Mercurial > repos > galaxyp > openms_proteinquantifier
comparison test-data/SequenceCoverageCalculator.idXML @ 7:9d9660679916 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Fri, 17 May 2019 04:41:54 -0400 |
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6:aa2a99daec3f | 7:9d9660679916 |
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1 <?xml version="1.0" encoding="UTF-8"?> | |
2 <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> | |
3 <IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
4 <SearchParameters id="SP_0" db="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="3,4,5,6,7" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0.2" peak_mass_tolerance_ppm="false" > | |
5 <UserParam type="string" name="input_consensusXML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.consensusXML"/> | |
6 <UserParam type="string" name="input_mzML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.mzML"/> | |
7 <UserParam type="string" name="input_decoys" value=""/> | |
8 <UserParam type="int" name="decoy_prefix" value="0"/> | |
9 <UserParam type="string" name="decoy_string" value="decoy"/> | |
10 <UserParam type="string" name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp"/> | |
11 <UserParam type="int" name="precursor:min_charge" value="3"/> | |
12 <UserParam type="int" name="precursor:max_charge" value="7"/> | |
13 <UserParam type="float" name="fragment:mass_tolerance_xlinks" value="0.3"/> | |
14 <UserParam type="int" name="peptide:min_size" value="5"/> | |
15 <UserParam type="stringList" name="cross_link:residue1" value="[K]"/> | |
16 <UserParam type="stringList" name="cross_link:residue2" value="[K]"/> | |
17 <UserParam type="float" name="cross_link:mass" value="138.0680796"/> | |
18 <UserParam type="float" name="cross_link:mass_isoshift" value="12.075321"/> | |
19 <UserParam type="floatList" name="cross_link:mass_monolink" value="[156.07864431, 155.094628715]"/> | |
20 <UserParam type="string" name="cross_link:name" value="DSS"/> | |
21 <UserParam type="int" name="modifications:variable_max_per_peptide" value="2"/> | |
22 <UserParam type="int" name="MS:1001029" value="329"/> | |
23 </SearchParameters> | |
24 <IdentificationRun date="2018-03-06T13:21:04" search_engine="OpenXQuest" search_engine_version="2.3.0" search_parameters_ref="SP_0" > | |
25 <ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" > | |
26 <ProteinHit id="PH_0" accession="Protein3" score="0" sequence="" > | |
27 <UserParam type="string" name="target_decoy" value="target"/> | |
28 </ProteinHit> | |
29 <ProteinHit id="PH_1" accession="Protein2" score="0" sequence="" > | |
30 <UserParam type="string" name="target_decoy" value="target"/> | |
31 </ProteinHit> | |
32 <ProteinHit id="PH_2" accession="Protein1" score="0" sequence="" > | |
33 <UserParam type="string" name="target_decoy" value="target"/> | |
34 </ProteinHit> | |
35 <UserParam type="string" name="SpectrumIdentificationProtocol" value="MS:1002494"/> | |
36 </ProteinIdentification> | |
37 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="728.411010742188" RT="2120.05249023438" spectrum_reference="spectrum=99,spectrum=48" > | |
38 <PeptideHit score="0.936605209529642" sequence="LAAPQLVQMFIGDGAK(Xlink:DSS)LVR" charge="3" aa_before="K" aa_after="D" start="249" end="267" protein_refs="PH_1" > | |
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43 <UserParam type="float" name="xl_mass" value="156.07864431"/> | |
44 <UserParam type="string" name="xl_chain" value="MS:1002509"/> | |
45 <UserParam type="int" name="xl_pos" value="15"/> | |
46 <UserParam type="string" name="xl_type" value="mono-link"/> | |
47 <UserParam type="int" name="xl_rank" value="2"/> | |
48 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> | |
49 <UserParam type="float" name="spec_heavy_RT" value="2099.09545898438"/> | |
50 <UserParam type="float" name="spec_heavy_MZ" value="732.436096191406"/> | |
51 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=48"/> | |
52 <UserParam type="int" name="spectrum_index_heavy" value="39"/> | |
53 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="-3.29631082786707"/> | |
54 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.000333623265276995"/> | |
55 <UserParam type="float" name="OpenXQuest:xcorr common" value="-0.0259976562688046"/> | |
56 <UserParam type="float" name="OpenXQuest:match-odds" value="0.00212489435959964"/> | |
57 <UserParam type="float" name="OpenXQuest:intsum" value="0.334201395511627"/> | |
58 <UserParam type="float" name="OpenXQuest:wTIC" value="0.0688459236181392"/> | |
59 <UserParam type="float" name="OpenXQuest:TIC" value="0.0688459236181392"/> | |
60 <UserParam type="float" name="OpenXQuest:prescore" value="0.00694444449618459"/> | |
61 <UserParam type="float" name="OpenXQuest:log_occupancy" value="0.0564614974779924"/> | |
62 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="0.0564614974779924"/> | |
63 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> | |
64 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="0.0231329371940407"/> | |
65 <UserParam type="float" name="HyperCommon" value="0"/> | |
66 <UserParam type="float" name="HyperXlink" value="0.288332907246581"/> | |
67 <UserParam type="float" name="HyperAlpha" value="2.58943363761124"/> | |
68 <UserParam type="float" name="HyperBeta" value="0"/> | |
69 <UserParam type="float" name="HyperBoth" value="2.58943363761124"/> | |
70 <UserParam type="int" name="matched_xlink_alpha" value="1"/> | |
71 <UserParam type="int" name="matched_xlink_beta" value="0"/> | |
72 <UserParam type="int" name="matched_common_alpha" value="0"/> | |
73 <UserParam type="int" name="matched_common_beta" value="0"/> | |
74 <UserParam type="string" name="selected" value="false"/> | |
75 <UserParam type="string" name="protein_references" value="unique"/> | |
76 </PeptideHit> | |
77 </PeptideIdentification> | |
78 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="467.945617675781" RT="2129.23608398438" spectrum_reference="spectrum=123,spectrum=77" > | |
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81 <UserParam type="string" name="spectrum_reference" value="spectrum=123"/> | |
82 <UserParam type="string" name="target_decoy" value="target"/> | |
83 <UserParam type="int" name="spectrum_index" value="101"/> | |
84 <UserParam type="float" name="xl_mass" value="156.07864431"/> | |
85 <UserParam type="string" name="xl_chain" value="MS:1002509"/> | |
86 <UserParam type="int" name="xl_pos" value="5"/> | |
87 <UserParam type="string" name="xl_type" value="mono-link"/> | |
88 <UserParam type="int" name="xl_rank" value="1"/> | |
89 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> | |
90 <UserParam type="float" name="spec_heavy_RT" value="2110.98901367188"/> | |
91 <UserParam type="float" name="spec_heavy_MZ" value="471.971282958984"/> | |
92 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=77"/> | |
93 <UserParam type="int" name="spectrum_index_heavy" value="63"/> | |
94 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="0.735970556846563"/> | |
95 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.237457299396362"/> | |
96 <UserParam type="float" name="OpenXQuest:xcorr common" value="0.529048564861274"/> | |
97 <UserParam type="float" name="OpenXQuest:match-odds" value="1.3649637673649"/> | |
98 <UserParam type="float" name="OpenXQuest:intsum" value="2.92258863151073"/> | |
99 <UserParam type="float" name="OpenXQuest:wTIC" value="0.660300024858228"/> | |
100 <UserParam type="float" name="OpenXQuest:TIC" value="0.660300024858228"/> | |
101 <UserParam type="float" name="OpenXQuest:prescore" value="0.0795454531908035"/> | |
102 <UserParam type="float" name="OpenXQuest:log_occupancy" value="3.16483711801473"/> | |
103 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="3.16483711801473"/> | |
104 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> | |
105 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="2.33666522248801"/> | |
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109 <UserParam type="float" name="HyperBeta" value="0"/> | |
110 <UserParam type="float" name="HyperBoth" value="11.9960758128656"/> | |
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114 <UserParam type="int" name="matched_common_beta" value="0"/> | |
115 <UserParam type="string" name="selected" value="false"/> | |
116 <UserParam type="string" name="protein_references" value="unique"/> | |
117 </PeptideHit> | |
118 </PeptideIdentification> | |
119 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="656.050903320313" RT="2228.50292963107" spectrum_reference="spectrum=238,spectrum=219" > | |
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156 <UserParam type="string" name="selected" value="false"/> | |
157 <UserParam type="string" name="protein_references" value="unique"/> | |
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159 </PeptideIdentification> | |
160 </IdentificationRun> | |
161 </IdXML> |