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diff test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML @ 6:aec819a9068b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Fri, 06 Oct 2017 15:00:11 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML	Fri Oct 06 15:00:11 2017 -0400
@@ -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 name="mzFidelity" value="25.381087340985"/>
+          <search_score name="xcorr" value="1.1044896737935341"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="TKPQIWPKMAK" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|27806963|ref|NP_776953.1|" num_tot_proteins="1" calc_neutral_pep_mass="1326.7482127568" massdiff="0.054030589181" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="22">
+          <search_score name="mvh" value="5.65200821354"/>
+          <search_score name="mzFidelity" value="16.183265741347"/>
+          <search_score name="xcorr" value="0.19536201572501194"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.2.2.3" spectrumNativeID="sample=1 period=1 cycle=1192 experiment=3" start_scan="2" end_scan="2" precursor_neutral_mass="1296.540613339326" assumed_charge="3" index="2" retention_time_sec="641.23099999998">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="GEIFGTCGEEQK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1296.5656165233" massdiff="0.025003183974" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="23">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="4.73735499523"/>
+          <search_score name="mzFidelity" value="20.706193451615"/>
+          <search_score name="xcorr" value="-0.027179517265532343"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.3.3.2" spectrumNativeID="sample=1 period=1 cycle=1193 experiment=2" start_scan="3" end_scan="3" precursor_neutral_mass="915.392372425296" assumed_charge="2" index="3" retention_time_sec="643.866">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="4">
+        <search_hit hit_rank="1" peptide="KQYSCCGK" peptide_prev_aa="R" peptide_next_aa="C" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" calc_neutral_pep_mass="915.3942578605" massdiff="0.001885435204" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="15">
+          <alternative_protein protein="XXX_gi|358418103|ref|XP_600387.4|"/>
+          <alternative_protein protein="XXX_gi|528923273|ref|XP_005196452.1|"/>
+          <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/>
+          <search_score name="mvh" value="7.006737263411"/>
+          <search_score name="mzFidelity" value="20.083610152632"/>
+          <search_score name="xcorr" value="0.10145246835947037"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.4.4.3" spectrumNativeID="sample=1 period=1 cycle=1202 experiment=2" start_scan="4" end_scan="4" precursor_neutral_mass="1464.686590506963" assumed_charge="3" index="4" retention_time_sec="680.352">
+      <search_result num_target_comparisons="8" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="LMLLSRDDSGSGSK" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1464.7242424303" massdiff="0.037651923337" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="28">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="9.626642757254"/>
+          <search_score name="mzFidelity" value="17.69444115758"/>
+          <search_score name="xcorr" value="0.63278641261563584"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.5.5.2" spectrumNativeID="sample=1 period=1 cycle=1203 experiment=2" start_scan="5" end_scan="5" precursor_neutral_mass="1065.469667444928" assumed_charge="2" index="5" retention_time_sec="685.11700000002">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="1">
+        <search_hit hit_rank="1" peptide="FAVSAEAEDK" peptide_prev_aa="R" peptide_next_aa="V" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1065.4978545341" massdiff="0.028187089172" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="19">
+          <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="7.875817776738"/>
+          <search_score name="mzFidelity" value="25.766451627541"/>
+          <search_score name="xcorr" value="0.25966326437518"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.6.6.3" spectrumNativeID="sample=1 period=1 cycle=1204 experiment=3" start_scan="6" end_scan="6" precursor_neutral_mass="2165.295835942044" assumed_charge="3" index="6" retention_time_sec="692.03200000002">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="VIPSTGSKLKRPTPAFHSSR" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="1" calc_neutral_pep_mass="2165.2069200887" massdiff="-0.088915853344" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="7" tot_num_ions="40">
+          <search_score name="mvh" value="5.152631021794"/>
+          <search_score name="mzFidelity" value="13.354233874427"/>
+          <search_score name="xcorr" value="1.5719721875880248"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.7.7.2" spectrumNativeID="sample=1 period=1 cycle=1207 experiment=3" start_scan="7" end_scan="7" precursor_neutral_mass="932.457605578544" assumed_charge="2" index="7" retention_time_sec="702.072">
+      <search_result num_target_comparisons="6" num_decoy_comparisons="8">
+        <search_hit hit_rank="1" peptide="LQTECLAR" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" calc_neutral_pep_mass="932.4749510225" massdiff="0.017345443956" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="15">
+          <search_score name="mvh" value="9.497597217689"/>
+          <search_score name="mzFidelity" value="22.30229794645"/>
+          <search_score name="xcorr" value="0.49551840232685207"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.7.7.3" spectrumNativeID="sample=1 period=1 cycle=1207 experiment=3" start_scan="7" end_scan="7" precursor_neutral_mass="1398.686408367816" assumed_charge="3" index="8" retention_time_sec="702.072">
+      <search_result num_target_comparisons="6" num_decoy_comparisons="8">
+        <search_hit hit_rank="1" peptide="TVMENFVAFVDK" peptide_prev_aa="K" peptide_next_aa="C" protein="gi|30794280|ref|NP_851335.1|" num_tot_proteins="1" calc_neutral_pep_mass="1398.6853377285" massdiff="-0.001070639316" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="24">
+          <search_score name="mvh" value="8.903431641574"/>
+          <search_score name="mzFidelity" value="21.428101764821"/>
+          <search_score name="xcorr" value="0.76171054159046059"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="EETTDTSARPHR" peptide_prev_aa="K" peptide_next_aa="A" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="2" calc_neutral_pep_mass="1398.6487693013" massdiff="-0.037639066516" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="24">
+          <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/>
+          <search_score name="mvh" value="7.119124685496"/>
+          <search_score name="mzFidelity" value="15.436374094438"/>
+          <search_score name="xcorr" value="0.45455168821457648"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.8.8.2" spectrumNativeID="sample=1 period=1 cycle=1209 experiment=2" start_scan="8" end_scan="8" precursor_neutral_mass="902.494736213322" assumed_charge="2" index="9" retention_time_sec="709.46800000002">
+      <search_result num_target_comparisons="6" num_decoy_comparisons="14">
+        <search_hit hit_rank="1" peptide="WNTLNKK" peptide_prev_aa="R" peptide_next_aa="V" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="902.4974010241" massdiff="0.002664810778" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="13">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="7.659026625056"/>
+          <search_score name="mzFidelity" value="24.386949005179"/>
+          <search_score name="xcorr" value="0.58527988406121734"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.8.8.3" spectrumNativeID="sample=1 period=1 cycle=1209 experiment=2" start_scan="8" end_scan="8" precursor_neutral_mass="1353.742104319983" assumed_charge="3" index="10" retention_time_sec="709.46800000002">
+      <search_result num_target_comparisons="6" num_decoy_comparisons="14">
+        <search_hit hit_rank="1" peptide="TFAHTIDLLAPR" peptide_prev_aa="K" peptide_next_aa="T" protein="XXX_gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="1353.740484842" massdiff="-0.001619477983" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="24">
+          <alternative_protein protein="XXX_gi|358414198|ref|XP_002700672.2|"/>
+          <alternative_protein protein="XXX_gi|528966552|ref|XP_005211956.1|"/>
+          <alternative_protein protein="XXX_gi|528966554|ref|XP_005211957.1|"/>
+          <search_score name="mvh" value="5.426956514787"/>
+          <search_score name="mzFidelity" value="14.207593940125"/>
+          <search_score name="xcorr" value="0.081095695108339055"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.9.9.3" spectrumNativeID="sample=1 period=1 cycle=1209 experiment=5" start_scan="9" end_scan="9" precursor_neutral_mass="1209.554789334543" assumed_charge="3" index="11" retention_time_sec="715.80799999998">
+      <search_result num_target_comparisons="5" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="FSEIQDRCGR" peptide_prev_aa="R" peptide_next_aa="K" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1209.55605489" massdiff="0.001265555457" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="6" tot_num_ions="20">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="9.356008366938"/>
+          <search_score name="mzFidelity" value="19.437122229364"/>
+          <search_score name="xcorr" value="0.57814169108246261"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.10.10.2" spectrumNativeID="sample=1 period=1 cycle=1210 experiment=2" start_scan="10" end_scan="10" precursor_neutral_mass="1192.563545399432" assumed_charge="2" index="12" retention_time_sec="718.45300000002">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="1">
+        <search_hit hit_rank="1" peptide="DTHKSEIAHR" peptide_prev_aa="R" peptide_next_aa="F" protein="gi|30794280|ref|NP_851335.1|" num_tot_proteins="1" calc_neutral_pep_mass="1192.5948832373" massdiff="0.031337837868" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="19">
+          <search_score name="mvh" value="9.6813936101"/>
+          <search_score name="mzFidelity" value="31.082800889076"/>
+          <search_score name="xcorr" value="0.82413857764303688"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.11.11.2" spectrumNativeID="sample=1 period=1 cycle=1210 experiment=3" start_scan="11" end_scan="11" precursor_neutral_mass="921.41789833277" assumed_charge="2" index="13" retention_time_sec="720.588">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="TCLASGNTR" peptide_prev_aa="R" peptide_next_aa="I" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="921.4338144893" massdiff="0.01591615653" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|528921180|ref|XP_005195747.1|"/>
+          <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/>
+          <search_score name="mvh" value="9.159765260459"/>
+          <search_score name="mzFidelity" value="26.480682982104"/>
+          <search_score name="xcorr" value="0.6390236904740334"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.12.12.2" spectrumNativeID="sample=1 period=1 cycle=1211 experiment=5" start_scan="12" end_scan="12" precursor_neutral_mass="994.45493277958" assumed_charge="2" index="14" retention_time_sec="731.703">
+      <search_result num_target_comparisons="5" num_decoy_comparisons="4">
+        <search_hit hit_rank="1" peptide="KAMGSNMEK" peptide_prev_aa="K" peptide_next_aa="V" protein="XXX_gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="994.4575863988" massdiff="0.00265361922" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="8" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|358414198|ref|XP_002700672.2|"/>
+          <alternative_protein protein="XXX_gi|528966552|ref|XP_005211956.1|"/>
+          <alternative_protein protein="XXX_gi|528966554|ref|XP_005211957.1|"/>
+          <search_score name="mvh" value="12.073735470826"/>
+          <search_score name="mzFidelity" value="36.65584101311"/>
+          <search_score name="xcorr" value="1.1047393040418625"/>
+        </search_hit>
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+        <search_hit hit_rank="2" peptide="LQGELDVNFNLQAAGR" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|358418103|ref|XP_600387.4|" num_tot_proteins="1" calc_neutral_pep_mass="1743.8903965562" massdiff="0.056511341036" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="7" tot_num_ions="32">
+          <search_score name="mvh" value="7.396562819256"/>
+          <search_score name="mzFidelity" value="16.597930481493"/>
+          <search_score name="xcorr" value="0.85658302524349561"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.29.29.3" spectrumNativeID="sample=1 period=1 cycle=1224 experiment=2" start_scan="29" end_scan="29" precursor_neutral_mass="1725.858220325283" assumed_charge="3" index="32" retention_time_sec="814.37500000002">
+      <search_result num_target_comparisons="5" num_decoy_comparisons="5">
+        <search_hit hit_rank="1" peptide="IHGFDLAAINLQRCR" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1725.9096922103" massdiff="0.051471885017" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="12" tot_num_ions="30">
+          <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="12.259750257107"/>
+          <search_score name="mzFidelity" value="34.970325461964"/>
+          <search_score name="xcorr" value="1.9202226581428345"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="ISELFDKLDSMSVDK" peptide_prev_aa="R" peptide_next_aa="I" protein="XXX_gi|528968108|ref|XP_005212569.1|" num_tot_proteins="1" calc_neutral_pep_mass="1725.8495025234" massdiff="-0.008717801883" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="11" tot_num_ions="30">
+          <search_score name="mvh" value="11.323857836871"/>
+          <search_score name="mzFidelity" value="36.756835575306"/>
+          <search_score name="xcorr" value="0.93184037338923231"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.30.30.3" spectrumNativeID="sample=1 period=1 cycle=1231 experiment=2" start_scan="30" end_scan="30" precursor_neutral_mass="1467.72458061501" assumed_charge="3" index="33" retention_time_sec="839.28400000002">
+      <search_result num_target_comparisons="8" num_decoy_comparisons="2">
+        <search_hit hit_rank="1" peptide="GVTEHSNQQQGRK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1467.7178519195" massdiff="-0.00672869551" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="25">
+          <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="6.653798251586"/>
+          <search_score name="mzFidelity" value="14.932769947598"/>
+          <search_score name="xcorr" value="0.028206144867315191"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.31.31.2" spectrumNativeID="sample=1 period=1 cycle=1234 experiment=2" start_scan="31" end_scan="31" precursor_neutral_mass="1030.473954852586" assumed_charge="2" index="34" retention_time_sec="842.98000000002">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="TFAHQENGK" peptide_prev_aa="R" peptide_next_aa="R" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="1030.4832075229" massdiff="0.009252670314" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|528921180|ref|XP_005195747.1|"/>
+          <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/>
+          <search_score name="mvh" value="6.979786912131"/>
+          <search_score name="mzFidelity" value="21.605021401289"/>
+          <search_score name="xcorr" value="0.49320911207199097"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.32.32.3" spectrumNativeID="sample=1 period=1 cycle=1283 experiment=2" start_scan="32" end_scan="32" precursor_neutral_mass="1770.954827198736" assumed_charge="3" index="35" retention_time_sec="883.49500000002">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="9">
+        <search_hit hit_rank="1" peptide="TEPHSFQRLSLTEVK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1770.9264477115" massdiff="-0.028379487236" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="30">
+          <search_score name="mvh" value="6.109846868339"/>
+          <search_score name="mzFidelity" value="13.900987096911"/>
+          <search_score name="xcorr" value="0.73578462478668327"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+  </msms_run_summary>
+</msms_pipeline_analysis>