Mercurial > repos > galaxyp > idpquery
view test-data/201208-378803-mm.pepXML @ 3:42dc8e9e58d8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
| author | galaxyp |
|---|---|
| date | Thu, 02 Nov 2017 14:15:35 -0400 |
| parents | 032c02d10694 |
| children |
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<?xml version="1.0" encoding="ISO-8859-1"?> <msms_pipeline_analysis date="2015-09-03T15:49:50" 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="2015-09-03T15:49:50"/> <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data=""> <sample_enzyme name="Trypsin/P" independent="false" fidelity="semispecific"> <specificity sense="C" cut="KR" no_cut="" 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/P" max_num_internal_cleavages="2" min_number_termini="1"/> <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0353846062" variable="Y" description="Oxidation"/> <aminoacid_modification aminoacid="Q" massdiff="-17.026" mass="111.0325775114" peptide_terminus="n" variable="Y"/> <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.0425935114" variable="Y" description="Deamidated"/> <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.0269434472" variable="Y" description="Deamidated"/> <aminoacid_modification aminoacid="C" massdiff="58.00548" mass="161.0146644778" variable="N" description="Carboxymethyl"/> <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="XXX_"/> <parameter name="Config: DynamicMods" value="M * 15.9949 (Q * -17.026 [QN] * 0.984016"/> <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="2"/> <parameter name="Config: MaxFragmentChargeState" value="0"/> <parameter name="Config: MaxMissedCleavages" value="2"/> <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="3"/> <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="1"/> <parameter name="Config: MonoPrecursorMzTolerance" value="50ppm"/> <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/> <parameter name="Config: NumBatches" value="50"/> <parameter name="Config: NumChargeStates" value="5"/> <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="C 58.00548"/> <parameter name="Config: StatusUpdateFrequency" value="5"/> <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/> <parameter name="Config: UseMultipleProcessors" value="1"/> <parameter name="Config: UseSmartPlusThreeModel" value="0"/> <parameter name="Config: WorkingDirectory" value="/galaxy-central"/> <parameter name="PeakCounts: 1stQuartile: Filtered" value="115"/> <parameter name="PeakCounts: 1stQuartile: Original" value="120"/> <parameter name="PeakCounts: 2ndQuartile: Filtered" value="145"/> <parameter name="PeakCounts: 2ndQuartile: Original" value="154"/> <parameter name="PeakCounts: 3rdQuartile: Filtered" value="177"/> <parameter name="PeakCounts: 3rdQuartile: Original" value="180"/> <parameter name="PeakCounts: Mean: Filtered" value="149"/> <parameter name="PeakCounts: Mean: Original" value="157"/> <parameter name="PeakCounts: Min/Max: Filtered" value="40 / 296"/> <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; 516261 peptides; 2500621 variants; 1034167 comparisons"/> <parameter name="SearchTime: Duration" value="15.5659609 seconds"/> <parameter name="SearchTime: Started" value="15:49:34 on 09/03/2015"/> <parameter name="SearchTime: Stopped" value="15:49:50 on 09/03/2015"/> </search_summary> <spectrum_query spectrum="201208-378803.1.1.2" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1011.474906260116" assumed_charge="2" index="1" retention_time_sec="614.35099999998"> <search_result num_target_comparisons="0" num_decoy_comparisons="0"> <search_hit hit_rank="1" peptide="RSPALGAANR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1011.557375519" massdiff="0.082469258884" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="9" tot_num_ions="19"> <alternative_protein protein="gi|528993971|ref|XP_005219929.1|"/> <alternative_protein protein="gi|528993973|ref|XP_005219930.1|"/> <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/> <search_score name="mvh" value="20.943884244483"/> <search_score name="mzFidelity" value="40.011435006046"/> <search_score name="xcorr" value="2.113353934546164"/> </search_hit> <search_hit hit_rank="2" peptide="RSPALGAANR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1012.541391519" massdiff="0.057820343284" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="8" tot_num_ions="19"> <alternative_protein protein="gi|528993971|ref|XP_005219929.1|"/> <alternative_protein protein="gi|528993973|ref|XP_005219930.1|"/> <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/> <modification_info> <mod_aminoacid_mass position="9" mass="115.0269434472"/> </modification_info> <search_score name="mvh" value="19.008347302137"/> <search_score name="mzFidelity" value="35.588423710657"/> <search_score name="xcorr" value="1.9616309176657931"/> </search_hit> <search_hit hit_rank="3" peptide="QLPKSNAPR" peptide_prev_aa="K" peptide_next_aa="V" protein="gi|32880221|ref|NP_872593.1|" num_tot_proteins="1" calc_neutral_pep_mass="1010.5508935728" massdiff="0.084652228284" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="6" tot_num_ions="17"> <modification_info> <mod_aminoacid_mass position="6" mass="115.0269434472"/> </modification_info> <search_score name="mvh" value="12.941640349312"/> <search_score name="mzFidelity" value="27.424896373573"/> <search_score name="xcorr" value="1.3971794629675336"/> </search_hit> <search_hit hit_rank="4" peptide="EDPQDAIPK" peptide_prev_aa="L" peptide_next_aa="G" protein="gi|297479727|ref|XP_002690982.1|" num_tot_proteins="2" calc_neutral_pep_mass="1012.4713058478" massdiff="-0.012265327916" num_tol_term="1" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="17"> <alternative_protein protein="gi|528966552|ref|XP_005211956.1|"/> <modification_info> <mod_aminoacid_mass position="4" mass="129.0425935114"/> </modification_info> <search_score name="mvh" value="10.776069653902"/> <search_score name="mzFidelity" value="21.773698015738"/> <search_score name="xcorr" value="0.714776080009772"/> </search_hit> <search_hit hit_rank="5" peptide="NAAGLAPSRR" peptide_prev_aa="R" peptide_next_aa="N" protein="XXX_gi|27806851|ref|NP_776358.1|" num_tot_proteins="3" calc_neutral_pep_mass="1011.557375519" massdiff="0.082469258884" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="19"> <alternative_protein protein="XXX_gi|528993971|ref|XP_005219929.1|"/> <alternative_protein protein="XXX_gi|528993973|ref|XP_005219930.1|"/> <search_score name="mvh" value="10.229701455942"/> <search_score name="mzFidelity" value="22.932400378615"/> <search_score name="xcorr" value="0.90139108915810939"/> </search_hit> <search_hit hit_rank="6" peptide="DQDILNHR" peptide_prev_aa="M" peptide_next_aa="V" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1010.4781225602" massdiff="0.011881215684" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="15"> <modification_info> <mod_aminoacid_mass position="6" mass="115.0269434472"/> </modification_info> <search_score name="mvh" value="10.003747281739"/> <search_score name="mzFidelity" value="25.386798535619"/> <search_score name="xcorr" value="1.2327418458265254"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.1.1.4" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="2022.949812520232" assumed_charge="4" index="2" retention_time_sec="614.35099999998"> <search_result num_target_comparisons="0" num_decoy_comparisons="0"> <search_hit hit_rank="1" peptide="VRAAALKLGQELCGMLHR" peptide_prev_aa="L" peptide_next_aa="P" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="2023.0819199626" massdiff="0.132107442368" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="19" tot_num_ions="99"> <alternative_protein protein="gi|528921180|ref|XP_005195747.1|"/> <alternative_protein protein="gi|528995523|ref|XP_002695913.2|"/> <modification_info> <mod_aminoacid_mass position="13" mass="161.0146644778"/> </modification_info> <search_score name="mvh" value="21.467037536913"/> <search_score name="mzFidelity" value="19.37024464526"/> <search_score name="xcorr" value="2.2623632236296167"/> </search_hit> <search_hit hit_rank="2" peptide="AQDTGLPFTGKERDPPVPP" peptide_prev_aa="R" peptide_next_aa="F" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" 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<alternative_protein protein="gi|528966554|ref|XP_005211957.1|"/> <modification_info> <mod_aminoacid_mass position="13" mass="115.0269434472"/> <mod_aminoacid_mass position="19" mass="115.0269434472"/> </modification_info> <search_score name="mvh" value="22.75395632061"/> <search_score name="mzFidelity" value="24.10812825654"/> <search_score name="xcorr" value="3.2616588403384505"/> </search_hit> <search_hit hit_rank="3" peptide="LELLLQIANKIQNGALNCEEKL" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="2526.3251069949" massdiff="-0.34482882419" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="24" tot_num_ions="154"> <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/> <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/> <modification_info> <mod_aminoacid_mass position="12" mass="129.0425935114"/> <mod_aminoacid_mass position="13" mass="115.0269434472"/> <mod_aminoacid_mass 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value="14.521473880124"/> <search_score name="mzFidelity" value="10.1620270721"/> <search_score name="xcorr" value="1.5544656865133089"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="201208-378803.2.2.2" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="830.315296606328" assumed_charge="2" index="4" retention_time_sec="617.50600000002"> <search_result num_target_comparisons="3908" num_decoy_comparisons="4324"> <search_hit hit_rank="1" peptide="EDVPSER" peptide_prev_aa="K" peptide_next_aa="Y" protein="gi|30794348|ref|NP_851372.1|" num_tot_proteins="6" calc_neutral_pep_mass="830.3770111169" massdiff="0.061714510572" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="13"> <alternative_protein protein="gi|528953234|ref|XP_005208080.1|"/> <alternative_protein protein="gi|528953236|ref|XP_005208081.1|"/> <alternative_protein protein="gi|528953238|ref|XP_005208082.1|"/> 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