1" length="178" id="DBSeq737">
20 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371739|ref|NP_715781.1| ferritin Ftn [Shewanella oneidensis MR-1]" name="protein description"/>
21 </DBSequence>
22 <DBSequence accession="gi|24371954|ref|NP_715996.1|" searchDatabase_ref="SearchDB_1" length="400" id="DBSeq1994">
23 <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"/>
24 </DBSequence>
25 <DBSequence accession="gi|24373023|ref|NP_717065.1|" searchDatabase_ref="SearchDB_1" length="188" id="DBSeq1805">
26 <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"/>
27 </DBSequence>
28 <Peptide id="Pep1">
29 <PeptideSequence>FKWNGTDTNSAAEK</PeptideSequence>
30 </Peptide>
31 <Peptide id="Pep2">
32 <PeptideSequence>GGESIMNAQSQPQA</PeptideSequence>
33 </Peptide>
34 <Peptide id="Pep3">
35 <PeptideSequence>VIYTTNAVEAVHRQFRKLTK</PeptideSequence>
36 </Peptide>
37 <Peptide id="Pep4">
38 <PeptideSequence>VMRMLR</PeptideSequence>
39 </Peptide>
40 <PeptideEvidence isDecoy="false" post="R" pre="R" end="556" start="543" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_543_1_543"/>
41 <PeptideEvidence isDecoy="false" post="-" pre="K" end="178" start="165" peptide_ref="Pep2" dBSequence_ref="DBSeq737" id="PepEv_901_2_165"/>
42 <PeptideEvidence isDecoy="false" post="T" pre="K" end="346" start="327" peptide_ref="Pep3" dBSequence_ref="DBSeq1994" id="PepEv_2320_3_327"/>
43 <PeptideEvidence isDecoy="false" post="H" pre="R" end="161" start="156" peptide_ref="Pep4" dBSequence_ref="DBSeq1805" id="PepEv_1960_4_156"/>
44 </SequenceCollection>
45 <AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
46 <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
47 <InputSpectra spectraData_ref="SID_1"/>
48 <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
49 </SpectrumIdentification>
50 </AnalysisCollection>
51 <AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
52 <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
53 <SearchType>
54 <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
55 </SearchType>
56 <AdditionalSearchParams>
57 <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
58 <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>
59 <userParam value="true" name="TargetDecoyApproach"/>
60 <userParam value="-1" name="MinIsotopeError"/>
61 <userParam value="2" name="MaxIsotopeError"/>
62 <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/>
63 <userParam value="LowRes" name="Instrument"/>
64 <userParam value="NoProtocol" name="Protocol"/>
65 <userParam value="1" name="NumTolerableTermini"/>
66 <userParam value="1" name="NumMatchesPerSpec"/>
67 <userParam value="6" name="MinPepLength"/>
68 <userParam value="40" name="MaxPepLength"/>
69 <userParam value="2" name="MinCharge"/>
70 <userParam value="3" name="MaxCharge"/>
71 </AdditionalSearchParams>
72 <ModificationParams>
73 <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
74 <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
75 </SearchModification>
76 </ModificationParams>
77 <Enzymes>
78 <Enzyme missedCleavages="1000" semiSpecific="true" id="Tryp">
79 <EnzymeName>
80 <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
81 </EnzymeName>
82 </Enzyme>
83 </Enzymes>
84 <ParentTolerance>
85 <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance plus value"/>
86 <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance minus value"/>
87 </ParentTolerance>
88 <Threshold>
89 <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
90 </Threshold>
91 </SpectrumIdentificationProtocol>
92 </AnalysisProtocolCollection>
93 <DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
94 <Inputs>
95 <SearchDatabase numDatabaseSequences="10" location="C:\cygwin\home\kims336\Data\SkylineDemo\Abbreviated.fasta" id="SearchDB_1">
96 <FileFormat>
97 <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
98 </FileFormat>
99 <DatabaseName>
100 <userParam name="Abbreviated.fasta"/>
101 </DatabaseName>
102 <cvParam accession="MS:1001197" cvRef="PSI-MS" name="DB composition target+decoy"/>
103 <cvParam accession="MS:1001283" cvRef="PSI-MS" value="^XXX" name="decoy DB accession regexp"/>
104 <cvParam accession="MS:1001195" cvRef="PSI-MS" name="decoy DB type reverse"/>
105 </SearchDatabase>
106 <SpectraData location="msgf-test.mzML" name="msgf-test.mzML" id="SID_1">
107 <FileFormat>
108 <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
109 </FileFormat>
110 <SpectrumIDFormat>
111 <cvParam accession="MS:1000768" cvRef="PSI-MS" name="Thermo nativeID format"/>
112 </SpectrumIDFormat>
113 </SpectraData>
114 </Inputs>
115 <AnalysisData>
116 <SpectrumIdentificationList id="SI_LIST_1">
117 <FragmentationTable>
118 <Measure id="Measure_MZ">
119 <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
120 </Measure>
121 </FragmentationTable>
122 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10073" id="SIR_3">
123 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="784.87060546875" experimentalMassToCharge="784.8652954101562" chargeState="2" id="SII_3_1">
124 <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/>
125 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="173" name="MS-GF:RawScore"/>
126 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="228" name="MS-GF:DeNovoScore"/>
127 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="3.3660747E-14" name="MS-GF:SpecEValue"/>
128 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="1.6083104E-10" name="MS-GF:EValue"/>
129 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
130 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
131 <userParam value="0" name="IsotopeError"/>
132 <userParam value="CID" name="AssumedDissociationMethod"/>
133 </SpectrumIdentificationItem>
134 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10073" name="scan number(s)"/>
135 </SpectrumIdentificationResult>
136 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10075" id="SIR_5">
137 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="523.5828247070312" experimentalMassToCharge="523.5802001953125" chargeState="3" id="SII_5_1">
138 <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/>
139 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="81" name="MS-GF:RawScore"/>
140 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="104" name="MS-GF:DeNovoScore"/>
141 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.2290536E-12" name="MS-GF:SpecEValue"/>
142 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="5.8724186E-9" name="MS-GF:EValue"/>
143 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
144 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
145 <userParam value="0" name="IsotopeError"/>
146 <userParam value="CID" name="AssumedDissociationMethod"/>
147 </SpectrumIdentificationItem>
148 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10075" name="scan number(s)"/>
149 </SpectrumIdentificationResult>
150 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10071" id="SIR_1">
151 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep2" calculatedMassToCharge="709.3224487304688" experimentalMassToCharge="709.3134765625" chargeState="2" id="SII_1_1">
152 <PeptideEvidenceRef peptideEvidence_ref="PepEv_901_2_165"/>
153 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="50" name="MS-GF:RawScore"/>
154 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="114" name="MS-GF:DeNovoScore"/>
155 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="9.0045643E-10" name="MS-GF:SpecEValue"/>
156 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="4.3023806E-6" name="MS-GF:EValue"/>
157 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
158 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
159 <userParam value="0" name="IsotopeError"/>
160 <userParam value="CID" name="AssumedDissociationMethod"/>
161 </SpectrumIdentificationItem>
162 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10071" name="scan number(s)"/>
163 </SpectrumIdentificationResult>
164 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10074" id="SIR_4">
165 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep3" calculatedMassToCharge="792.1166381835938" experimentalMassToCharge="792.4600219726562" chargeState="3" id="SII_4_1">
166 <PeptideEvidenceRef peptideEvidence_ref="PepEv_2320_3_327"/>
167 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="25" name="MS-GF:RawScore"/>
168 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="123" name="MS-GF:DeNovoScore"/>
169 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="4.4064498E-7" name="MS-GF:SpecEValue"/>
170 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0021054016" name="MS-GF:EValue"/>
171 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
172 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
173 <userParam value="1" name="IsotopeError"/>
174 <userParam value="CID" name="AssumedDissociationMethod"/>
175 </SpectrumIdentificationItem>
176 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10074" name="scan number(s)"/>
177 </SpectrumIdentificationResult>
178 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10072" id="SIR_2">
179 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep4" calculatedMassToCharge="403.2303771972656" experimentalMassToCharge="403.7300109863281" chargeState="2" id="SII_2_1">
180 <PeptideEvidenceRef peptideEvidence_ref="PepEv_1960_4_156"/>
181 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="27" name="MS-GF:RawScore"/>
182 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="50" name="MS-GF:DeNovoScore"/>
183 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.4847345E-6" name="MS-GF:SpecEValue"/>
184 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0070940615" name="MS-GF:EValue"/>
185 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/>
186 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/>
187 <userParam value="1" name="IsotopeError"/>
188 <userParam value="CID" name="AssumedDissociationMethod"/>
189 </SpectrumIdentificationItem>
190 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10072" name="scan number(s)"/>
191 </SpectrumIdentificationResult>
192 </SpectrumIdentificationList>
193 </AnalysisData>
194 </DataCollection>
195 </MzIdentML>