annotate test-data/201208-378803-mm.pepXML @ 2:dd33125925d9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?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" calc_neutral_pep_mass="2021.0218046597" massdiff="0.089321970668" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="16" tot_num_ions="102">
          <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="21.038913054038"/>
          <search_score name="mzFidelity" value="20.708945557204"/>
          <search_score name="xcorr" value="1.7484519315798444"/>
        </search_hit>
        <search_hit hit_rank="3" 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="2024.0659359626" massdiff="0.107458526768" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="18" 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="10" mass="129.0425935114"/>
            <mod_aminoacid_mass position="13" mass="161.0146644778"/>
          </modification_info>
          <search_score name="mvh" value="19.477768930341"/>
          <search_score name="mzFidelity" value="19.862979428176"/>
          <search_score name="xcorr" value="2.5029671826385758"/>
        </search_hit>
        <search_hit hit_rank="4" peptide="AAALKLGQELCGMLHRPR" peptide_prev_aa="R" peptide_next_aa="H" protein="gi|528995523|ref|XP_002695913.2|" num_tot_proteins="1" calc_neutral_pep_mass="2021.0662698984" massdiff="0.133787209368" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="15" tot_num_ions="96">
          <modification_info>
            <mod_aminoacid_mass position="11" mass="161.0146644778"/>
          </modification_info>
          <search_score name="mvh" value="15.095047502377"/>
          <search_score name="mzFidelity" value="16.115018508678"/>
          <search_score name="xcorr" value="1.9267737457763163"/>
        </search_hit>
        <search_hit hit_rank="5" peptide="PRHLMGCLEQGLKLAAAR" peptide_prev_aa="R" peptide_next_aa="V" protein="XXX_gi|528995523|ref|XP_002695913.2|" num_tot_proteins="1" calc_neutral_pep_mass="2021.0662698984" massdiff="0.133787209368" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="13" tot_num_ions="99">
          <modification_info>
            <mod_aminoacid_mass position="7" mass="161.0146644778"/>
          </modification_info>
          <search_score name="mvh" value="12.532513600259"/>
          <search_score name="mzFidelity" value="12.691293478724"/>
          <search_score name="xcorr" value="1.32307615270207"/>
        </search_hit>
      </search_result>
    </spectrum_query>
    <spectrum_query spectrum="201208-378803.1.1.5" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="2526.66993581909" assumed_charge="5" index="3" retention_time_sec="614.35099999998">
      <search_result num_target_comparisons="0" num_decoy_comparisons="0">
        <search_hit hit_rank="1" 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="25" tot_num_ions="154">
          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
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            <mod_aminoacid_mass position="12" mass="129.0425935114"/>
            <mod_aminoacid_mass position="17" mass="115.0269434472"/>
            <mod_aminoacid_mass position="18" mass="161.0146644778"/>
          </modification_info>
          <search_score name="mvh" value="24.555168021719"/>
          <search_score name="mzFidelity" value="13.158130753361"/>
          <search_score name="xcorr" value="2.6769549653109732"/>
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        <search_hit hit_rank="1" 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="25" tot_num_ions="154">
          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
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            <mod_aminoacid_mass position="13" mass="115.0269434472"/>
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          </modification_info>
          <search_score name="mvh" value="24.555168021719"/>
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          <search_score name="xcorr" value="2.6858516440138747"/>
        </search_hit>
        <search_hit hit_rank="2" peptide="QERLALEATIKDNESEEGNGGIR" peptide_prev_aa="E" peptide_next_aa="G" protein="gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="2530.214704231" massdiff="0.518773665111" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="25" tot_num_ions="162">
          <alternative_protein protein="gi|358414198|ref|XP_002700672.2|"/>
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          <modification_info>
            <mod_aminoacid_mass position="13" mass="115.0269434472"/>
            <mod_aminoacid_mass position="19" mass="115.0269434472"/>
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          <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|"/>
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            <mod_aminoacid_mass position="12" mass="129.0425935114"/>
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            <mod_aminoacid_mass position="18" mass="161.0146644778"/>
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          <search_score name="mvh" value="22.352043722256"/>
          <search_score name="mzFidelity" value="10.775997964917"/>
          <search_score name="xcorr" value="2.5918696638942031"/>
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        <search_hit hit_rank="4" peptide="GVTVAQHVDAAHSEIEEELAKHR" peptide_prev_aa="Q" peptide_next_aa="I" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2526.2462787157" massdiff="-0.42365710339" num_tol_term="1" num_missed_cleavages="1" num_matched_ions="22" tot_num_ions="159">
          <modification_info>
            <mod_aminoacid_mass position="6" mass="129.0425935114"/>
          </modification_info>
          <search_score name="mvh" value="19.580449224809"/>
          <search_score name="mzFidelity" value="13.402506848624"/>
          <search_score name="xcorr" value="2.9697220446115864"/>
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        <search_hit hit_rank="5" peptide="QMLDLLDIKEATNPDILNKSSR" peptide_prev_aa="R" peptide_next_aa="L" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="2530.2948537701" massdiff="0.59892320421" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="16" tot_num_ions="155">
          <modification_info>
            <mod_aminoacid_mass position="2" mass="147.0353846062"/>
            <mod_aminoacid_mass position="18" mass="115.0269434472"/>
          </modification_info>
          <search_score name="mvh" value="15.920923377675"/>
          <search_score name="mzFidelity" value="11.187293576294"/>
          <search_score name="xcorr" value="1.3435728884597988"/>
        </search_hit>
        <search_hit hit_rank="6" peptide="THFQHLLKSMENEDKEETVAK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2530.2009533849" massdiff="0.50502281901" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="17" tot_num_ions="145">
          <modification_info>
            <mod_aminoacid_mass position="10" mass="147.0353846062"/>
            <mod_aminoacid_mass position="12" mass="115.0269434472"/>
          </modification_info>
          <search_score name="mvh" 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|"/>
          <alternative_protein protein="gi|528953240|ref|XP_005208083.1|"/>
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</msms_pipeline_analysis>