Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer

comparison test-data/SequenceCoverageCalculator.idXML @ 7:e98ae1229a67 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Fri, 17 May 2019 04:41:30 -0400
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6:d4a5a5f3497f 7:e98ae1229a67
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" >
39 <UserParam type="string" name="fragment_annotation" value="1004.99096679688,0.334201395511627,2,&quot;[alpha|xi$b18]&quot;"/>
40 <UserParam type="string" name="spectrum_reference" value="spectrum=99"/>
41 <UserParam type="string" name="target_decoy" value="target"/>
42 <UserParam type="int" name="spectrum_index" value="81"/>
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"/>
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53 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="-3.29631082786707"/>
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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" >
79 <PeptideHit score="28.2731402412177" sequence="GGVHVK(Xlink:DSS)LAHLSK" charge="3" aa_before="R" aa_after="H" start="292" end="303" protein_refs="PH_0" >
80 <UserParam type="string" name="fragment_annotation" value="396.987884521484,0.384458035230637,3,&quot;[alpha|xi$y9]&quot;|449.323913574219,0.387931138277054,3,&quot;[alpha|xi$y11]&quot;|450.284820556641,0.393777251243591,1,&quot;[alpha|ci$b5]&quot;|484.207611083984,0.215591758489609,1,&quot;[alpha|ci$y4]&quot;|555.274353027344,0.297201305627823,1,&quot;[alpha|ci$y5]&quot;|595.053527832031,1,2,&quot;[alpha|xi$y9]&quot;|668.345275878906,0.243629142642021,1,&quot;[alpha|ci$y6]&quot;"/>
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"/>
106 <UserParam type="float" name="HyperCommon" value="5.59770114368979"/>
107 <UserParam type="float" name="HyperXlink" value="4.32762764114041"/>
108 <UserParam type="float" name="HyperAlpha" value="11.9960758128656"/>
109 <UserParam type="float" name="HyperBeta" value="0"/>
110 <UserParam type="float" name="HyperBoth" value="11.9960758128656"/>
111 <UserParam type="int" name="matched_xlink_alpha" value="3"/>
112 <UserParam type="int" name="matched_xlink_beta" value="0"/>
113 <UserParam type="int" name="matched_common_alpha" value="4"/>
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" >
120 <PeptideHit score="30.0056519661123" sequence="EVIELPLK(Xlink:DSS)NPELFLR" charge="3" aa_before="R" aa_after="V" start="145" end="159" protein_refs="PH_2" >
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122 <UserParam type="string" name="spectrum_reference" value="spectrum=238"/>
123 <UserParam type="string" name="target_decoy" value="target"/>
124 <UserParam type="int" name="spectrum_index" value="195"/>
125 <UserParam type="float" name="xl_mass" value="156.07864431"/>
126 <UserParam type="string" name="xl_chain" value="MS:1002509"/>
127 <UserParam type="int" name="xl_pos" value="7"/>
128 <UserParam type="string" name="xl_type" value="mono-link"/>
129 <UserParam type="int" name="xl_rank" value="1"/>
130 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/>
131 <UserParam type="float" name="spec_heavy_RT" value="2221.23388666232"/>
132 <UserParam type="float" name="spec_heavy_MZ" value="660.072448730469"/>
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135 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="6.2016465793789"/>
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138 <UserParam type="float" name="OpenXQuest:match-odds" value="2.59304858228082"/>
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142 <UserParam type="float" name="OpenXQuest:prescore" value="0.107142858207226"/>
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156 <UserParam type="string" name="selected" value="false"/>
157 <UserParam type="string" name="protein_references" value="unique"/>
158 </PeptideHit>
159 </PeptideIdentification>
160 </IdentificationRun>
161 </IdXML>