Mercurial > repos > galaxyp > myrimatch
diff 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 | |
| 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 Wed Feb 01 20:53:23 2017 -0500 @@ -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 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