Mercurial > repos > iracooke > xtandem
comparison test-data/bsa.pepXML @ 8:16080891c80d
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author | iracooke |
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date | Tue, 05 Mar 2013 00:48:00 -0500 |
parents | 5d2228f63b53 |
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7:f16d64131371 | 8:16080891c80d |
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1 <?xml version="1.0" encoding="UTF-8"?> | |
2 <?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?> | |
3 <msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2013:02:27:09:50:15" summary_xml="/data/galaxy/galaxy/database/job_working_directory/004/4155//data/galaxy/galaxy/database/files/004/dataset_4786.dat" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"> | |
4 <msms_run_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783.dat" search_engine="X! Tandem (k-score)" raw_data_type="raw" raw_data="mzML"> | |
5 <sample_enzyme name="trypsin"> | |
6 <specificity cut="KR" no_cut="P" sense="C"/> | |
7 </sample_enzyme> | |
8 <search_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> | |
9 <search_database local_path="/data/galaxy/galaxy/database/files/004/dataset_4785.dat" type="AA"/> | |
10 <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1"/> | |
11 <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/> | |
12 <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification--> | |
13 <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification--> | |
14 <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification--> | |
15 | |
16 <!-- Input parameters --> | |
17 <parameter name="list path, default parameters" value="/data/galaxy/tools/tpp/default/bin/isb_default_input_kscore.xml"/> | |
18 <parameter name="list path, taxonomy information" value="/data/galaxy/galaxy/database/files/004/dataset_4783.taxonomy.xml"/> | |
19 <parameter name="output, histogram column width" value="30"/> | |
20 <parameter name="output, histograms" value="no"/> | |
21 <parameter name="output, log path" value=""/> | |
22 <parameter name="output, maximum valid expectation value" value="0.1"/> | |
23 <parameter name="output, message" value="1234567890"/> | |
24 <parameter name="output, one sequence copy" value="no"/> | |
25 <parameter name="output, parameters" value="yes"/> | |
26 <parameter name="output, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem"/> | |
27 <parameter name="output, path hashing" value="no"/> | |
28 <parameter name="output, performance" value="yes"/> | |
29 <parameter name="output, proteins" value="yes"/> | |
30 <parameter name="output, results" value="all"/> | |
31 <parameter name="output, sequence path" value=""/> | |
32 <parameter name="output, sequences" value="no"/> | |
33 <parameter name="output, sort results by" value="spectrum"/> | |
34 <parameter name="output, spectra" value="yes"/> | |
35 <parameter name="output, xsl path" value="tandem-style.xsl"/> | |
36 <parameter name="protein, C-terminal residue modification mass" value=""/> | |
37 <parameter name="protein, N-terminal residue modification mass" value=""/> | |
38 <parameter name="protein, cleavage semi" value="yes"/> | |
39 <parameter name="protein, cleavage site" value="[RK]|{P}"/> | |
40 <parameter name="protein, homolog management" value="no"/> | |
41 <parameter name="protein, modified residue mass file" value=""/> | |
42 <parameter name="protein, taxon" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/> | |
43 <parameter name="refine" value="no"/> | |
44 <parameter name="refine, maximum valid expectation value" value="0.1"/> | |
45 <parameter name="refine, sequence path" value=""/> | |
46 <parameter name="refine, spectrum synthesis" value="yes"/> | |
47 <parameter name="residue, modification mass" value="57.021464@C"/> | |
48 <parameter name="residue, potential modification mass" value=""/> | |
49 <parameter name="residue, potential modification motif" value=""/> | |
50 <parameter name="scoring, a ions" value="no"/> | |
51 <parameter name="scoring, algorithm" value="k-score"/> | |
52 <parameter name="scoring, b ions" value="yes"/> | |
53 <parameter name="scoring, c ions" value="no"/> | |
54 <parameter name="scoring, cyclic permutation" value="no"/> | |
55 <parameter name="scoring, include reverse" value="no"/> | |
56 <parameter name="scoring, maximum missed cleavage sites" value="2"/> | |
57 <parameter name="scoring, minimum ion count" value="1"/> | |
58 <parameter name="scoring, x ions" value="no"/> | |
59 <parameter name="scoring, y ions" value="yes"/> | |
60 <parameter name="scoring, z ions" value="no"/> | |
61 <parameter name="spectrum, dynamic range" value="10000.0"/> | |
62 <parameter name="spectrum, fragment mass type" value="monoisotopic"/> | |
63 <parameter name="spectrum, fragment monoisotopic mass error" value="0.65"/> | |
64 <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/> | |
65 <parameter name="spectrum, maximum parent charge" value="5"/> | |
66 <parameter name="spectrum, minimum fragment mz" value="125.0"/> | |
67 <parameter name="spectrum, minimum parent m+h" value="600.0"/> | |
68 <parameter name="spectrum, minimum peaks" value="10"/> | |
69 <parameter name="spectrum, parent monoisotopic mass error minus" value="50.0"/> | |
70 <parameter name="spectrum, parent monoisotopic mass error plus" value="50.0"/> | |
71 <parameter name="spectrum, parent monoisotopic mass error units" value="ppm"/> | |
72 <parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/> | |
73 <parameter name="spectrum, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783.dat"/> | |
74 <parameter name="spectrum, sequence batch size" value="1000"/> | |
75 <parameter name="spectrum, threads" value="1"/> | |
76 <parameter name="spectrum, total peaks" value="400"/> | |
77 <parameter name="spectrum, use conditioning" value="no"/> | |
78 <parameter name="spectrum, use noise suppression" value="yes"/> | |
79 <!-- Unused input parameters --> | |
80 <parameter name="refine, cleavage semi" value="yes"/> | |
81 <parameter name="refine, modification mass" value="57.012@C"/> | |
82 <parameter name="refine, point mutations" value="no"/> | |
83 <parameter name="refine, potential C-terminus modifications" value=""/> | |
84 <parameter name="refine, potential N-terminus modifications" value=""/> | |
85 <parameter name="refine, potential modification mass" value="15.994915@M"/> | |
86 <parameter name="refine, potential modification motif" value=""/> | |
87 <parameter name="refine, tic percent" value="10"/> | |
88 <parameter name="refine, unanticipated cleavage" value="no"/> | |
89 <parameter name="refine, use potential modifications for full refinement" value="no"/> | |
90 <parameter name="scoring, pluggable scoring" value="yes"/> | |
91 <!-- Performance parameters --> | |
92 <parameter name="list path, sequence source #1" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/> | |
93 <parameter name="list path, sequence source description #1" value="no description"/> | |
94 <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/> | |
95 <parameter name="modelling, total peptides used" value="1"/> | |
96 <parameter name="modelling, total proteins used" value="2"/> | |
97 <parameter name="modelling, total spectra used" value="1"/> | |
98 <parameter name="process, start time" value="2013:02:27:09:50:15"/> | |
99 <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/> | |
100 <parameter name="quality values" value="0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/> | |
101 <parameter name="refining, # input models" value="0"/> | |
102 <parameter name="refining, # input spectra" value="0"/> | |
103 <parameter name="refining, # partial cleavage" value="0"/> | |
104 <parameter name="refining, # point mutations" value="0"/> | |
105 <parameter name="refining, # potential C-terminii" value="0"/> | |
106 <parameter name="refining, # potential N-terminii" value="0"/> | |
107 <parameter name="refining, # unanticipated cleavage" value="0"/> | |
108 <parameter name="timing, initial modelling total (sec)" value="0.00"/> | |
109 <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/> | |
110 <parameter name="timing, load sequence models (sec)" value="0.00"/> | |
111 <parameter name="timing, refinement/spectrum (sec)" value="0.000"/> | |
112 </search_summary> | |
113 | |
114 <spectrum_query spectrum="dataset_4783.dat.00000.00000.2" start_scan="0" end_scan="0" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1"> | |
115 <search_result> | |
116 <search_hit hit_rank="1" peptide="YICDNQDTISSK" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|ALBU_BOVIN|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="22" calc_neutral_pep_mass="1442.6347" massdiff="0.055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> | |
117 <modification_info> | |
118 <mod_aminoacid_mass position="3" mass="160.0306"/> | |
119 </modification_info> | |
120 <search_score name="hyperscore" value="491"/> | |
121 <search_score name="nextscore" value="287"/> | |
122 <search_score name="bscore" value="0"/> | |
123 <search_score name="yscore" value="2"/> | |
124 <search_score name="cscore" value="0"/> | |
125 <search_score name="zscore" value="0"/> | |
126 <search_score name="ascore" value="0"/> | |
127 <search_score name="xscore" value="0"/> | |
128 <search_score name="expect" value="0.12"/> | |
129 </search_hit> | |
130 </search_result> | |
131 </spectrum_query> | |
132 </msms_run_summary> | |
133 </msms_pipeline_analysis> |