Mercurial > repos > galaxyp > idpquery
diff test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML @ 2:032c02d10694 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
| author | galaxyp |
|---|---|
| date | Fri, 06 Oct 2017 15:01:05 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML Fri Oct 06 15:01:05 2017 -0400 @@ -0,0 +1,499 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<msms_pipeline_analysis date="2015-09-03T17:55:14" summary_xml="201208-378803.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"> + <analysis_summary analysis="MyriMatch" version="2.2.8634" time="2015-09-03T17:55:14"/> + <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data=""> + <sample_enzyme name="Trypsin" independent="false" fidelity="specific"> + <specificity sense="C" cut="KR" no_cut="P" min_spacing="1"/> + </sample_enzyme> + <search_summary base_name="201208-378803" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data=""> + <search_database local_path="cow.protein.PRG2012-subset.fasta" database_name="SDB" type="AA"/> + <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="4" min_number_termini="2"/> + <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/> + <parameter name="Config: ClassSizeMultiplier" value="2"/> + <parameter name="Config: CleavageRules" value="Trypsin"/> + <parameter name="Config: ComputeXCorr" value="1"/> + <parameter name="Config: DecoyPrefix" value="XXX_"/> + <parameter name="Config: DynamicMods" value=""/> + <parameter name="Config: EstimateSearchTimeOnly" value="0"/> + <parameter name="Config: FragmentMzTolerance" value="0.5mz"/> + <parameter name="Config: FragmentationAutoRule" value="1"/> + <parameter name="Config: FragmentationRule" value="cid"/> + <parameter name="Config: KeepUnadjustedPrecursorMz" value="0"/> + <parameter name="Config: MaxDynamicMods" value="4"/> + <parameter name="Config: MaxFragmentChargeState" value="0"/> + <parameter name="Config: MaxMissedCleavages" value="4"/> + <parameter name="Config: MaxPeakCount" value="300"/> + <parameter name="Config: MaxPeptideLength" value="75"/> + <parameter name="Config: MaxPeptideMass" value="10000"/> + <parameter name="Config: MaxPeptideVariants" value="1000000"/> + <parameter name="Config: MaxResultRank" value="1"/> + <parameter name="Config: MinMatchedFragments" value="5"/> + <parameter name="Config: MinPeptideLength" value="5"/> + <parameter name="Config: MinPeptideMass" value="0"/> + <parameter name="Config: MinResultScore" value="9.9999999999999995e-08"/> + <parameter name="Config: MinTerminiCleavages" value="2"/> + <parameter name="Config: MonoPrecursorMzTolerance" value="15ppm"/> + <parameter name="Config: MonoisotopeAdjustmentSet" value="[0,0] "/> + <parameter name="Config: NumBatches" value="50"/> + <parameter name="Config: NumChargeStates" value="3"/> + <parameter name="Config: NumIntensityClasses" value="3"/> + <parameter name="Config: NumMzFidelityClasses" value="3"/> + <parameter name="Config: OutputFormat" value="pepXML"/> + <parameter name="Config: OutputSuffix" value=""/> + <parameter name="Config: PrecursorMzToleranceRule" value="mono"/> + <parameter name="Config: PreferIntenseComplements" value="1"/> + <parameter name="Config: ProteinDatabase" value="cow.protein.PRG2012-subset.fasta"/> + <parameter name="Config: ProteinListFilters" value=""/> + <parameter name="Config: ProteinSamplingTime" value="15"/> + <parameter name="Config: ResultsPerBatch" value="200000"/> + <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/> + <parameter name="Config: StaticMods" value=""/> + <parameter name="Config: StatusUpdateFrequency" value="5"/> + <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/> + <parameter name="Config: UseMultipleProcessors" value="1"/> + <parameter name="Config: UseSmartPlusThreeModel" value="1"/> + <parameter name="Config: WorkingDirectory" value="/galaxy-central"/> + <parameter name="PeakCounts: 1stQuartile: Filtered" value="116"/> + <parameter name="PeakCounts: 1stQuartile: Original" value="120"/> + <parameter name="PeakCounts: 2ndQuartile: Filtered" value="146"/> + <parameter name="PeakCounts: 2ndQuartile: Original" value="154"/> + <parameter name="PeakCounts: 3rdQuartile: Filtered" value="178"/> + <parameter name="PeakCounts: 3rdQuartile: Original" value="180"/> + <parameter name="PeakCounts: Mean: Filtered" value="151"/> + <parameter name="PeakCounts: Mean: Original" value="157"/> + <parameter name="PeakCounts: Min/Max: Filtered" value="41 / 298"/> + <parameter name="PeakCounts: Min/Max: Original" value="42 / 471"/> + <parameter name="SearchEngine: Name" value="MyriMatch"/> + <parameter name="SearchEngine: Version" value="2.2.8634"/> + <parameter name="SearchStats: Nodes" value="1"/> + <parameter name="SearchStats: Overall" value="144 proteins; 49480 peptides; 27944 variants; 401 comparisons"/> + <parameter name="SearchTime: Duration" value="0.342288971 seconds"/> + <parameter name="SearchTime: Started" value="17:55:14 on 09/03/2015"/> + <parameter name="SearchTime: Stopped" value="17:55:14 on 09/03/2015"/> + </search_summary> + <spectrum_query spectrum="201208-378803.1.1.3" spectrumNativeID="sample=1 period=1 cycle=1192 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1326.694182167619" assumed_charge="3" index="1" retention_time_sec="639.111"> + <search_result num_target_comparisons="0" num_decoy_comparisons="0"> + <search_hit hit_rank="1" peptide="GDRADKQLVVAR" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1326.7367964476" massdiff="0.042614279981" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="7" tot_num_ions="23"> + <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/> + <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/> + <search_score name="mvh" value="9.156783954627"/> + <search_score name="mzFidelity" value="25.381087340985"/> + <search_score name="xcorr" value="1.1044896737935341"/> + </search_hit> + <search_hit hit_rank="2" peptide="TKPQIWPKMAK" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|27806963|ref|NP_776953.1|" num_tot_proteins="1" calc_neutral_pep_mass="1326.7482127568" massdiff="0.054030589181" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="22"> + <search_score name="mvh" value="5.65200821354"/> + <search_score name="mzFidelity" value="16.183265741347"/> + <search_score name="xcorr" value="0.19536201572501194"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.2.2.3" spectrumNativeID="sample=1 period=1 cycle=1192 experiment=3" start_scan="2" end_scan="2" precursor_neutral_mass="1296.540613339326" assumed_charge="3" index="2" retention_time_sec="641.23099999998"> + <search_result num_target_comparisons="3" num_decoy_comparisons="0"> + <search_hit hit_rank="1" peptide="GEIFGTCGEEQK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1296.5656165233" massdiff="0.025003183974" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="23"> + <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/> + <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/> + <search_score name="mvh" value="4.73735499523"/> + <search_score name="mzFidelity" value="20.706193451615"/> + <search_score name="xcorr" value="-0.027179517265532343"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.3.3.2" spectrumNativeID="sample=1 period=1 cycle=1193 experiment=2" start_scan="3" end_scan="3" precursor_neutral_mass="915.392372425296" assumed_charge="2" index="3" retention_time_sec="643.866"> + <search_result num_target_comparisons="0" num_decoy_comparisons="4"> + <search_hit hit_rank="1" peptide="KQYSCCGK" peptide_prev_aa="R" peptide_next_aa="C" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" calc_neutral_pep_mass="915.3942578605" massdiff="0.001885435204" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="15"> + <alternative_protein protein="XXX_gi|358418103|ref|XP_600387.4|"/> + <alternative_protein protein="XXX_gi|528923273|ref|XP_005196452.1|"/> + <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/> + <search_score name="mvh" value="7.006737263411"/> + <search_score name="mzFidelity" value="20.083610152632"/> + <search_score name="xcorr" value="0.10145246835947037"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.4.4.3" spectrumNativeID="sample=1 period=1 cycle=1202 experiment=2" start_scan="4" end_scan="4" precursor_neutral_mass="1464.686590506963" assumed_charge="3" index="4" retention_time_sec="680.352"> + <search_result num_target_comparisons="8" num_decoy_comparisons="3"> + <search_hit hit_rank="1" peptide="LMLLSRDDSGSGSK" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1464.7242424303" massdiff="0.037651923337" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="28"> + <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/> + <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/> + <search_score name="mvh" value="9.626642757254"/> + <search_score name="mzFidelity" value="17.69444115758"/> + <search_score name="xcorr" value="0.63278641261563584"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.5.5.2" spectrumNativeID="sample=1 period=1 cycle=1203 experiment=2" start_scan="5" end_scan="5" precursor_neutral_mass="1065.469667444928" assumed_charge="2" index="5" retention_time_sec="685.11700000002"> + <search_result num_target_comparisons="3" num_decoy_comparisons="1"> + <search_hit hit_rank="1" peptide="FAVSAEAEDK" peptide_prev_aa="R" peptide_next_aa="V" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1065.4978545341" massdiff="0.028187089172" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="19"> + <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/> + <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/> + <search_score name="mvh" value="7.875817776738"/> + <search_score name="mzFidelity" value="25.766451627541"/> + <search_score name="xcorr" value="0.25966326437518"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.6.6.3" spectrumNativeID="sample=1 period=1 cycle=1204 experiment=3" start_scan="6" end_scan="6" precursor_neutral_mass="2165.295835942044" assumed_charge="3" index="6" retention_time_sec="692.03200000002"> + <search_result num_target_comparisons="1" num_decoy_comparisons="0"> + <search_hit hit_rank="1" peptide="VIPSTGSKLKRPTPAFHSSR" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="1" calc_neutral_pep_mass="2165.2069200887" massdiff="-0.088915853344" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="7" tot_num_ions="40"> + <search_score name="mvh" value="5.152631021794"/> + <search_score name="mzFidelity" value="13.354233874427"/> + <search_score name="xcorr" value="1.5719721875880248"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.7.7.2" spectrumNativeID="sample=1 period=1 cycle=1207 experiment=3" start_scan="7" end_scan="7" precursor_neutral_mass="932.457605578544" assumed_charge="2" index="7" retention_time_sec="702.072"> + <search_result num_target_comparisons="6" num_decoy_comparisons="8"> + <search_hit hit_rank="1" peptide="LQTECLAR" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" calc_neutral_pep_mass="932.4749510225" massdiff="0.017345443956" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="15"> + <search_score name="mvh" value="9.497597217689"/> + <search_score name="mzFidelity" value="22.30229794645"/> + <search_score name="xcorr" value="0.49551840232685207"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.7.7.3" spectrumNativeID="sample=1 period=1 cycle=1207 experiment=3" start_scan="7" end_scan="7" precursor_neutral_mass="1398.686408367816" assumed_charge="3" index="8" retention_time_sec="702.072"> + <search_result num_target_comparisons="6" num_decoy_comparisons="8"> + <search_hit hit_rank="1" peptide="TVMENFVAFVDK" peptide_prev_aa="K" peptide_next_aa="C" protein="gi|30794280|ref|NP_851335.1|" num_tot_proteins="1" calc_neutral_pep_mass="1398.6853377285" massdiff="-0.001070639316" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="24"> + <search_score name="mvh" value="8.903431641574"/> + <search_score name="mzFidelity" value="21.428101764821"/> + <search_score name="xcorr" value="0.76171054159046059"/> + </search_hit> + <search_hit hit_rank="2" peptide="EETTDTSARPHR" peptide_prev_aa="K" peptide_next_aa="A" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="2" calc_neutral_pep_mass="1398.6487693013" massdiff="-0.037639066516" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="24"> + <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/> + <search_score name="mvh" value="7.119124685496"/> + <search_score name="mzFidelity" value="15.436374094438"/> + <search_score name="xcorr" value="0.45455168821457648"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.8.8.2" spectrumNativeID="sample=1 period=1 cycle=1209 experiment=2" start_scan="8" end_scan="8" precursor_neutral_mass="902.494736213322" assumed_charge="2" index="9" retention_time_sec="709.46800000002"> + <search_result num_target_comparisons="6" num_decoy_comparisons="14"> + <search_hit hit_rank="1" peptide="WNTLNKK" peptide_prev_aa="R" peptide_next_aa="V" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="902.4974010241" massdiff="0.002664810778" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="13"> + <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/> + <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/> + <search_score name="mvh" value="7.659026625056"/> + <search_score name="mzFidelity" value="24.386949005179"/> + <search_score name="xcorr" value="0.58527988406121734"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.8.8.3" spectrumNativeID="sample=1 period=1 cycle=1209 experiment=2" start_scan="8" end_scan="8" precursor_neutral_mass="1353.742104319983" assumed_charge="3" index="10" retention_time_sec="709.46800000002"> + <search_result num_target_comparisons="6" num_decoy_comparisons="14"> + <search_hit hit_rank="1" peptide="TFAHTIDLLAPR" peptide_prev_aa="K" peptide_next_aa="T" protein="XXX_gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="1353.740484842" massdiff="-0.001619477983" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="24"> + <alternative_protein protein="XXX_gi|358414198|ref|XP_002700672.2|"/> + <alternative_protein protein="XXX_gi|528966552|ref|XP_005211956.1|"/> + <alternative_protein protein="XXX_gi|528966554|ref|XP_005211957.1|"/> + <search_score name="mvh" value="5.426956514787"/> + <search_score name="mzFidelity" value="14.207593940125"/> + <search_score name="xcorr" value="0.081095695108339055"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="201208-378803.9.9.3" 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