Mercurial > repos > galaxyp > myrimatch
view test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML @ 1:1881935e5351 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
| author | galaxyp |
|---|---|
| date | Wed, 01 Feb 2017 20:53:23 -0500 |
| parents | |
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<?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 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tot_num_ions="20"> <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/> <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/> <search_score name="mvh" value="9.356008366938"/> <search_score name="mzFidelity" value="19.437122229364"/> <search_score name="xcorr" value="0.57814169108246261"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.10.10.2" spectrumNativeID="sample=1 period=1 cycle=1210 experiment=2" start_scan="10" end_scan="10" precursor_neutral_mass="1192.563545399432" assumed_charge="2" index="12" retention_time_sec="718.45300000002"> <search_result num_target_comparisons="1" num_decoy_comparisons="1"> <search_hit hit_rank="1" peptide="DTHKSEIAHR" peptide_prev_aa="R" peptide_next_aa="F" protein="gi|30794280|ref|NP_851335.1|" num_tot_proteins="1" calc_neutral_pep_mass="1192.5948832373" massdiff="0.031337837868" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="19"> <search_score name="mvh" value="9.6813936101"/> <search_score name="mzFidelity" value="31.082800889076"/> <search_score name="xcorr" value="0.82413857764303688"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.11.11.2" spectrumNativeID="sample=1 period=1 cycle=1210 experiment=3" start_scan="11" end_scan="11" precursor_neutral_mass="921.41789833277" assumed_charge="2" index="13" retention_time_sec="720.588"> <search_result num_target_comparisons="3" num_decoy_comparisons="3"> <search_hit hit_rank="1" peptide="TCLASGNTR" peptide_prev_aa="R" peptide_next_aa="I" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="921.4338144893" massdiff="0.01591615653" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="17"> <alternative_protein protein="XXX_gi|528921180|ref|XP_005195747.1|"/> <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/> <search_score name="mvh" value="9.159765260459"/> <search_score name="mzFidelity" value="26.480682982104"/> <search_score name="xcorr" value="0.6390236904740334"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.12.12.2" spectrumNativeID="sample=1 period=1 cycle=1211 experiment=5" start_scan="12" end_scan="12" precursor_neutral_mass="994.45493277958" assumed_charge="2" index="14" retention_time_sec="731.703"> <search_result num_target_comparisons="5" num_decoy_comparisons="4"> <search_hit hit_rank="1" peptide="KAMGSNMEK" peptide_prev_aa="K" peptide_next_aa="V" protein="XXX_gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="994.4575863988" massdiff="0.00265361922" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="8" tot_num_ions="17"> <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="12.073735470826"/> <search_score name="mzFidelity" value="36.65584101311"/> <search_score name="xcorr" value="1.1047393040418625"/> </search_hit> <search_hit hit_rank="2" peptide="EVASTTMEK" peptide_prev_aa="K" peptide_next_aa="N" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="994.4641115647" massdiff="0.00917878512" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="17"> <search_score name="mvh" value="8.907421620351"/> <search_score name="mzFidelity" value="36.65584101311"/> <search_score name="xcorr" value="0.71224422781467434"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.13.13.3" spectrumNativeID="sample=1 period=1 cycle=1212 experiment=2" start_scan="13" end_scan="13" precursor_neutral_mass="1956.908783163726" assumed_charge="3" index="15" retention_time_sec="734.343"> <search_result num_target_comparisons="4" num_decoy_comparisons="0"> <search_hit 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protein="XXX_gi|528921180|ref|XP_005195747.1|"/> <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/> <search_score name="mvh" value="6.979786912131"/> <search_score name="mzFidelity" value="21.605021401289"/> <search_score name="xcorr" value="0.49320911207199097"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.32.32.3" spectrumNativeID="sample=1 period=1 cycle=1283 experiment=2" start_scan="32" end_scan="32" precursor_neutral_mass="1770.954827198736" assumed_charge="3" index="35" retention_time_sec="883.49500000002"> <search_result num_target_comparisons="1" num_decoy_comparisons="9"> <search_hit hit_rank="1" peptide="TEPHSFQRLSLTEVK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1770.9264477115" massdiff="-0.028379487236" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="30"> <search_score name="mvh" value="6.109846868339"/> <search_score name="mzFidelity" value="13.900987096911"/> <search_score name="xcorr" value="0.73578462478668327"/> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis>