Mercurial > repos > galaxyp > idpquery
diff test-data/201208-378803-mm.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.pepXML Fri Oct 06 15:01:05 2017 -0400 @@ -0,0 +1,20531 @@ +<?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|" 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