Mercurial > repos > galaxyp > idconvert
view test-data/Rpal_01.pepXML @ 2:edb33e8224c6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
| author | galaxyp |
|---|---|
| date | Sat, 23 Feb 2019 06:21:11 -0500 |
| parents | 4f7d6bec667f |
| children |
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<?xml version="1.0" encoding="ISO-8859-1"?> <msms_pipeline_analysis date="2011-10-31T11:08:11" summary_xml="Rpal_01.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="2.1.101" time="2011-10-31T11:08:11"/> <msms_run_summary base_name="Rpal_01" raw_data_type="" raw_data=""> <sample_enzyme name="Trypsin/P" independent="false" fidelity="specific"> <specificity sense="C" cut="KR" no_cut="" min_spacing="1"/> </sample_enzyme> <search_summary base_name="Rpal_01" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data=""> <search_database local_path="Mark12-Rpal-20050929-reverse.fasta" database_name="SDB" type="AA"/> <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="100000" min_number_termini="2"/> <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/> <parameter name="Config: ClassSizeMultiplier" value="2"/> <parameter name="Config: CleavageRules" value="trypsin/p"/> <parameter name="Config: ComputeXCorr" value="1"/> <parameter name="Config: DecoyPrefix" value="rev_"/> <parameter name="Config: DynamicMods" value=""/> <parameter name="Config: EstimateSearchTimeOnly" value="0"/> <parameter name="Config: FragmentMzTolerance" value="30ppm"/> <parameter name="Config: FragmentationAutoRule" value="1"/> <parameter name="Config: FragmentationRule" value="cid"/> <parameter name="Config: MaxDynamicMods" value="2"/> <parameter name="Config: MaxFragmentChargeState" value="0"/> <parameter name="Config: MaxMissedCleavages" value="100000"/> <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="2"/> <parameter name="Config: MinPeptideLength" value="5"/> <parameter name="Config: MinPeptideMass" value="0"/> <parameter name="Config: MinResultScore" value="9.9999999999999995e-008"/> <parameter name="Config: MinTerminiCleavages" value="2"/> <parameter name="Config: MonoPrecursorMzTolerance" value="10ppm"/> <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/> <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="auto"/> <parameter name="Config: PreferIntenseComplements" value="1"/> <parameter name="Config: ProteinDatabase" value="Mark12-Rpal-20050929-reverse.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="C:\test\rpal-orbi-orbi\raw"/> <parameter name="PeakCounts: 1stQuartile: Filtered" value="94"/> <parameter name="PeakCounts: 1stQuartile: Original" value="109"/> <parameter name="PeakCounts: 2ndQuartile: Filtered" value="130"/> <parameter name="PeakCounts: 2ndQuartile: Original" value="148"/> <parameter name="PeakCounts: 3rdQuartile: Filtered" value="162"/> <parameter name="PeakCounts: 3rdQuartile: Original" value="182"/> <parameter name="PeakCounts: Mean: Filtered" value="127"/> <parameter name="PeakCounts: Mean: Original" value="143"/> <parameter name="PeakCounts: Min/Max: Filtered" value="9 / 299"/> <parameter name="PeakCounts: Min/Max: Original" value="9 / 365"/> <parameter name="SearchEngine: Name" value="MyriMatch"/> <parameter name="SearchEngine: Version" value="2.1.101"/> <parameter name="SearchStats: Nodes" value="1"/> <parameter name="SearchStats: Overall" value="9696 proteins; 2367559 peptides; 1463799 variants; 1624470 comparisons"/> <parameter name="SearchTime: Duration" value="18.9302578 seconds"/> <parameter name="SearchTime: Started" value="11:07:52 on 10/31/2011"/> <parameter name="SearchTime: Stopped" value="11:08:11 on 10/31/2011"/> </search_summary> <spectrum_query spectrum="Rpal_01.4.4.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=4" start_scan="4" end_scan="4" precursor_neutral_mass="971.24544706624" assumed_charge="2" index="2"> <search_result num_target_comparisons="2774" num_decoy_comparisons="2735"> <search_hit hit_rank="1" peptide="VMKNVIDR" peptide_prev_aa="R" peptide_next_aa="G" protein="rev_RPA0498" num_tot_proteins="1" calc_neutral_pep_mass="974.1791" massdiff="2.93365293376" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="14"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="13"/> <search_score name="mvh" value="5.705950021744"/> <search_score name="mzFidelity" value="7.087171850592"/> <search_score name="xcorr" value="0.12372587929479778"/> </search_hit> <search_hit hit_rank="2" peptide="RTTPLDLR" peptide_prev_aa="R" peptide_next_aa="R" protein="RPA1332" num_tot_proteins="1" calc_neutral_pep_mass="971.11226" massdiff="-0.13318706624" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="15"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="14"/> <search_score name="mvh" value="5.637738227844"/> <search_score name="mzFidelity" value="6.950056555619"/> <search_score name="xcorr" value="0.16826496059233614"/> </search_hit> <search_hit hit_rank="2" peptide="MYDFGSPR" peptide_prev_aa="K" peptide_next_aa="G" protein="rev_RPA3341" num_tot_proteins="1" calc_neutral_pep_mass="972.07534" massdiff="0.82989293376" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="1" tot_num_ions="15"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="14"/> <search_score name="mvh" value="5.637738227844"/> <search_score name="mzFidelity" value="6.950056555619"/> <search_score name="xcorr" value="0.24158960944600402"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.4.4.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=4" start_scan="4" end_scan="4" precursor_neutral_mass="1456.86817059936" assumed_charge="3" index="3"> <search_result num_target_comparisons="2774" num_decoy_comparisons="2735"> <search_hit hit_rank="1" peptide="AAAEGERVLGFALR" peptide_prev_aa="R" peptide_next_aa="S" protein="RPA1259" num_tot_proteins="1" calc_neutral_pep_mass="1459.64904" massdiff="2.78086940064" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="2" tot_num_ions="27"> <search_score name="number of matched peaks" value="2"/> <search_score name="number of unmatched peaks" value="25"/> <search_score name="mvh" value="9.639448642731"/> <search_score name="mzFidelity" value="12.288225127384"/> <search_score name="xcorr" value="0.24297397212008945"/> </search_hit> <search_hit hit_rank="1" peptide="ARDSAPSFLYGGGR" peptide_prev_aa="-" peptide_next_aa="I" protein="rev_RPA4791" num_tot_proteins="1" calc_neutral_pep_mass="1453.55834" massdiff="-3.30983059936" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="2" tot_num_ions="27"> <search_score name="number of matched peaks" value="2"/> <search_score name="number of unmatched peaks" value="25"/> <search_score name="mvh" value="9.639448642731"/> <search_score name="mzFidelity" value="12.288225127384"/> <search_score name="xcorr" value="0.29122955967718733"/> </search_hit> <search_hit hit_rank="2" peptide="YQFGSCGGGEVSIR" peptide_prev_aa="K" peptide_next_aa="L" protein="rev_RPA2856" num_tot_proteins="1" calc_neutral_pep_mass="1459.58276" massdiff="2.71458940064" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="2" tot_num_ions="28"> <search_score name="number of matched peaks" value="2"/> <search_score name="number of unmatched peaks" value="26"/> <search_score name="mvh" value="9.566092014313"/> <search_score name="mzFidelity" value="12.143032047397"/> <search_score name="xcorr" value="0.32399273418844676"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.6.6.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=6" start_scan="6" end_scan="6" precursor_neutral_mass="1435.68817059936" assumed_charge="3" index="5"> <search_result num_target_comparisons="2664" num_decoy_comparisons="2703"> <search_hit hit_rank="1" peptide="WTCTHREPDMR" peptide_prev_aa="K" peptide_next_aa="L" protein="rev_RPA0358" num_tot_proteins="1" calc_neutral_pep_mass="1431.5991" massdiff="-4.08907059936" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="22"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="21"/> <search_score name="mvh" value="4.771549940109"/> <search_score name="mzFidelity" value="6.19199306784"/> <search_score name="xcorr" value="0.33668218702788"/> </search_hit> <search_hit hit_rank="2" peptide="ALDAPEITEYWK" peptide_prev_aa="R" peptide_next_aa="S" protein="RPA2211" num_tot_proteins="1" calc_neutral_pep_mass="1435.57622" massdiff="-0.11195059936" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="1" tot_num_ions="23"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="22"/> <search_score name="mvh" value="4.72772860527"/> <search_score name="mzFidelity" value="6.104439812757"/> <search_score name="xcorr" value="0.50852873161295431"/> </search_hit> <search_hit hit_rank="2" peptide="GLTEVFGEFRER" peptide_prev_aa="R" peptide_next_aa="G" protein="rev_RPA2234" num_tot_proteins="1" calc_neutral_pep_mass="1439.57152" massdiff="3.88334940064" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="23"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="22"/> <search_score name="mvh" value="4.72772860527"/> <search_score name="mzFidelity" value="6.104439812757"/> <search_score name="xcorr" value="0.090642644567764358"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.18.18.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=18" start_scan="18" end_scan="18" precursor_neutral_mass="2444.86544706624" assumed_charge="2" index="7"> <search_result num_target_comparisons="2396" num_decoy_comparisons="2378"> <search_hit hit_rank="1" peptide="EAGVAVTVRLTVRRPRLGQPLR" peptide_prev_aa="K" peptide_next_aa="V" protein="rev_RPA0929" num_tot_proteins="1" calc_neutral_pep_mass="2444.8806" massdiff="0.01515293376" num_tol_term="2" num_missed_cleavages="4" num_matched_ions="1" tot_num_ions="29"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="28"/> <search_score name="mvh" value="6.366468429565"/> <search_score name="mzFidelity" value="5.650373022565"/> <search_score name="xcorr" value="0.19870963499199726"/> </search_hit> <search_hit hit_rank="2" peptide="PGRVRDEVLVPLPRPRTAEMR" peptide_prev_aa="R" peptide_next_aa="S" protein="RPA4163" num_tot_proteins="1" calc_neutral_pep_mass="2444.85738" massdiff="-0.00806706624" num_tol_term="2" num_missed_cleavages="4" num_matched_ions="1" tot_num_ions="28"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="27"/> <search_score name="mvh" value="5.484818696976"/> <search_score name="mzFidelity" value="5.718845762685"/> <search_score name="xcorr" value="0.21646692322489985"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.18.18.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=18" start_scan="18" end_scan="18" precursor_neutral_mass="3667.29817059936" assumed_charge="3" index="8"> <search_result num_target_comparisons="2396" num_decoy_comparisons="2378"> <search_hit hit_rank="1" peptide="WAEMEEFQGDKLAADLARTAETCDALIALDVDR" peptide_prev_aa="R" peptide_next_aa="I" protein="rev_RPA2760" num_tot_proteins="1" calc_neutral_pep_mass="3668.02742" massdiff="0.72924940064" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="1" tot_num_ions="62"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="61"/> <search_score name="mvh" value="5.621503353119"/> <search_score name="mzFidelity" value="4.220733811822"/> <search_score name="xcorr" value="0.23354606578336706"/> </search_hit> <search_hit hit_rank="2" peptide="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" peptide_prev_aa="K" peptide_next_aa="V" protein="rev_RPA3091" num_tot_proteins="1" calc_neutral_pep_mass="3664.2889" massdiff="-3.009270599361" num_tol_term="2" num_missed_cleavages="7" num_matched_ions="1" tot_num_ions="62"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="61"/> <search_score name="mvh" value="4.705212593079"/> <search_score name="mzFidelity" value="4.220733811822"/> <search_score name="xcorr" value="0.33999514155915078"/> </search_hit> <search_hit hit_rank="3" peptide="YGRPLRLNAPWWFWNMFGEQGVFLLSRAQK" peptide_prev_aa="R" peptide_next_aa="K" protein="RPA4436" num_tot_proteins="1" calc_neutral_pep_mass="3669.22194" massdiff="1.92376940064" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="1" tot_num_ions="56"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="55"/> <search_score name="mvh" value="4.216502189636"/> <search_score name="mzFidelity" value="4.403077095805"/> <search_score name="xcorr" value="0.31230731711549931"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.20.20.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=20" start_scan="20" end_scan="20" precursor_neutral_mass="836.62544706624" assumed_charge="2" index="10"> <search_result num_target_comparisons="2377" num_decoy_comparisons="2359"> <search_hit hit_rank="1" peptide="PPSHSRR" peptide_prev_aa="R" peptide_next_aa="A" protein="RPA2556" num_tot_proteins="1" calc_neutral_pep_mass="835.91088" massdiff="-0.71456706624" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="12"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="11"/> <search_score name="mvh" value="5.165723323822"/> <search_score name="mzFidelity" value="7.39388253707"/> <search_score name="xcorr" value="0.15096145810186862"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.20.20.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=20" start_scan="20" end_scan="20" precursor_neutral_mass="1254.93817059936" assumed_charge="3" index="11"> <search_result num_target_comparisons="2377" num_decoy_comparisons="2359"> <search_hit hit_rank="1" peptide="GRKKRRWDR" peptide_prev_aa="-" peptide_next_aa="K" protein="rev_RPA2576" num_tot_proteins="1" calc_neutral_pep_mass="1257.45118" massdiff="2.51300940064" num_tol_term="2" num_missed_cleavages="5" num_matched_ions="1" tot_num_ions="17"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="16"/> <search_score name="mvh" value="5.514616966248"/> <search_score name="mzFidelity" value="6.701621452441"/> <search_score name="xcorr" value="0.11619574564043432"/> </search_hit> <search_hit hit_rank="2" peptide="KRRDKKRLR" peptide_prev_aa="K" peptide_next_aa="E" protein="RPA3081" num_tot_proteins="1" calc_neutral_pep_mass="1255.51988" massdiff="0.58170940064" num_tol_term="2" num_missed_cleavages="6" num_matched_ions="1" tot_num_ions="18"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="17"/> <search_score name="mvh" value="5.458269119263"/> <search_score name="mzFidelity" value="6.588355047646"/> <search_score name="xcorr" value="0.44604161430476236"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.21.21.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=21" start_scan="21" end_scan="21" precursor_neutral_mass="1996.44544706624" assumed_charge="2" index="13"> <search_result num_target_comparisons="2376" num_decoy_comparisons="2457"> <search_hit hit_rank="1" peptide="VPRKPQPRKAAVRRPSR" peptide_prev_aa="K" peptide_next_aa="A" protein="rev_RPA2589" num_tot_proteins="1" calc_neutral_pep_mass="1999.3734" massdiff="2.92795293376" num_tol_term="2" num_missed_cleavages="6" num_matched_ions="1" tot_num_ions="29"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="28"/> <search_score name="mvh" value="5.263653278351"/> <search_score name="mzFidelity" value="5.650519300492"/> <search_score name="xcorr" value="0.38562970847777772"/> </search_hit> <search_hit hit_rank="2" peptide="KALEGDEHPDIIVFRKK" peptide_prev_aa="K" peptide_next_aa="D" protein="rev_RPA0865" num_tot_proteins="1" calc_neutral_pep_mass="1995.28208" massdiff="-1.16336706624" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="1" tot_num_ions="30"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="29"/> <search_score name="mvh" value="5.230051994324"/> <search_score name="mzFidelity" value="5.584485484559"/> <search_score name="xcorr" value="0.1350407991673217"/> </search_hit> <search_hit hit_rank="2" peptide="SVTPEYLICLEDGKRFK" peptide_prev_aa="K" peptide_next_aa="S" protein="RPA1852" num_tot_proteins="1" calc_neutral_pep_mass="1998.30256" massdiff="1.85711293376" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="1" tot_num_ions="30"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="29"/> <search_score name="mvh" value="5.230051994324"/> <search_score name="mzFidelity" value="5.584485484559"/> <search_score name="xcorr" value="0.21671201714405447"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Rpal_01.21.21.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=21" start_scan="21" end_scan="21" precursor_neutral_mass="2994.66817059936" assumed_charge="3" index="14"> <search_result num_target_comparisons="2376" num_decoy_comparisons="2457"> <search_hit hit_rank="1" peptide="FLMERYDRRNTETSEVGIVDFRKK" peptide_prev_aa="R" peptide_next_aa="I" protein="rev_RPA0940" num_tot_proteins="1" calc_neutral_pep_mass="2990.35276" massdiff="-4.31541059936" num_tol_term="2" num_missed_cleavages="5" num_matched_ions="1" tot_num_ions="45"> <search_score name="number of matched peaks" value="1"/> <search_score name="number of unmatched peaks" value="44"/> <search_score name="mvh" value="4.829092979431"/> <search_score name="mzFidelity" value="4.807287883047"/> <search_score name="xcorr" value="0.056497040579923996"/> </search_hit> <search_hit hit_rank="1" peptide="LIVQFQYYHQLRNPNEGYRGDKPR" peptide_prev_aa="K" peptide_next_aa="R" protein="rev_RPA1045" num_tot_proteins="1" calc_neutral_pep_mass="2992.30882" massdiff="-2.35935059936" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="1" 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