diff test-data/Rpal_01.pepXML @ 0:4f7d6bec667f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
author galaxyp
date Fri, 08 Apr 2016 16:07:32 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Rpal_01.pepXML	Fri Apr 08 16:07:32 2016 -0400
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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"/>
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+        <search_hit hit_rank="3" peptide="EADFTDWGLSSLMVNR" peptide_prev_aa="R" peptide_next_aa="L" protein="rev_RPA2968" num_tot_proteins="1" calc_neutral_pep_mass="1839.84614848" massdiff="0.001810541835" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="28">
+          <search_score name="number of matched peaks" value="6"/>
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+          <search_score name="mvh" value="19.410739660263"/>
+          <search_score name="mzFidelity" value="41.306898838258"/>
+          <search_score name="xcorr" value="0.78919111921824514"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="Rpal_01.2430.2430.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=2430" start_scan="2430" end_scan="2430" precursor_neutral_mass="1968.104831831865" assumed_charge="2" index="4037">
+      <search_result num_target_comparisons="194" num_decoy_comparisons="194">
+        <search_hit hit_rank="1" peptide="TISPNLLAGQALELLNSSK" peptide_prev_aa="K" peptide_next_aa="I" protein="RPA0879" num_tot_proteins="1" calc_neutral_pep_mass="1968.0891559434" massdiff="-0.015675888465" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="11" tot_num_ions="33">
+          <search_score name="number of matched peaks" value="11"/>
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+          <search_score name="mzFidelity" value="78.400661306264"/>
+          <search_score name="xcorr" value="0.78784737513214353"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="PIMREIAKEVVREPFR" peptide_prev_aa="R" peptide_next_aa="G" protein="rev_RPA2767" num_tot_proteins="1" calc_neutral_pep_mass="1969.0931358843" massdiff="-0.020360863165" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="4" tot_num_ions="28">
+          <search_score name="number of matched peaks" value="4"/>
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+          <search_score name="mvh" value="14.913594961166"/>
+          <search_score name="mzFidelity" value="26.189812145934"/>
+          <search_score name="xcorr" value="0.3146208707690239"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="Rpal_01.2433.2433.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=2433" start_scan="2433" end_scan="2433" precursor_neutral_mass="1783.937229292803" assumed_charge="2" index="4039">
+      <search_result num_target_comparisons="248" num_decoy_comparisons="263">
+        <search_hit hit_rank="1" peptide="SGEVTPIEVLDVLEER" peptide_prev_aa="K" peptide_next_aa="I" protein="RPA1734" num_tot_proteins="1" calc_neutral_pep_mass="1783.9203592806" massdiff="-0.016870012203" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="22" tot_num_ions="28">
+          <search_score name="number of matched peaks" value="22"/>
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+          <search_score name="mzFidelity" value="185.709221374132"/>
+          <search_score name="xcorr" value="5.4402822087663223"/>
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+        <search_hit hit_rank="2" peptide="TVEGWPVTPLAGAFGAGR" peptide_prev_aa="K" peptide_next_aa="S" protein="RPA0753" num_tot_proteins="1" calc_neutral_pep_mass="1784.9209684031" massdiff="-0.024925805303" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="31">
+          <search_score name="number of matched peaks" value="8"/>
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+          <search_score name="mvh" value="32.320402622223"/>
+          <search_score name="mzFidelity" value="55.524611432896"/>
+          <search_score name="xcorr" value="1.6306462675628719"/>
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+        <search_hit hit_rank="3" peptide="SREQPKEAVAKDDSPK" peptide_prev_aa="R" peptide_next_aa="K" protein="rev_RPA2658" num_tot_proteins="1" calc_neutral_pep_mass="1783.9064405509" massdiff="-0.030788741903" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="7" tot_num_ions="29">
+          <search_score name="number of matched peaks" value="7"/>
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+          <search_score name="mvh" value="28.938888072968"/>
+          <search_score name="mzFidelity" value="48.686009810194"/>
+          <search_score name="xcorr" value="0.80805631181364879"/>
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+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="Rpal_01.2434.2434.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=2434" start_scan="2434" end_scan="2434" precursor_neutral_mass="1081.63681425374" assumed_charge="2" index="4041">
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+        <search_hit hit_rank="1" peptide="QLGGPVWVVK" peptide_prev_aa="K" peptide_next_aa="S" protein="RPA0191" num_tot_proteins="1" calc_neutral_pep_mass="1081.6284151971" massdiff="-0.00839905664" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="18">
+          <search_score name="number of matched peaks" value="8"/>
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+          <search_score name="mvh" value="38.772735834122"/>
+          <search_score name="mzFidelity" value="65.054646326801"/>
+          <search_score name="xcorr" value="1.6667071547922678"/>
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+        <search_hit hit_rank="2" peptide="NPALRREVK" peptide_prev_aa="K" peptide_next_aa="L" protein="RPA2977" num_tot_proteins="1" calc_neutral_pep_mass="1081.63562584" massdiff="-0.00118841374" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="4" tot_num_ions="16">
+          <search_score name="number of matched peaks" value="4"/>
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+          <search_score name="mvh" value="17.102844238281"/>
+          <search_score name="mzFidelity" value="30.837907609603"/>
+          <search_score name="xcorr" value="0.44266026132227854"/>
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+        <search_hit hit_rank="3" peptide="AVFVGTLAFR" peptide_prev_aa="K" peptide_next_aa="S" protein="rev_RPA4668" num_tot_proteins="1" calc_neutral_pep_mass="1079.6127651329" massdiff="-0.00671928964" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="4" tot_num_ions="18">
+          <search_score name="number of matched peaks" value="4"/>
+          <search_score name="number of unmatched peaks" value="14"/>
+          <search_score name="mvh" value="16.589879512787"/>
+          <search_score name="mzFidelity" value="29.849243245154"/>
+          <search_score name="xcorr" value="0.67468716832110653"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="Rpal_01.2436.2436.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=2436" start_scan="2436" end_scan="2436" precursor_neutral_mass="1149.62544706624" assumed_charge="2" index="4043">
+      <search_result num_target_comparisons="871" num_decoy_comparisons="890">
+        <search_hit hit_rank="1" peptide="NPWEVFVEK" peptide_prev_aa="R" peptide_next_aa="H" protein="RPA0064" num_tot_proteins="1" calc_neutral_pep_mass="1147.27922" massdiff="-2.34622706624" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="10" tot_num_ions="16">
+          <search_score name="number of matched peaks" value="10"/>
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+          <search_score name="mvh" value="50.194524645805"/>
+          <search_score name="mzFidelity" value="86.851865019713"/>
+          <search_score name="xcorr" value="1.6098698580488562"/>
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+        <search_hit hit_rank="2" peptide="AWLDFVAEKA" peptide_prev_aa="R" peptide_next_aa="-" protein="RPA3576" num_tot_proteins="1" calc_neutral_pep_mass="1149.2951" massdiff="-0.33034706624" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="9" tot_num_ions="17">
+          <search_score name="number of matched peaks" value="9"/>
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+          <search_score name="mzFidelity" value="75.613555668398"/>
+          <search_score name="xcorr" value="1.9848502265699208"/>
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+        <search_hit hit_rank="3" peptide="DYGLRAGGSTR" peptide_prev_aa="R" peptide_next_aa="V" protein="rev_RPA4459" num_tot_proteins="1" calc_neutral_pep_mass="1152.21798" massdiff="2.59253293376" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="20">
+          <search_score name="number of matched peaks" value="7"/>
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+          <search_score name="mvh" value="29.204201936722"/>
+          <search_score name="mzFidelity" value="54.274397630421"/>
+          <search_score name="xcorr" value="1.0154997527897358"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+  </msms_run_summary>
+</msms_pipeline_analysis>