# HG changeset patch
# User galaxyp
# Date 1481579805 18000
# Node ID f962717ca1db41a739a4715b57c3da56d4914c69
# Parent  d239e445e2e6afd77cad931de63a30fe41c73027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit d571b106668cb1e749d6235abf5d2b6224c47d74

diff -r d239e445e2e6 -r f962717ca1db COPYING
diff -r d239e445e2e6 -r f962717ca1db README.md
diff -r d239e445e2e6 -r f962717ca1db idpQonvertEmbedder.xml
--- a/idpQonvertEmbedder.xml	Thu Nov 05 11:54:46 2015 -0500
+++ b/idpQonvertEmbedder.xml	Mon Dec 12 16:56:45 2016 -0500
@@ -2,7 +2,7 @@
 <tool id="idpqonvertEmbedder" name="idpEmbedder" version="0.1.0">
     <description>Embed human/mouse gene metadata into IDPicker files</description>
     <requirements>
-        <requirement type="package" version="3.0.8789">bumbershoot</requirement>
+        <requirement type="package" version="3.0.10185">bumbershoot</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
diff -r d239e445e2e6 -r f962717ca1db idpqonvert.xml
--- a/idpqonvert.xml	Thu Nov 05 11:54:46 2015 -0500
+++ b/idpqonvert.xml	Mon Dec 12 16:56:45 2016 -0500
@@ -9,7 +9,7 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="3.0.8789">bumbershoot</requirement>
+        <requirement type="package" version="3.0.10185">bumbershoot</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -19,7 +19,7 @@
 <![CDATA[
         #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
         #set $input_name = $input.display_name
-        #set $output_name = $input_name.replace(".pep.xml", "").replace(".pepXML", "").replace(".mzid", "") + ".idpDB"
+        #set $output_name = $input_name.split(".")[0] + ".idpDB"
         ln -s '$input' '${input_name}' &&
         ln -s '$ProteinDatabase' '${db_name}' &&
 
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-cm.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-embeddedGenes.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-embeddedGenesAndQuantitation.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-embeddedGenesAndScanTimes.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-embeddedGenesAndSpectra.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-embeddedGenesAndSpectra2.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-msgf.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/201208-378803-myrimatch.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803-cm.pep.xml
--- a/test-data/input/201208-378803-cm.pep.xml	Thu Nov 05 11:54:46 2015 -0500
+++ b/test-data/input/201208-378803-cm.pep.xml	Mon Dec 12 16:56:45 2016 -0500
@@ -1,10303 +1,10303 @@
-<?xml version="1.0" encoding="UTF-8"?>
- <msms_pipeline_analysis date="2014-09-19T11:13:55" 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" summary_xml="C:\idpicker\branches\IDPicker-3\TestData\201208-378803.pep.xml">
- <msms_run_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" msManufacturer="unknown" msModel="unknown" raw_data_type="raw" raw_data=".mzML">
- <sample_enzyme name="Trypsin/P">
-  <specificity cut="KR" no_cut="-" sense="C"/>
- </sample_enzyme>
- <search_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" search_engine="Comet" search_engine_version="2014.02 rev. 0" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
-  <search_database local_path="cow.protein.PRG2012-subset.fasta" type="AA"/>
-  <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>
-  <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/>
-  <aminoacid_modification aminoacid="Q" massdiff="-17.026000" mass="111.032578" variable="Y" symbol="#"/>
-  <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.042594" variable="Y" symbol="@"/>
-  <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.026943" variable="Y" symbol="@"/>
-  <aminoacid_modification aminoacid="C" massdiff="58.005480" mass="161.014665" variable="N"/>
-  <parameter name="# comet_version " value="2014.02"/>
-  <parameter name="activation_method" value="ALL"/>
-  <parameter name="add_A_alanine" value="0.000000"/>
-  <parameter name="add_B_user_amino_acid" value="0.000000"/>
-  <parameter name="add_C_cysteine" value="58.005480"/>
-  <parameter name="add_Cterm_peptide" value="0.000000"/>
-  <parameter name="add_Cterm_protein" value="0.000000"/>
-  <parameter name="add_D_aspartic_acid" value="0.000000"/>
-  <parameter name="add_E_glutamic_acid" value="0.000000"/>
-  <parameter name="add_F_phenylalanine" value="0.000000"/>
-  <parameter name="add_G_glycine" value="0.000000"/>
-  <parameter name="add_H_histidine" value="0.000000"/>
-  <parameter name="add_I_isoleucine" value="0.000000"/>
-  <parameter name="add_J_user_amino_acid" value="0.000000"/>
-  <parameter name="add_K_lysine" value="0.000000"/>
-  <parameter name="add_L_leucine" value="0.000000"/>
-  <parameter name="add_M_methionine" value="0.000000"/>
-  <parameter name="add_N_asparagine" value="0.000000"/>
-  <parameter name="add_Nterm_peptide" value="0.000000"/>
-  <parameter name="add_Nterm_protein" value="0.000000"/>
-  <parameter name="add_O_ornithine" value="0.000000"/>
-  <parameter name="add_P_proline" value="0.000000"/>
-  <parameter name="add_Q_glutamine" value="0.000000"/>
-  <parameter name="add_R_arginine" value="0.000000"/>
-  <parameter name="add_S_serine" value="0.000000"/>
-  <parameter name="add_T_threonine" value="0.000000"/>
-  <parameter name="add_U_user_amino_acid" value="0.000000"/>
-  <parameter name="add_V_valine" value="0.000000"/>
-  <parameter name="add_W_tryptophan" value="0.000000"/>
-  <parameter name="add_X_user_amino_acid" value="0.000000"/>
-  <parameter name="add_Y_tyrosine" value="0.000000"/>
-  <parameter name="add_Z_user_amino_acid" value="0.000000"/>
-  <parameter name="allowed_missed_cleavage" value="2"/>
-  <parameter name="clear_mz_range" value="0.000000 0.000000"/>
-  <parameter name="clip_nterm_methionine" value="1"/>
-  <parameter name="database_name" value="cow.protein.PRG2012-subset.fasta"/>
-  <parameter name="decoy_prefix" value="XXX_"/>
-  <parameter name="decoy_search" value="1"/>
-  <parameter name="digest_mass_range" value="600.000000 5000.000000"/>
-  <parameter name="fragment_bin_offset" value="0.020000"/>
-  <parameter name="fragment_bin_tol" value="0.020000"/>
-  <parameter name="isotope_error" value="1"/>
-  <parameter name="mass_type_fragment" value="1"/>
-  <parameter name="mass_type_parent" value="1"/>
-  <parameter name="max_fragment_charge" value="3"/>
-  <parameter name="max_precursor_charge" value="6"/>
-  <parameter name="max_variable_mods_in_peptide" value="5"/>
-  <parameter name="minimum_intensity" value="0"/>
-  <parameter name="minimum_peaks" value="10"/>
-  <parameter name="ms_level" value="2"/>
-  <parameter name="nucleotide_reading_frame" value="0"/>
-  <parameter name="num_enzyme_termini" value="1"/>
-  <parameter name="num_output_lines" value="5"/>
-  <parameter name="num_results" value="50"/>
-  <parameter name="num_threads" value="0"/>
-  <parameter name="output_outfiles" value="0"/>
-  <parameter name="output_pepxmlfile" value="1"/>
-  <parameter name="output_percolatorfile" value="0"/>
-  <parameter name="output_sqtfile" value="0"/>
-  <parameter name="output_sqtstream" value="0"/>
-  <parameter name="output_suffix" value="-cm"/>
-  <parameter name="output_txtfile" value="0"/>
-  <parameter name="override_charge" value="0"/>
-  <parameter name="peptide_mass_tolerance" value="20.000000"/>
-  <parameter name="peptide_mass_units" value="2"/>
-  <parameter name="precursor_charge" value="1 5"/>
-  <parameter name="print_expect_score" value="1"/>
-  <parameter name="remove_precursor_peak" value="0"/>
-  <parameter name="remove_precursor_tolerance" value="1.500000"/>
-  <parameter name="sample_enzyme_number" value="2"/>
-  <parameter name="scan_range" value="0 0"/>
-  <parameter name="search_enzyme_number" value="2"/>
-  <parameter name="show_fragment_ions" value="0"/>
-  <parameter name="skip_researching" value="1"/>
-  <parameter name="spectrum_batch_size" value="0"/>
-  <parameter name="theoretical_fragment_ions" value="0"/>
-  <parameter name="use_A_ions" value="0"/>
-  <parameter name="use_B_ions" value="1"/>
-  <parameter name="use_C_ions" value="0"/>
-  <parameter name="use_NL_ions" value="1"/>
-  <parameter name="use_X_ions" value="0"/>
-  <parameter name="use_Y_ions" value="1"/>
-  <parameter name="use_Z_ions" value="0"/>
-  <parameter name="use_sparse_matrix" value="0"/>
-  <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/>
-  <parameter name="variable_mod02" value="-17.026000 Q 0 1 0 0"/>
-  <parameter name="variable_mod03" value="0.984016 QN 0 3 -1 0"/>
-  <parameter name="variable_mod04" value="0.000000 X 0 3 -1 0"/>
-  <parameter name="variable_mod05" value="0.000000 X 0 3 -1 0"/>
-  <parameter name="variable_mod06" value="0.000000 X 0 3 -1 0"/>
-  <parameter name="variable_mod07" value="0.000000 X 0 3 -1 0"/>
-  <parameter name="variable_mod08" value="0.000000 X 0 3 -1 0"/>
-  <parameter name="variable_mod09" value="0.000000 X 0 3 -1 0"/>
- </search_summary>
- <spectrum_query spectrum="201208-378803.00001.00001.3" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1517.212359" assumed_charge="3" index="1" retention_time_sec="614.4">
-  <search_result>
-  </search_result>
- </spectrum_query>
- <spectrum_query spectrum="201208-378803.00001.00001.2" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1011.474906" assumed_charge="2" index="2" retention_time_sec="614.4">
-  <search_result>
-   <search_hit hit_rank="1" peptide="AEPESDLPR" peptide_prev_aa="H" peptide_next_aa="N" protein="XXX_gi|528920173|ref|XP_001788336.2|" num_tot_proteins="2" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1012.482539" massdiff="-1.007633" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
-    <search_score name="xcorr" value="0.474"/>
-    <search_score name="deltacn" value="0.001"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="7"/>
-    <search_score name="expect" value="9.70E+000"/>
-   </search_hit>
-   <search_hit hit_rank="2" peptide="ASQGMTPFR" peptide_prev_aa="G" peptide_next_aa="S" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1009.465100" massdiff="2.009806" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
-    <modification_info modified_peptide="ASQGM[147]TPFR">
-     <mod_aminoacid_mass position="5" mass="147.035385"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.473"/>
-    <search_score name="deltacn" value="0.043"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="7"/>
-    <search_score name="expect" value="9.74E+000"/>
-   </search_hit>
-   <search_hit hit_rank="3" peptide="NESLDLYR" peptide_prev_aa="L" peptide_next_aa="L" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="14" calc_neutral_pep_mass="1009.471640" massdiff="2.003266" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
-    <modification_info modified_peptide="N[115]ESLDLYR">
-     <mod_aminoacid_mass position="1" mass="115.026943"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.453"/>
-    <search_score name="deltacn" value="0.208"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="2.8"/>
-    <search_score name="sprank" value="3"/>
-    <search_score name="expect" value="1.20E+001"/>
-   </search_hit>
-   <search_hit hit_rank="4" peptide="LMQQSSVSK" peptide_prev_aa="I" peptide_next_aa="F" protein="XXX_gi|30466252|ref|NP_848667.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="16" calc_neutral_pep_mass="1008.479763" massdiff="2.995144" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
-    <modification_info modified_peptide="LMQ[129]Q[129]SSVSK">
-     <mod_aminoacid_mass position="3" mass="129.042594"/>
-     <mod_aminoacid_mass position="4" mass="129.042594"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.359"/>
-    <search_score name="deltacn" value="0.019"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="3.9"/>
-    <search_score name="sprank" value="2"/>
-    <search_score name="expect" value="3.16E+001"/>
-   </search_hit>
-   <search_hit hit_rank="5" peptide="KAMGSNMEK" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|358414198|ref|XP_002700672.2|" num_tot_proteins="4" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1010.452487" massdiff="1.022420" num_tol_term="2" num_missed_cleavages="1" num_matched_peptides="622">
-    <modification_info modified_peptide="KAM[147]GSNMEK">
-     <mod_aminoacid_mass position="3" mass="147.035385"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.352"/>
-    <search_score name="deltacn" value="1.000"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="7"/>
-    <search_score name="expect" value="3.39E+001"/>
-   </search_hit>
-  </search_result>
- </spectrum_query>
- <spectrum_query spectrum="201208-378803.00002.00002.2" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="830.315297" assumed_charge="2" index="3" retention_time_sec="617.5">
-  <search_result>
-   <search_hit hit_rank="1" peptide="DGCHWR" peptide_prev_aa="P" peptide_next_aa="G" protein="XXX_gi|528961840|ref|XP_005211303.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.312972" massdiff="0.002325" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
-    <modification_info modified_peptide="DGCHWR">
-     <mod_aminoacid_mass position="3" mass="161.014665"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.208"/>
-    <search_score name="deltacn" value="0.166"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="1.20E+001"/>
-   </search_hit>
-   <search_hit hit_rank="2" peptide="YYNEDQ" peptide_prev_aa="R" peptide_next_aa="L" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.308263" massdiff="0.007034" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
-    <search_score name="xcorr" value="0.173"/>
-    <search_score name="deltacn" value="0.133"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="2.36E+001"/>
-   </search_hit>
-   <search_hit hit_rank="3" peptide="TMEEMR" peptide_prev_aa="F" peptide_next_aa="K" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="827.315310" massdiff="2.999987" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
-    <modification_info modified_peptide="TM[147]EEM[147]R">
-     <mod_aminoacid_mass position="2" mass="147.035385"/>
-     <mod_aminoacid_mass position="5" mass="147.035385"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.150"/>
-    <search_score name="deltacn" value="0.081"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="3.72E+001"/>
-   </search_hit>
-   <search_hit hit_rank="4" peptide="WHCGDR" peptide_prev_aa="P" peptide_next_aa="G" protein="gi|528961840|ref|XP_005211303.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.312972" massdiff="0.002325" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
-    <modification_info modified_peptide="WHCGDR">
-     <mod_aminoacid_mass position="3" mass="161.014665"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.138"/>
-    <search_score name="deltacn" value="0.035"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="4.73E+001"/>
-   </search_hit>
-   <search_hit hit_rank="5" peptide="MEEMTR" peptide_prev_aa="F" peptide_next_aa="K" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="827.315310" massdiff="2.999987" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
-    <modification_info modified_peptide="M[147]EEM[147]TR">
-     <mod_aminoacid_mass position="1" mass="147.035385"/>
-     <mod_aminoacid_mass position="4" mass="147.035385"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.133"/>
-    <search_score name="deltacn" value="1.000"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.0"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="5.20E+001"/>
-   </search_hit>
-  </search_result>
- </spectrum_query>
- <spectrum_query spectrum="201208-378803.00002.00002.3" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="1245.472945" assumed_charge="3" index="4" retention_time_sec="617.5">
-  <search_result>
-   <search_hit hit_rank="1" peptide="VNSGCMAMENK" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="1" tot_num_ions="40" calc_neutral_pep_mass="1242.456662" massdiff="3.016283" num_tol_term="2" num_missed_cleavages="0" num_matched_peptides="54">
-    <modification_info modified_peptide="VN[115]SGCMAMEN[115]K">
-     <mod_aminoacid_mass position="2" mass="115.026943"/>
-     <mod_aminoacid_mass position="5" mass="161.014665"/>
-     <mod_aminoacid_mass position="10" mass="115.026943"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.288"/>
-    <search_score name="deltacn" value="0.321"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="0.4"/>
-    <search_score name="sprank" value="6"/>
-    <search_score name="expect" value="5.57E+000"/>
-   </search_hit>
-   <search_hit hit_rank="2" peptide="MMTDKEADGSE" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" num_matched_ions="2" tot_num_ions="40" calc_neutral_pep_mass="1244.453654" massdiff="1.019291" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="54">
-    <modification_info modified_peptide="M[147]M[147]TDKEADGSE">
-     <mod_aminoacid_mass position="1" mass="147.035385"/>
-     <mod_aminoacid_mass position="2" mass="147.035385"/>
-    </modification_info>
-    <search_score name="xcorr" value="0.196"/>
-    <search_score name="deltacn" value="0.168"/>
-    <search_score name="deltacnstar" value="0.000"/>
-    <search_score name="spscore" value="3.2"/>
-    <search_score name="sprank" value="1"/>
-    <search_score name="expect" value="2.71E+001"/>
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-    <search_score name="expect" value="2.60E+000"/>
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-   <search_hit hit_rank="5" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="3" tot_num_ions="20" calc_neutral_pep_mass="1162.528837" massdiff="-0.013263" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
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-    <search_score name="expect" value="4.02E+000"/>
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- </spectrum_query>
- </msms_run_summary>
-</msms_pipeline_analysis>
+<?xml version="1.0" encoding="UTF-8"?>
+ <msms_pipeline_analysis date="2014-09-19T11:13:55" 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" summary_xml="C:\idpicker\branches\IDPicker-3\TestData\201208-378803.pep.xml">
+ <msms_run_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" msManufacturer="unknown" msModel="unknown" raw_data_type="raw" raw_data=".mzML">
+ <sample_enzyme name="Trypsin/P">
+  <specificity cut="KR" no_cut="-" sense="C"/>
+ </sample_enzyme>
+ <search_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" search_engine="Comet" search_engine_version="2014.02 rev. 0" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
+  <search_database local_path="cow.protein.PRG2012-subset.fasta" type="AA"/>
+  <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>
+  <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/>
+  <aminoacid_modification aminoacid="Q" massdiff="-17.026000" mass="111.032578" variable="Y" symbol="#"/>
+  <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.042594" variable="Y" symbol="@"/>
+  <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.026943" variable="Y" symbol="@"/>
+  <aminoacid_modification aminoacid="C" massdiff="58.005480" mass="161.014665" variable="N"/>
+  <parameter name="# comet_version " value="2014.02"/>
+  <parameter name="activation_method" value="ALL"/>
+  <parameter name="add_A_alanine" value="0.000000"/>
+  <parameter name="add_B_user_amino_acid" value="0.000000"/>
+  <parameter name="add_C_cysteine" value="58.005480"/>
+  <parameter name="add_Cterm_peptide" value="0.000000"/>
+  <parameter name="add_Cterm_protein" value="0.000000"/>
+  <parameter name="add_D_aspartic_acid" value="0.000000"/>
+  <parameter name="add_E_glutamic_acid" value="0.000000"/>
+  <parameter name="add_F_phenylalanine" value="0.000000"/>
+  <parameter name="add_G_glycine" value="0.000000"/>
+  <parameter name="add_H_histidine" value="0.000000"/>
+  <parameter name="add_I_isoleucine" value="0.000000"/>
+  <parameter name="add_J_user_amino_acid" value="0.000000"/>
+  <parameter name="add_K_lysine" value="0.000000"/>
+  <parameter name="add_L_leucine" value="0.000000"/>
+  <parameter name="add_M_methionine" value="0.000000"/>
+  <parameter name="add_N_asparagine" value="0.000000"/>
+  <parameter name="add_Nterm_peptide" value="0.000000"/>
+  <parameter name="add_Nterm_protein" value="0.000000"/>
+  <parameter name="add_O_ornithine" value="0.000000"/>
+  <parameter name="add_P_proline" value="0.000000"/>
+  <parameter name="add_Q_glutamine" value="0.000000"/>
+  <parameter name="add_R_arginine" value="0.000000"/>
+  <parameter name="add_S_serine" value="0.000000"/>
+  <parameter name="add_T_threonine" value="0.000000"/>
+  <parameter name="add_U_user_amino_acid" value="0.000000"/>
+  <parameter name="add_V_valine" value="0.000000"/>
+  <parameter name="add_W_tryptophan" value="0.000000"/>
+  <parameter name="add_X_user_amino_acid" value="0.000000"/>
+  <parameter name="add_Y_tyrosine" value="0.000000"/>
+  <parameter name="add_Z_user_amino_acid" value="0.000000"/>
+  <parameter name="allowed_missed_cleavage" value="2"/>
+  <parameter name="clear_mz_range" value="0.000000 0.000000"/>
+  <parameter name="clip_nterm_methionine" value="1"/>
+  <parameter name="database_name" value="cow.protein.PRG2012-subset.fasta"/>
+  <parameter name="decoy_prefix" value="XXX_"/>
+  <parameter name="decoy_search" value="1"/>
+  <parameter name="digest_mass_range" value="600.000000 5000.000000"/>
+  <parameter name="fragment_bin_offset" value="0.020000"/>
+  <parameter name="fragment_bin_tol" value="0.020000"/>
+  <parameter name="isotope_error" value="1"/>
+  <parameter name="mass_type_fragment" value="1"/>
+  <parameter name="mass_type_parent" value="1"/>
+  <parameter name="max_fragment_charge" value="3"/>
+  <parameter name="max_precursor_charge" value="6"/>
+  <parameter name="max_variable_mods_in_peptide" value="5"/>
+  <parameter name="minimum_intensity" value="0"/>
+  <parameter name="minimum_peaks" value="10"/>
+  <parameter name="ms_level" value="2"/>
+  <parameter name="nucleotide_reading_frame" value="0"/>
+  <parameter name="num_enzyme_termini" value="1"/>
+  <parameter name="num_output_lines" value="5"/>
+  <parameter name="num_results" value="50"/>
+  <parameter name="num_threads" value="0"/>
+  <parameter name="output_outfiles" value="0"/>
+  <parameter name="output_pepxmlfile" value="1"/>
+  <parameter name="output_percolatorfile" value="0"/>
+  <parameter name="output_sqtfile" value="0"/>
+  <parameter name="output_sqtstream" value="0"/>
+  <parameter name="output_suffix" value="-cm"/>
+  <parameter name="output_txtfile" value="0"/>
+  <parameter name="override_charge" value="0"/>
+  <parameter name="peptide_mass_tolerance" value="20.000000"/>
+  <parameter name="peptide_mass_units" value="2"/>
+  <parameter name="precursor_charge" value="1 5"/>
+  <parameter name="print_expect_score" value="1"/>
+  <parameter name="remove_precursor_peak" value="0"/>
+  <parameter name="remove_precursor_tolerance" value="1.500000"/>
+  <parameter name="sample_enzyme_number" value="2"/>
+  <parameter name="scan_range" value="0 0"/>
+  <parameter name="search_enzyme_number" value="2"/>
+  <parameter name="show_fragment_ions" value="0"/>
+  <parameter name="skip_researching" value="1"/>
+  <parameter name="spectrum_batch_size" value="0"/>
+  <parameter name="theoretical_fragment_ions" value="0"/>
+  <parameter name="use_A_ions" value="0"/>
+  <parameter name="use_B_ions" value="1"/>
+  <parameter name="use_C_ions" value="0"/>
+  <parameter name="use_NL_ions" value="1"/>
+  <parameter name="use_X_ions" value="0"/>
+  <parameter name="use_Y_ions" value="1"/>
+  <parameter name="use_Z_ions" value="0"/>
+  <parameter name="use_sparse_matrix" value="0"/>
+  <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/>
+  <parameter name="variable_mod02" value="-17.026000 Q 0 1 0 0"/>
+  <parameter name="variable_mod03" value="0.984016 QN 0 3 -1 0"/>
+  <parameter name="variable_mod04" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod05" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod06" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod07" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod08" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod09" value="0.000000 X 0 3 -1 0"/>
+ </search_summary>
+ <spectrum_query spectrum="201208-378803.00001.00001.3" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1517.212359" assumed_charge="3" index="1" retention_time_sec="614.4">
+  <search_result>
+  </search_result>
+ </spectrum_query>
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+    <search_score name="expect" value="1.00E+000"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="ISDMNQN[115]IGAT">
+     <mod_aminoacid_mass position="7" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.675"/>
+    <search_score name="deltacn" value="0.242"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="28.2"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.00E+000"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="VIDEGLMDEK" peptide_prev_aa="E" peptide_next_aa="L" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="18" calc_neutral_pep_mass="1163.537991" massdiff="-1.022417" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="VIDEGLM[147]DEK">
+     <mod_aminoacid_mass position="7" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.512"/>
+    <search_score name="deltacn" value="0.077"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="3.7"/>
+    <search_score name="sprank" value="3"/>
+    <search_score name="expect" value="2.60E+000"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="3" tot_num_ions="20" calc_neutral_pep_mass="1162.528837" massdiff="-0.013263" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <search_score name="xcorr" value="0.473"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="15.4"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="4.02E+000"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ </msms_run_summary>
+</msms_pipeline_analysis>
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803-mm.pepXML
--- a/test-data/input/201208-378803-mm.pepXML	Thu Nov 05 11:54:46 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20531 +0,0 @@
-<?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|"/>
-          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
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-            <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"/>
-        </search_hit>
-        <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|"/>
-          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
-          <modification_info>
-            <mod_aminoacid_mass position="13" mass="115.0269434472"/>
-            <mod_aminoacid_mass position="17" mass="115.0269434472"/>
-            <mod_aminoacid_mass position="18" mass="161.0146644778"/>
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-          <search_score name="mvh" value="24.555168021719"/>
-          <search_score name="mzFidelity" value="13.158130753361"/>
-          <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|"/>
-          <alternative_protein protein="gi|528966552|ref|XP_005211956.1|"/>
-          <alternative_protein protein="gi|528966554|ref|XP_005211957.1|"/>
-          <modification_info>
-            <mod_aminoacid_mass position="13" mass="115.0269434472"/>
-            <mod_aminoacid_mass position="19" mass="115.0269434472"/>
-          </modification_info>
-          <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|"/>
-          <modification_info>
-            <mod_aminoacid_mass position="12" mass="129.0425935114"/>
-            <mod_aminoacid_mass position="13" mass="115.0269434472"/>
-            <mod_aminoacid_mass position="18" mass="161.0146644778"/>
-          </modification_info>
-          <search_score name="mvh" value="22.352043722256"/>
-          <search_score name="mzFidelity" value="10.775997964917"/>
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-        <search_hit hit_rank="3" peptide="LLLNTSKRIMDDVETSSLHLDESFK" peptide_prev_aa="T" peptide_next_aa="L" protein="XXX_gi|115497338|ref|NP_001069884.1|" num_tot_proteins="4" calc_neutral_pep_mass="2906.4695232566" massdiff="0.18058826829" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="20" tot_num_ions="171">
-          <alternative_protein protein="XXX_gi|528968104|ref|XP_005212567.1|"/>
-          <alternative_protein protein="XXX_gi|528968106|ref|XP_005212568.1|"/>
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-          <search_score name="mzFidelity" value="6.815403335045"/>
-          <search_score name="xcorr" value="2.564456180282789"/>
-        </search_hit>
-        <search_hit hit_rank="4" peptide="QIFVKTLTGKTITLEVEPSDTIENVK" peptide_prev_aa="M" peptide_next_aa="A" protein="gi|115496708|ref|NP_001069831.1|" num_tot_proteins="4" calc_neutral_pep_mass="2904.5583369414" massdiff="0.28673178429" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="20" tot_num_ions="179">
-          <alternative_protein protein="gi|27807503|ref|NP_777203.1|"/>
-          <alternative_protein protein="gi|528968221|ref|XP_005212615.1|"/>
-          <alternative_protein protein="gi|528995063|ref|XP_005220352.1|"/>
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-          <search_score name="mvh" value="16.196711830419"/>
-          <search_score name="mzFidelity" value="8.384634792566"/>
-          <search_score name="xcorr" value="1.9797285930138711"/>
-        </search_hit>
-        <search_hit hit_rank="5" peptide="ELNGSLQEMQGESSGVSTVWDLLADIK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2907.369549893" massdiff="0.07194998909" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="18" tot_num_ions="188">
-          <modification_info>
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-            <mod_aminoacid_mass position="10" mass="129.0425935114"/>
-          </modification_info>
-          <search_score name="mvh" value="13.019234366281"/>
-          <search_score name="mzFidelity" value="6.610442990057"/>
-          <search_score name="xcorr" value="1.709385507643441"/>
-        </search_hit>
-      </search_result>
-    </spectrum_query>
-  </msms_run_summary>
-</msms_pipeline_analysis>
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803-msgf.mzid
--- a/test-data/input/201208-378803-msgf.mzid	Thu Nov 05 11:54:46 2015 -0500
+++ b/test-data/input/201208-378803-msgf.mzid	Mon Dec 12 16:56:45 2016 -0500
@@ -1,17 +1,17 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2014-09-05T13:19:45" >
+<?xml version="1.0" encoding="UTF-8"?>
+<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2014-09-05T13:19:45" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>
     <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
     <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>
-</cvList>
+</cvList>
 <AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <AnalysisSoftware version="Beta (v10072)" name="MS-GF+" id="ID_software">
         <SoftwareName>
             <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>
         </SoftwareName>
     </AnalysisSoftware>
-</AnalysisSoftwareList>
+</AnalysisSoftwareList>
 <SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <DBSequence accession="gi|30794280|ref|NP_851335.1|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq43937">
         <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|30794280|ref|NP_851335.1| serum albumin precursor [Bos taurus]" name="protein description"/>
@@ -1362,13 +1362,13 @@
     <PeptideEvidence isDecoy="true" post="K" pre="N" end="1374" start="1364" peptide_ref="Pep123" dBSequence_ref="DBSeq65480" id="PepEv_66843_123_1364"/>
     <PeptideEvidence isDecoy="true" post="K" pre="N" end="1304" start="1294" peptide_ref="Pep123" dBSequence_ref="DBSeq73091" id="PepEv_74384_123_1294"/>
     <PeptideEvidence isDecoy="true" post="K" pre="N" end="1304" start="1294" peptide_ref="Pep123" dBSequence_ref="DBSeq94489" id="PepEv_95782_123_1294"/>
-</SequenceCollection>
+</SequenceCollection>
 <AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
         <InputSpectra spectraData_ref="SID_1"/>
         <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
     </SpectrumIdentification>
-</AnalysisCollection>
+</AnalysisCollection>
 <AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
         <SearchType>
@@ -1426,7 +1426,7 @@
             <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
         </Threshold>
     </SpectrumIdentificationProtocol>
-</AnalysisProtocolCollection>
+</AnalysisProtocolCollection>
 <DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
     <Inputs>
         <SearchDatabase numDatabaseSequences="144" location="C:\idpicker\branches\IDPicker-3\TestData\cow.protein.PRG2012-subset.fasta" id="SearchDB_1">
@@ -4627,5 +4627,5 @@
             </SpectrumIdentificationResult>
         </SpectrumIdentificationList>
     </AnalysisData>
-</DataCollection>
-</MzIdentML>
+</DataCollection>
+</MzIdentML>
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803-myrimatch.pepXML
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803.idpDB
diff -r d239e445e2e6 -r f962717ca1db test-data/input/201208-378803.mzML
diff -r d239e445e2e6 -r f962717ca1db test-data/input/F003098.dat
--- a/test-data/input/F003098.dat	Thu Nov 05 11:54:46 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4078 +0,0 @@
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-TOL=50
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-A=71.037114
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-    <umod:elem avge_mass="6.941" full_name="Lithium" mono_mass="7.016003" title="Li"/>
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-    <umod:elem avge_mass="30.973761" full_name="Phosphorous" mono_mass="30.973762" title="P"/>
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-      <umod:specificity classification="Artefact" hidden="true" position="Any N-term" site="N-term" spec_group="3"/>
-      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="K" spec_group="2"/>
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-      <umod:specificity classification="Post-translational" hidden="false" position="Protein N-term" site="N-term" spec_group="5"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="S" spec_group="4"/>
-      <umod:specificity classification="Multiple" hidden="false" position="Any N-term" site="N-term" spec_group="2">
-        <umod:misc_notes>GIST acetyl light</umod:misc_notes>
-      </umod:specificity>
-      <umod:specificity classification="Multiple" hidden="false" position="Anywhere" site="K" spec_group="1">
-        <umod:misc_notes>PT and GIST acetyl light</umod:misc_notes>
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-      <umod:delta avge_mass="42.0367" composition="H(2) C(2) O" mono_mass="42.010565">
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-        <umod:element number="2" symbol="C"/>
-        <umod:element number="1" symbol="O"/>
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-      <umod:xref>
-        <umod:text>AA0052</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0051</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0050</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0049</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0048</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0047</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0046</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0056</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0045</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0354</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0043</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0044</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>11999733</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>IonSource acetylation tutorial</umod:text>
-        <umod:source>Misc. URL</umod:source>
-        <umod:url>http://www.ionsource.com/Card/acetylation/acetylation.htm</umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0055</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0364</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>14730666</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>15350136</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>11857757</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>12175151</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0042</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0041</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0053</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0054</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>ACET</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-    </umod:mod>
-    <umod:mod approved="false" date_time_modified="2006-11-14 11:11:50" date_time_posted="2002-08-19 19:17:11" full_name="Deamidation" group_of_poster="admin" title="Deamidated" username_of_poster="unimod">
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="R" spec_group="2">
-        <umod:misc_notes>Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline</umod:misc_notes>
-      </umod:specificity>
-      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="N" spec_group="1">
-        <umod:misc_notes>Convertion of glycosylated asparagine residues upon deglycosylation with PGNase F in H2O</umod:misc_notes>
-      </umod:specificity>
-      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="Q" spec_group="1"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Protein N-term" site="F" spec_group="3"/>
-      <umod:delta avge_mass="0.9848" composition="H(-1) N(-1) O" mono_mass="0.984016">
-        <umod:element number="-1" symbol="H"/>
-        <umod:element number="-1" symbol="N"/>
-        <umod:element number="1" symbol="O"/>
-      </umod:delta>
-      <umod:alt_name>phenyllactyl from N-term Phe</umod:alt_name>
-      <umod:alt_name>Citrullination</umod:alt_name>
-      <umod:xref>
-        <umod:text>IonSource tutorial</umod:text>
-        <umod:source>Misc. URL</umod:source>
-        <umod:url>http://www.ionsource.com/Card/Deamidation/deamidation.htm</umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>CITR</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>FLAC</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0128</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0214</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>6838602</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>15700232</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>DEAM</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-    </umod:mod>
-    <umod:mod approved="true" date_time_modified="2006-10-13 17:06:57" date_time_posted="2002-08-19 19:17:11" full_name="Pyro-glu from Q" group_of_poster="admin" title="Gln->pyro-Glu" username_of_poster="unimod">
-      <umod:specificity classification="Artefact" hidden="false" position="Any N-term" site="Q" spec_group="1"/>
-      <umod:delta avge_mass="-17.0305" composition="H(-3) N(-1)" mono_mass="-17.026549">
-        <umod:element number="-3" symbol="H"/>
-        <umod:element number="-1" symbol="N"/>
-      </umod:delta>
-      <umod:xref>
-        <umod:text>AA0031</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>PYRR</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-    </umod:mod>
-    <umod:mod approved="false" date_time_modified="2007-02-14 09:23:15" date_time_posted="2002-08-19 19:17:11" full_name="Oxidation or Hydroxylation" group_of_poster="admin" title="Oxidation" username_of_poster="unimod">
-      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="W" spec_group="10"/>
-      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="H" spec_group="10"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="C" spec_group="9">
-        <umod:misc_notes>Cysteine sulfenic acid</umod:misc_notes>
-      </umod:specificity>
-      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="M" spec_group="8">
-        <umod:NeutralLoss avge_mass="64.1069" composition="H(4) C O S" flag="false" mono_mass="63.998285">
-          <umod:element number="4" symbol="H"/>
-          <umod:element number="1" symbol="C"/>
-          <umod:element number="1" symbol="O"/>
-          <umod:element number="1" symbol="S"/>
-        </umod:NeutralLoss>
-        <umod:NeutralLoss avge_mass="0.0000" composition="0" flag="false" mono_mass="0.000000"/>
-      </umod:specificity>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="R" spec_group="7"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="Y" spec_group="6"/>
-      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="F" spec_group="5"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="P" spec_group="4">
-        <umod:misc_notes>Proline oxidation to glutamic semialdehyde</umod:misc_notes>
-      </umod:specificity>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="N" spec_group="3"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="K" spec_group="2"/>
-      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="D" spec_group="1"/>
-      <umod:delta avge_mass="15.9994" composition="O" mono_mass="15.994915">
-        <umod:element number="1" symbol="O"/>
-      </umod:delta>
-      <umod:xref>
-        <umod:text>14661085</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0146</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0235</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0027</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>11461766</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0028</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>9004526</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0030</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0029</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0215</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>Lagerwerf FM, van de Weert M, Heerma W, Haverkamp J, Rapid Commun Mass Spectrom. 1996;10(15):1905-10</umod:text>
-        <umod:source>Journal</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0205</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0026</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text>
-        <umod:source>Journal</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>15569593</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>14661084</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>CSEA</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>DOPA</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>11120890</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>11212008</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>AA0322</umod:text>
-        <umod:source>RESID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>HYDR</umod:text>
-        <umod:source>FindMod</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-      <umod:xref>
-        <umod:text>12781462</umod:text>
-        <umod:source>PubMed PMID</umod:source>
-        <umod:url></umod:url>
-      </umod:xref>
-    </umod:mod>
-  </umod:modifications>
-  <umod:amino_acids>
-    <umod:aa avge_mass="0.0000" full_name="" mono_mass="0.000000" three_letter="" title="-"/>
-    <umod:aa avge_mass="71.0779" full_name="Alanine" mono_mass="71.037114" three_letter="Ala" title="A">
-      <umod:element number="5" symbol="H"/>
-      <umod:element number="3" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="156.1857" full_name="Arginine" mono_mass="156.101111" three_letter="Arg" title="R">
-      <umod:element number="12" symbol="H"/>
-      <umod:element number="6" symbol="C"/>
-      <umod:element number="4" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="114.1026" full_name="Asparagine" mono_mass="114.042927" three_letter="Asn" title="N">
-      <umod:element number="6" symbol="H"/>
-      <umod:element number="4" symbol="C"/>
-      <umod:element number="2" symbol="N"/>
-      <umod:element number="2" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="115.0874" full_name="Aspartic acid" mono_mass="115.026943" three_letter="Asp" title="D">
-      <umod:element number="5" symbol="H"/>
-      <umod:element number="4" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="3" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="103.1429" full_name="Cysteine" mono_mass="103.009185" three_letter="Cys" title="C">
-      <umod:element number="5" symbol="H"/>
-      <umod:element number="3" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-      <umod:element number="1" symbol="S"/>
-    </umod:aa>
-    <umod:aa avge_mass="129.1140" full_name="Glutamic acid" mono_mass="129.042593" three_letter="Glu" title="E">
-      <umod:element number="7" symbol="H"/>
-      <umod:element number="5" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="3" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="128.1292" full_name="Glutamine" mono_mass="128.058578" three_letter="Gln" title="Q">
-      <umod:element number="8" symbol="H"/>
-      <umod:element number="5" symbol="C"/>
-      <umod:element number="2" symbol="N"/>
-      <umod:element number="2" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="57.0513" full_name="Glycine" mono_mass="57.021464" three_letter="Gly" title="G">
-      <umod:element number="3" symbol="H"/>
-      <umod:element number="2" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="137.1393" full_name="Histidine" mono_mass="137.058912" three_letter="His" title="H">
-      <umod:element number="7" symbol="H"/>
-      <umod:element number="6" symbol="C"/>
-      <umod:element number="3" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="113.1576" full_name="Isoleucine" mono_mass="113.084064" three_letter="Ile" title="I">
-      <umod:element number="11" symbol="H"/>
-      <umod:element number="6" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="113.1576" full_name="Leucine" mono_mass="113.084064" three_letter="Leu" title="L">
-      <umod:element number="11" symbol="H"/>
-      <umod:element number="6" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="128.1723" full_name="Lysine" mono_mass="128.094963" three_letter="Lys" title="K">
-      <umod:element number="12" symbol="H"/>
-      <umod:element number="6" symbol="C"/>
-      <umod:element number="2" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="131.1961" full_name="Methionine" mono_mass="131.040485" three_letter="Met" title="M">
-      <umod:element number="9" symbol="H"/>
-      <umod:element number="5" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-      <umod:element number="1" symbol="S"/>
-    </umod:aa>
-    <umod:aa avge_mass="147.1739" full_name="Phenylalanine" mono_mass="147.068414" three_letter="Phe" title="F">
-      <umod:element number="9" symbol="H"/>
-      <umod:element number="9" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="97.1152" full_name="Proline" mono_mass="97.052764" three_letter="Pro" title="P">
-      <umod:element number="7" symbol="H"/>
-      <umod:element number="5" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="87.0773" full_name="Serine" mono_mass="87.032028" three_letter="Ser" title="S">
-      <umod:element number="5" symbol="H"/>
-      <umod:element number="3" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="2" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="101.1039" full_name="Threonine" mono_mass="101.047679" three_letter="Thr" title="T">
-      <umod:element number="7" symbol="H"/>
-      <umod:element number="4" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="2" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="186.2099" full_name="Tryptophan" mono_mass="186.079313" three_letter="Trp" title="W">
-      <umod:element number="10" symbol="H"/>
-      <umod:element number="11" symbol="C"/>
-      <umod:element number="2" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="163.1733" full_name="Tyrosine" mono_mass="163.063329" three_letter="Tyr" title="Y">
-      <umod:element number="9" symbol="H"/>
-      <umod:element number="9" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="2" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="99.1311" full_name="Valine" mono_mass="99.068414" three_letter="Val" title="V">
-      <umod:element number="9" symbol="H"/>
-      <umod:element number="5" symbol="C"/>
-      <umod:element number="1" symbol="N"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-    <umod:aa avge_mass="1.0079" full_name="N-term" mono_mass="1.007825" three_letter="N-term" title="N-term">
-      <umod:element number="1" symbol="H"/>
-    </umod:aa>
-    <umod:aa avge_mass="17.0073" full_name="C-term" mono_mass="17.002740" three_letter="C-term" title="C-term">
-      <umod:element number="1" symbol="H"/>
-      <umod:element number="1" symbol="O"/>
-    </umod:aa>
-  </umod:amino_acids>
-</umod:unimod>
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-q37_p1=1,1458.695038,0.013058,4,LVNIRNDDITDGN,18,000200000000000,2.48,2002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:229:241:81,"gi|528944678|ref|XP_005204735.1|":0:229:241:67,"gi|219804516|ref|NP_001137332.1|":0:153:165:67
-q37_p1_terms=K,P:K,P:K,P
-q37_p2=1,1457.754807,0.953289,2,SPDHMLKSTISVK,9,000004000000000,2.42,0002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:940:952:81,"gi|528944678|ref|XP_005204735.1|":0:938:950:67,"gi|219804516|ref|NP_001137332.1|":0:862:874:67
-q37_p2_terms=R,A:R,A:R,A
-q37_p2_primary_nl=000001000000000
-q37_p3=1,1457.711029,0.997067,2,LVNIRNDDITDGN,9,000000000000000,1.86,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:229:241:81,"gi|528944678|ref|XP_005204735.1|":0:229:241:67,"gi|219804516|ref|NP_001137332.1|":0:153:165:67
-q37_p3_terms=K,P:K,P:K,P
-q37_p4=1,1458.695038,0.013058,2,LVNIRNDDITDGN,9,000000000000020,1.86,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:229:241:81,"gi|528944678|ref|XP_005204735.1|":0:229:241:67,"gi|219804516|ref|NP_001137332.1|":0:153:165:67
-q37_p4_terms=K,P:K,P:K,P
-q37_p5=1,1458.695038,0.013058,2,LVNIRNDDITDGN,9,000000200000000,1.36,2000000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:229:241:81,"gi|528944678|ref|XP_005204735.1|":0:229:241:67,"gi|219804516|ref|NP_001137332.1|":0:153:165:67
-q37_p5_terms=K,P:K,P:K,P
-q37_p6=0,1458.668076,0.040020,2,LVQFHFHWGSSD,9,00000000000000,1.36,2000000000000000000,0,0;"gi|30466252|ref|NP_848667.1|":0:90:101:3
-q37_p6_terms=R,D
-q38_p1=0,1464.549698,-0.072806,13,TCVADESHAGCEK,70,000000000000000,20.82,1000002020000000000,0,0;"gi|30794280|ref|NP_851335.1|":0:76:88:1
-q38_p1_terms=K,S
-q39_p1=0,976.486557,-0.028829,3,LLDDWTSK,16,0000000000,13.54,1001012010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:4415:4422:79,"gi|528944678|ref|XP_005204735.1|":0:2373:2380:54,"gi|219804516|ref|NP_001137332.1|":0:2297:2304:53
-q39_p1_terms=D,G:D,G:D,G
-q39_p2=1,974.482162,1.975566,4,QDVFRSLQ,16,3000000000,7.95,1002002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:809:816:79,"gi|528944678|ref|XP_005204735.1|":0:809:816:54,"gi|219804516|ref|NP_001137332.1|":0:733:740:53
-q39_p2_terms=K,D:K,D:K,D
-q39_p3=0,975.502533,0.955195,2,LISGWGNTK,8,00000002000,1.25,2000000000000000000,0,0;"gi|528903801|ref|XP_871686.4|":0:140:148:3,"gi|528947854|ref|XP_002687054.3|":0:140:148:3,"gi|165973958|ref|NP_001107199.1|":0:140:148:3
-q39_p3_terms=C,S:C,S:C,S
-q40_p1=0,978.429413,-0.035867,4,QPEQNFSK,37,0000220000,2.53,0002000000000000000,0,0;"gi|139948503|ref|NP_001077142.1|":0:432:439:2
-q40_p1_terms=Y,N
-q40_p2=0,978.429413,-0.035867,4,QPEQNFSK,44,0200020000,2.17,0002001000000000000,0,0;"gi|139948503|ref|NP_001077142.1|":0:432:439:2
-q40_p2_terms=Y,N
-q41_p1=1,1465.687119,2.037462,3,MTQQQENPKFLS,16,04000000000000,5.42,1000012000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p1_terms=R,H:R,H:R,H
-q41_p1_primary_nl=02000000000000
-q41_p2=1,1466.671127,1.053454,3,MTQQQENPKFLS,16,04000200000000,0.95,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p2_terms=R,H:R,H:R,H
-q41_p2_primary_nl=02000000000000
-q41_p3=1,1466.671127,1.053454,3,MTQQQENPKFLS,16,04002000000000,0.95,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p3_terms=R,H:R,H:R,H
-q41_p3_primary_nl=02000000000000
-q41_p4=1,1467.655136,0.069445,3,MTQQQENPKFLS,16,04002200000000,0.95,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p4_terms=R,H:R,H:R,H
-q41_p4_primary_nl=02000000000000
-q41_p5=1,1466.671127,1.053454,3,MTQQQENPKFLS,16,04020000000000,0.22,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p5_terms=R,H:R,H:R,H
-q41_p5_primary_nl=02000000000000
-q41_p6=1,1467.655136,0.069445,3,MTQQQENPKFLS,16,04020200000000,0.22,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p6_terms=R,H:R,H:R,H
-q41_p6_primary_nl=02000000000000
-q41_p7=1,1467.655136,0.069445,3,MTQQQENPKFLS,16,04022000000000,0.22,1000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:1004:1015:15,"gi|528921180|ref|XP_005195747.1|":0:949:960:15,"gi|528995523|ref|XP_002695913.2|":0:1051:1062:14
-q41_p7_terms=R,H:R,H:R,H
-q41_p7_primary_nl=02000000000000
-q42_p1=-1
-q43_p1=-1
-q44_p1=1,991.418152,1.961556,2,QREPYCR,8,300000000,2.70,2010001000000000000,0,0;"gi|528961840|ref|XP_005211303.1|":0:699:705:3,"gi|528961845|ref|XP_005211304.1|":0:656:662:3,"gi|156523214|ref|NP_001096021.1|":0:656:662:3
-q44_p1_terms=L,D:L,D:L,D
-q45_p1=-1
-q46_p1=-1
-q47_p1=-1
-q48_p1=1,1001.514130,-0.040140,4,LAEAEKEGR,18,00000000000,2.71,2001002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2678:2686:43
-q48_p1_terms=T,L
-q48_p2=0,1000.434921,1.039069,2,LATSGSSDTY,18,000000000000,0.99,2011000000000000000,0,0;"gi|139948503|ref|NP_001077142.1|":0:227:236:1
-q48_p2_terms=R,S
-q48_p3=1,1001.496399,-0.022409,2,LVKNDPCR,18,0000000000,0.73,2010001000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7344:7351:43,"gi|528944678|ref|XP_005204735.1|":0:5292:5299:29,"gi|219804516|ref|NP_001137332.1|":0:5216:5223:29
-q48_p3_terms=F,V:F,A:F,A
-q49_p1=1,1011.498505,-0.023597,3,QDNALRIAE,14,30000000000,3.61,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:1163:1171:36,"gi|528944678|ref|XP_005204735.1|":0:1161:1169:28,"gi|219804516|ref|NP_001137332.1|":0:1085:1093:27
-q49_p1_terms=R,Q:R,Q:R,Q
-q49_p2=0,1011.469513,0.005395,4,IYLDQMGR,14,0000024000,3.12,0000002020000000000,0,0;"gi|528928354|ref|XP_005193233.1|":0:277:284:4
-q49_p2_terms=R,L
-q49_p2_primary_nl=0000001000
-q50_p1=1,1516.708527,1.956009,2,ALNEINQFYQKF,8,00020022000000,2.79,2001000000000000000,0,0;"gi|27806963|ref|NP_776953.1|":0:96:107:6
-q50_p1_terms=K,P
-q50_p2=1,1517.692535,0.972001,2,ALNEINQFYQKF,8,00020022002000,2.79,2001000000000000000,0,0;"gi|27806963|ref|NP_776953.1|":0:96:107:6
-q50_p2_terms=K,P
-q51_p1=1,1015.461044,1.038338,2,IEYYRNTG,8,0000002000,6.89,2000001000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:112:119:8,"gi|528966552|ref|XP_005211956.1|":0:112:119:8,"gi|528966554|ref|XP_005211957.1|":0:112:119:8,"gi|297479727|ref|XP_002690982.1|":0:112:119:8
-q51_p1_terms=K,S:K,S:K,S:K,S
-q52_p1=0,1018.373550,0.028622,4,MMSASSYNE,21,00000000000,6.59,1002012010000000000,0,0;"gi|528928354|ref|XP_005193233.1|":0:472:480:1
-q52_p1_terms=R,D
-q52_p2=1,1016.427307,1.974865,2,KNNMFAQF,21,0022400000,0.56,0000002010000000000,0,0;"gi|528968104|ref|XP_005212567.1|":0:781:788:2,"gi|528968106|ref|XP_005212568.1|":0:777:784:2
-q52_p2_terms=R,R:R,R
-q52_p2_primary_nl=0000200000
-q53_p1=-1
-q54_p1=1,1030.475342,-0.001386,5,SPDHMLKST,40,00000400000,4.54,0002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:940:948:58,"gi|528944678|ref|XP_005204735.1|":0:938:946:42,"gi|219804516|ref|NP_001137332.1|":0:862:870:41
-q54_p1_terms=R,I:R,I:R,I
-q54_p1_primary_nl=00000100000
-q55_p1=-1
-q56_p1=0,1036.449493,2.012817,5,ALGSQACSNK,62,000000000200,4.32,0010002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5086:5095:50,"gi|528944678|ref|XP_005204735.1|":0:3044:3053:42,"gi|219804516|ref|NP_001137332.1|":0:2968:2977:42
-q56_p1_terms=D,N:D,N:D,N
-q56_p2=0,1037.433502,1.028808,5,ALGSQACSNK,62,000002000200,2.64,0000002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5086:5095:50,"gi|528944678|ref|XP_005204735.1|":0:3044:3053:42,"gi|219804516|ref|NP_001137332.1|":0:2968:2977:42
-q56_p2_terms=D,N:D,N:D,N
-q56_p3=0,1038.486938,-0.024628,5,QTVEAYSAAV,62,020000000000,0.71,2001001000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:831:840:50,"gi|528944678|ref|XP_005204735.1|":0:831:840:42,"gi|219804516|ref|NP_001137332.1|":0:755:764:42
-q56_p3_terms=K,Q:K,Q:K,Q
-q57_p1=-1
-q58_p1=-1
-q59_p1=-1
-q60_p1=0,1064.469574,0.033672,4,VLNDMTTAAE,9,000200000000,10.58,1000002020000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5287:5296:73,"gi|528944678|ref|XP_005204735.1|":0:3245:3254:51,"gi|219804516|ref|NP_001137332.1|":0:3169:3178:51
-q60_p1_terms=K,E:K,E:K,E
-q60_p2=0,1062.465149,2.038097,3,LQQMEQAAQ,27,00004020000,5.41,2011011000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:3651:3659:73
-q60_p2_terms=R,V
-q60_p2_primary_nl=00001000000
-q60_p3=0,1063.449158,1.054088,3,LQQMEQAAQ,27,00004020020,4.74,2011010000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:3651:3659:73
-q60_p3_terms=R,V
-q60_p3_primary_nl=00001000000
-q60_p4=0,1063.485565,1.017681,2,VLNDMTTAAE,18,000000000000,2.48,2001000010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5287:5296:73,"gi|528944678|ref|XP_005204735.1|":0:3245:3254:51,"gi|219804516|ref|NP_001137332.1|":0:3169:3178:51
-q60_p4_terms=K,E:K,E:K,E
-q61_p1=1,1595.775253,0.989711,2,LVNELTEFAKTCVA,8,0002000000000000,0.15,2000010000000000000,0,0;"gi|30794280|ref|NP_851335.1|":0:66:79:3
-q61_p1_terms=K,D
-q62_p1=0,1065.453583,0.016085,2,QMLEEEGTL,18,02400000000,0.04,2000000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5233:5241:67,"gi|528944678|ref|XP_005204735.1|":0:3191:3199:49,"gi|219804516|ref|NP_001137332.1|":0:3115:3123:49
-q62_p1_terms=R,D:R,D:R,D
-q62_p1_primary_nl=00100000000
-q63_p1=1,1615.741272,1.974279,4,RIHSGERPFVCQQ,9,000000000000220,4.92,0002020010000000000,0,0;"gi|528908802|ref|XP_005199340.1|":0:322:334:6,"gi|528908804|ref|XP_005199341.1|":0:322:334:6,"gi|528908806|ref|XP_005199342.1|":0:322:334:6,"gi|528908808|ref|XP_005199343.1|":0:321:333:6,"gi|528908810|ref|XP_005199344.1|":0:302:314:4,"gi|528908812|ref|XP_609847.5|":0:294:306:4,"gi|528959647|ref|XP_005210511.1|":0:322:334:6,"gi|528959649|ref|XP_005210512.1|":0:322:334:6,"gi|528959651|ref|XP_005210513.1|":0:322:334:6,"gi|528959653|ref|XP_005210514.1|":0:321:333:6,"gi|528959655|ref|XP_005210515.1|":0:302:314:4,"gi|528959657|ref|XP_002689899.2|":0:294:306:4
-q63_p1_terms=K,C:K,C:K,C:K,C:K,C:K,C:K,C:K,C:K,C:K,C:K,C:K,C
-q64_p1=-1
-q65_p1=-1
-q66_p1=-1
-q67_p1=-1
-q68_p1=-1
-q69_p1=-1
-q70_p1=-1
-q71_p1=-1
-q72_p1=-1
-q73_p1=0,1148.560089,1.034831,6,APLTEIENYV,57,000000002000,2.29,0002001000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:788:797:12,"gi|528966552|ref|XP_005211956.1|":0:820:829:12,"gi|528966554|ref|XP_005211957.1|":0:788:797:12,"gi|297479727|ref|XP_002690982.1|":0:788:797:12
-q73_p1_terms=K,G:K,G:K,G:K,G
-q73_p2=0,1147.576080,2.018840,6,APLTEIENYV,66,000000000000,0.59,0002001000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:788:797:12,"gi|528966552|ref|XP_005211956.1|":0:820:829:12,"gi|528966554|ref|XP_005211957.1|":0:788:797:12,"gi|297479727|ref|XP_002690982.1|":0:788:797:12
-q73_p2_terms=K,G:K,G:K,G:K,G
-q74_p1=-1
-q75_p1=0,1151.494202,0.985944,3,SSDEETLSER,10,000000000000,10.70,2001001000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:79:88:37,"gi|528944678|ref|XP_005204735.1|":0:79:88:34,"gi|219804516|ref|NP_001137332.1|":0:3:12:34
-q75_p1_terms=S,S:S,S:S,S
-q75_p2=1,1152.531189,-0.051043,6,RWQEYQSR,44,0002000000,3.78,2002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:391:398:37,"gi|528944678|ref|XP_005204735.1|":0:391:398:34,"gi|219804516|ref|NP_001137332.1|":0:315:322:34
-q75_p2_terms=A,V:A,V:A,V
-q76_p1=-1
-q77_p1=-1
-q78_p1=1,1160.574722,1.981202,3,QTMKGLDIQK,20,300400000200,2.97,1002000000000000000,0,0;"gi|528969819|ref|XP_005213230.1|":0:21:30:4,"gi|87196497|ref|NP_776354.2|":0:21:30:4
-q78_p1_terms=T,V:T,V
-q78_p1_primary_nl=000100000000
-q78_p2=0,1161.576492,0.979432,2,IVVETEGSSIE,10,0000000000000,1.74,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2150:2160:90
-q78_p2_terms=K,N
-q78_p3=1,1160.603668,1.952256,3,ALESELRSEK,20,000000000000,1.29,0012000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2294:2303:90
-q78_p3_terms=L,D
-q78_p4=0,1160.520569,2.035355,2,MSVLDHALMA,20,140000000400,0.10,1001012000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:1:10:3,"gi|528959655|ref|XP_005210515.1|":0:1:10:3
-q78_p4_terms=-,F:-,F
-q78_p4_primary_nl=010000000100
-q79_p1=1,1748.862106,2.029640,3,VIGQFPFQDAELEKQ,18,00002000000000000,0.24,2001000010000000000,0,0;"gi|528968104|ref|XP_005212567.1|":0:468:482:9,"gi|528968106|ref|XP_005212568.1|":0:468:482:9,"gi|528968108|ref|XP_005212569.1|":0:468:482:8,"gi|115497338|ref|NP_001069884.1|":0:468:482:10
-q79_p1_terms=K,P:K,P:K,P:K,P
-q79_p2=1,1749.846115,1.045631,3,VIGQFPFQDAELEKQ,18,00002000200000000,0.24,2001000010000000000,0,0;"gi|528968104|ref|XP_005212567.1|":0:468:482:9,"gi|528968106|ref|XP_005212568.1|":0:468:482:9,"gi|528968108|ref|XP_005212569.1|":0:468:482:8,"gi|115497338|ref|NP_001069884.1|":0:468:482:10
-q79_p2_terms=K,P:K,P:K,P:K,P
-q80_p1=-1
-q81_p1=-1
-q82_p1=-1
-q83_p1=-1
-q84_p1=0,1192.554657,0.008889,4,IVSWGSGCAQK,38,0000000000000,2.95,1000002000000000000,0,0;"gi|528903801|ref|XP_871686.4|":0:213:223:5,"gi|528947854|ref|XP_002687054.3|":0:213:223:5,"gi|165973958|ref|NP_001107199.1|":0:213:223:5
-q84_p1_terms=G,N:G,N:G,N
-q84_p2=0,1192.561157,0.002389,4,VLNQYEQLEG,21,000000020000,2.36,2001002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:3536:3545:84
-q84_p2_terms=R,R
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-q21_p3=1,900.452744,2.041994,2,RALYFMT,8,000000000,5.80,1000002000000000000,0,0;"gi|30794280|ref|NP_851335.1|":0:589:595:9
-q21_p3_terms=K,R
-q21_p4=0,900.491638,2.003100,4,GAPLSLDTK,36,00000000000,3.21,0000002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2316:2324:59
-q21_p4_terms=R,F
-q21_p5=1,902.522552,-0.027814,5,QKIFSIGK,22,3000000000,3.04,2000020000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3243:3250:50
-q21_p5_terms=C,E
-q22_p1=-1
-q23_p1=0,915.437164,-0.044790,4,QSMVTPAAK,46,32000000000,1.60,1000002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:3768:3776:24
-q23_p1_terms=T,S
-q23_p2=0,914.434494,0.957880,4,QPEEGINK,46,0200000000,1.02,0000002000000000000,0,0;"gi|528908812|ref|XP_609847.5|":0:193:200:5,"gi|528959657|ref|XP_002689899.2|":0:193:200:5
-q23_p2_terms=Q,G:Q,G
-q23_p3=0,914.423294,0.969080,4,QNVTVQEL,32,3200002000,0.36,0000002000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:900:907:5
-q23_p3_terms=R,Q
-q23_p4=0,913.414124,1.978250,2,IDQHSSQV,16,0000000200,0.24,2011000000000000000,0,0;"gi|528993973|ref|XP_005219930.1|":0:651:658:3,"gi|27806851|ref|NP_776358.1|":0:651:658:3
-q23_p4_terms=K,E:K,E
-q23_p5=0,913.414124,1.978250,2,IDQHSSQV,16,0002000000,0.24,2011000000000000000,0,0;"gi|528993973|ref|XP_005219930.1|":0:651:658:3,"gi|27806851|ref|NP_776358.1|":0:651:658:3
-q23_p5_terms=K,E:K,E
-q24_p1=0,921.447708,-0.029808,5,EAMEVSLK,15,0004000000,12.91,2002001010000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3258:3265:26
-q24_p1_terms=Q,S
-q24_p1_primary_nl=0002000000
-q24_p2=1,919.388260,2.029640,4,EASQARQQ,15,0000200220,3.80,2002000000000000000,0,0;"gi|528954392|ref|XP_005208526.1|":0:54:61:2,"gi|115496708|ref|NP_001069831.1|":0:54:61:2
-q24_p2_terms=K,S:K,S
-q24_p3=0,921.392700,0.025200,3,ELSEGSSNV,15,00000000200,1.87,2000001000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3967:3975:38
-q24_p3_terms=K,N
-q24_p4=0,921.386169,0.031731,2,EANQMVGR,15,0002240000,1.44,2001001010000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:568:575:38
-q24_p4_terms=H,Q
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-q24_p5=0,921.374939,0.042961,2,EAGCDLQK,15,0000000200,0.95,2001001010000000000,0,0;"gi|528968108|ref|XP_005212569.1|":0:195:202:5
-q24_p5_terms=T,M
-q24_p6=0,921.447739,-0.029839,2,TVDVMTEK,15,0000000000,0.95,1002001010000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3121:3128:26
-q24_p6_terms=E,F
-q24_p7=0,921.411316,0.006584,2,AEVAEMEK,15,0000004000,0.82,1001002010000000000,0,0;"gi|528920173|ref|XP_001788336.2|":0:391:398:2
-q24_p7_terms=R,F
-q24_p7_primary_nl=0000002000
-q24_p8=0,919.418152,1.999748,3,EANQMVGR,22,0000040000,0.71,2001000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:568:575:38
-q24_p8_terms=H,Q
-q24_p8_primary_nl=0000010000
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-q26_p1=1,926.449799,-0.033815,2,FEGKGFSGV,7,00000000000,8.59,1001002000000000000,0,0;"gi|528995523|ref|XP_002695913.2|":0:645:653:2
-q26_p1_terms=K,E
-q26_p2=0,925.414124,1.001860,2,QFSTEGTR,7,0200000000,3.51,1002000000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:527:534:9
-q26_p2_terms=P,D
-q26_p3=0,926.405518,0.010466,2,MEDLFEK,14,040000000,1.77,1002001000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:4142:4148:24
-q26_p3_terms=S,A
-q26_p3_primary_nl=020000000
-q26_p4=0,925.439270,0.976714,2,YDQTGLTK,7,0002000000,1.71,2000000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:2485:2492:24
-q26_p4_terms=R,L
-q27_p1=0,932.423935,0.033671,2,QPAQNLNF,7,0200000200,7.35,1000002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3962:3969:54
-q27_p1_terms=R,Q
-q27_p2=0,932.427322,0.030284,4,LLGCDLNQ,14,0000000000,6.76,2001002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2048:2055:57
-q27_p2_terms=R,L
-q27_p3=0,932.481461,-0.023855,4,LLTNDQTK,14,0000002000,6.76,2001002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1971:1978:54
-q27_p3_terms=Q,F
-q27_p4=0,932.481461,-0.023855,4,LLTNDQTK,14,0000200000,6.76,2001002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1971:1978:54
-q27_p4_terms=Q,F
-q27_p5=0,932.416077,0.041529,2,LLPCTEAE,7,0000000000,2.91,2000001000000000000,0,0;"gi|528993973|ref|XP_005219930.1|":0:169:176:5,"gi|27806851|ref|NP_776358.1|":0:169:176:5
-q27_p5_terms=R,R:R,R
-q27_p6=0,931.439926,1.017680,2,QPAQNLNF,7,0000000200,2.01,0010002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3962:3969:54
-q27_p6_terms=R,Q
-q27_p7=0,931.439926,1.017680,2,QPAQNLNF,7,0000020000,2.01,0010002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3962:3969:54
-q27_p7_terms=R,Q
-q27_p8=0,932.423935,0.033671,2,QPAQNLNF,7,0200020000,2.01,1000002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:3962:3969:54
-q27_p8_terms=R,Q
-q27_p9=0,930.436813,2.020793,2,LGLLECPE,7,0000000000,0.69,1000020000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:1532:1539:57
-q27_p9_terms=R,D
-q27_p10=0,931.497452,0.960154,2,LLTNDQTK,7,0000000000,0.69,2000000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1971:1978:54
-q27_p10_terms=Q,F
-q28_p1=0,1410.674774,-0.047060,6,CLGIQPGQHMLR,23,00000000200000,4.24,0000002020000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:2494:2505:40
-q28_p1_terms=T,L
-q29_p1=0,946.387955,0.018481,2,QGQDGQLEA,7,02000020000,8.84,1001002010000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4986:4994:24
-q29_p1_terms=K,V
-q29_p2=0,946.406601,-0.000165,2,QTSMGEKPA,7,30004000000,5.45,0002011000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:391:399:5,"gi|528959655|ref|XP_005210515.1|":0:391:399:5
-q29_p2_terms=K,K:K,K
-q29_p2_primary_nl=00002000000
-q29_p3=0,945.415176,0.991260,4,PSTGENGER,61,00000000000,2.04,2001001010000000000,0,0;"gi|528966552|ref|XP_005211956.1|":0:783:791:8
-q29_p3_terms=E,E
-q29_p4=1,945.440308,0.966128,2,NAQGDLQKA,7,02000002000,0.69,1002000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1651:1659:24
-q29_p4_terms=K,Y
-q30_p1=0,949.406250,1.974910,4,AVCDLEDK,9,0000000000,6.69,0000002020000000000,0,0;"gi|528968106|ref|XP_005212568.1|":0:144:151:3
-q30_p1_terms=E,G
-q30_p2=1,950.382874,0.998286,4,ATDEQGDKS,18,00000200000,0.35,0000002020000000000,0,0;"gi|32880221|ref|NP_872593.1|":0:279:287:3
-q30_p2_terms=K,T
-q31_p1=0,1429.730011,1.979129,5,VLENVTSALLQEN,15,000020000000000,6.60,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3526:3538:65
-q31_p1_terms=K,K
-q31_p2=0,1430.714020,0.995120,5,VLENVTSALLQEN,15,000020000000020,6.60,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3526:3538:65
-q31_p2_terms=K,K
-q31_p3=0,1430.714020,0.995120,5,VLENVTSALLQEN,15,000020000002000,6.60,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3526:3538:65
-q31_p3_terms=K,K
-q31_p4=0,1431.698029,0.011111,5,VLENVTSALLQEN,15,000020000002020,6.60,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3526:3538:65
-q31_p4_terms=K,K
-q31_p5=1,1430.776917,0.932223,4,IVKAFGQAVEEQI,15,000000000000000,4.49,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:4302:4314:65
-q31_p5_terms=R,G
-q31_p6=0,1431.672882,0.036258,4,VLSQENAIAAQGTE,15,0000202000000000,4.15,2012000000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:703:716:10
-q31_p6_terms=R,G
-q31_p7=1,1431.760925,-0.051785,4,IVKAFGQAVEEQI,15,000000000000200,3.42,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:4302:4314:65
-q31_p7_terms=R,G
-q31_p8=1,1431.663025,0.046115,4,QTQGPSVYLNRGE,22,300200000000000,1.43,2021000000000000000,0,0;"gi|27806963|ref|NP_776953.1|":0:158:170:6
-q31_p8_terms=K,D
-q31_p9=0,1430.696289,1.012851,3,LVEIDSGVLASPCA,15,0000000000000000,1.26,2001000000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:459:472:13,"gi|528959655|ref|XP_005210515.1|":0:459:472:13
-q31_p9_terms=K,R:K,R
-q31_p10=0,1431.672882,0.036258,4,VLSQENAIAAQGTE,15,0000002000020000,0.95,2012000000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:703:716:10
-q31_p10_terms=R,G
-q32_p1=-1
-q33_p1=0,962.449097,-0.040441,4,IAGESMAER,16,00000000000,4.51,2012001000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:484:492:4,"gi|528959655|ref|XP_005210515.1|":0:484:492:4
-q33_p1_terms=G,A:G,A
-q34_p1=0,960.469849,1.969903,4,CVNADLLR,32,0000000000,4.01,0000002000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:813:820:11,"gi|528966554|ref|XP_005211957.1|":0:813:820:11
-q34_p1_terms=L,V:L,V
-q35_p1=0,1453.570068,2.020473,2,MENAECDAVEIR,8,04020000000000,2.28,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:6461:6472:22
-q35_p1_terms=G,A
-q35_p1_primary_nl=01000000000000
-q36_p1=0,971.442245,1.024277,6,LVAQYFCA,43,0000000000,1.60,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:2177:2184:37
-q36_p1_terms=R,L
-q37_p1=1,971.442062,1.030002,3,PDGGADQRR,18,00000002000,8.06,1001002000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:200:208:5,"gi|528959655|ref|XP_005210515.1|":0:200:208:5
-q37_p1_terms=I,F:I,F
-q37_p2=0,972.426254,0.045810,2,LVAQYFCA,9,0000200000,3.33,2000001000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:2177:2184:37
-q37_p2_terms=R,L
-q37_p3=0,971.442245,1.029819,4,LVAQYFCA,18,0000000000,2.51,2002000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:2177:2184:37
-q37_p3_terms=R,L
-q37_p4=0,970.497086,1.974978,2,EIPGNLAEK,9,00000200000,0.96,0020000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1272:1280:32
-q37_p4_terms=G,G
-q37_p5=0,971.455978,1.016086,2,QGPINTNVE,9,02000000000,0.96,0020000000000000000,0,0;"gi|28849955|ref|NP_788795.1|":0:332:340:11
-q37_p5_terms=R,L
-q37_p6=1,971.503571,0.968493,3,PNISEQRK,34,0020000000,0.78,0000002000000000000,0,0;"gi|28849955|ref|NP_788795.1|":0:316:323:11
-q37_p6_terms=A,E
-q38_p1=-1
-q39_p1=0,1462.719086,1.967506,4,LIQPYEISQNQK,16,00000000022200,5.58,2001002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4479:4490:32
-q39_p1_terms=F,G
-q39_p2=0,1462.719086,1.967506,4,LIQPYEISQNQK,16,00020000002200,5.58,2001012000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4479:4490:32
-q39_p2_terms=F,G
-q39_p3=0,1463.703094,0.983498,4,LIQPYEISQNQK,16,00020000022200,5.58,2001012000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4479:4490:32
-q39_p3_terms=F,G
-q39_p4=0,1464.757278,-0.070686,2,ILGSGAHVPTQGTLGG,8,000000000002000000,1.12,2000000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:4395:4410:59
-q39_p4_terms=K,S
-q39_p5=0,1462.719086,1.967506,2,LIQPYEISQNQK,8,00020000020200,1.12,2000000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4479:4490:32
-q39_p5_terms=F,G
-q39_p6=0,1462.719086,1.967506,2,LIQPYEISQNQK,8,00020000022000,1.12,2000000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4479:4490:32
-q39_p6_terms=F,G
-q40_p1=0,977.358261,1.035285,4,SSSMSFCR,57,0000400000,1.38,0002011000000000000,0,0;"gi|528968106|ref|XP_005212568.1|":0:648:655:2
-q40_p1_terms=S,E
-q40_p1_primary_nl=0000100000
-q41_p1=1,1465.730881,1.993700,4,LREMMLAFLETP,16,00000400000000,10.26,2010000000000000000,0,0;"gi|528995523|ref|XP_002695913.2|":0:793:804:15
-q41_p1_terms=R,A
-q41_p1_primary_nl=00000200000000
-q41_p2=1,1465.730881,1.993700,4,LREMMLAFLETP,16,00004000000000,10.26,2010000000000000000,0,0;"gi|528995523|ref|XP_002695913.2|":0:793:804:15
-q41_p2_terms=R,A
-q41_p2_primary_nl=00002000000000
-q41_p3=0,1465.712250,2.012331,4,QAAVAAYLMQDIAT,16,0200000000000000,4.18,2010002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7457:7470:45
-q41_p3_terms=R,D
-q41_p4=0,1466.696259,1.028322,4,QAAVAAYLMQDIAT,16,0200000000200000,4.18,2010002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7457:7470:45
-q41_p4_terms=R,D
-q41_p5=0,1466.761658,0.962923,5,FLLSSEQGLSTSAK,24,0000000000000000,3.49,2010002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:644:657:45
-q41_p5_terms=S,F
-q41_p6=0,1467.745667,-0.021086,4,FLLSSEQGLSTSAK,24,0000000200000000,2.45,2000002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:644:657:45
-q41_p6_terms=S,F
-q41_p7=1,1465.723511,2.001070,3,FVIRQVGMGEEGK,16,000002004000000,1.99,2000001000000000000,0,0;"gi|528961845|ref|XP_005211304.1|":0:227:239:8,"gi|156523214|ref|NP_001096021.1|":0:227:239:8
-q41_p7_terms=S,A:S,A
-q41_p7_primary_nl=000000002000000
-q42_p1=-1
-q43_p1=-1
-q44_p1=-1
-q45_p1=1,992.459702,1.995232,4,LSVTGDRDM,16,00000000000,3.28,1010002020000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:1898:1906:62
-q45_p1_terms=K,S
-q46_p1=-1
-q47_p1=0,1498.642319,1.945255,2,SEASQQETQGLYSA,9,0000020000000000,2.61,0001001020000000000,0,0;"gi|528908802|ref|XP_005199340.1|":0:514:527:3,"gi|528908804|ref|XP_005199341.1|":0:514:527:3,"gi|528908806|ref|XP_005199342.1|":0:514:527:3,"gi|528959647|ref|XP_005210511.1|":0:514:527:3,"gi|528959649|ref|XP_005210512.1|":0:514:527:3,"gi|528959651|ref|XP_005210513.1|":0:514:527:3
-q47_p1_terms=R,R:R,R:R,R:R,R:R,R:R,R
-q47_p2=0,1498.642319,1.945255,2,SEASQQETQGLYSA,9,0000002000000000,1.87,0000001020000000000,0,0;"gi|528908802|ref|XP_005199340.1|":0:514:527:3,"gi|528908804|ref|XP_005199341.1|":0:514:527:3,"gi|528908806|ref|XP_005199342.1|":0:514:527:3,"gi|528959647|ref|XP_005210511.1|":0:514:527:3,"gi|528959649|ref|XP_005210512.1|":0:514:527:3,"gi|528959651|ref|XP_005210513.1|":0:514:527:3
-q47_p2_terms=R,R:R,R:R,R:R,R:R,R:R,R
-q47_p3=0,1498.613358,1.974216,2,YCVVESGQENDVV,9,000000000020000,1.87,0001020000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:5198:5210:13
-q47_p3_terms=K,M
-q47_p4=0,1498.613358,1.974216,2,YCVVESGQENDVV,9,000000002000000,1.87,0001020000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:5198:5210:13
-q47_p4_terms=K,M
-q48_p1=0,1001.460022,0.013968,3,LVCSGNHSK,18,00000000000,6.65,2000001010000000000,0,0;"gi|528993971|ref|XP_005219929.1|":0:701:709:3
-q48_p1_terms=F,E
-q48_p2=1,1000.472641,1.001349,2,LAGEGRHFD,18,00000000000,1.00,2001010000000000000,0,0;"gi|528993971|ref|XP_005219929.1|":0:88:96:3
-q48_p2_terms=K,P
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-q48_p3_terms=L,K
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-q50_p1=0,1010.485489,1.957535,3,NPQCLHLK,24,0200000000,6.12,1011002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:2389:2396:31
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-q50_p2=1,1010.460358,1.982666,3,AHSVDMHKS,16,00000000000,1.56,0002001010000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:11:19:6
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-q51_p1_terms=R,A:R,A:R,A:R,A
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-q51_p2_terms=F,S
-q51_p3=0,1015.475662,1.023720,4,GAQPAMGVQR,64,000200000200,2.20,2001001000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:4063:4072:33
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-q51_p5_terms=K,N
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-q51_p6_terms=Q,I:Q,I
-q51_p7=0,1014.461761,2.037621,3,EPQIQENR,16,0002020000,1.06,1000002010000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:505:512:5,"gi|528966554|ref|XP_005211957.1|":0:505:512:5
-q51_p7_terms=Q,I:Q,I
-q51_p8=0,1014.459290,2.040092,5,PSYSFMQR,56,0000000000,0.57,2001000000000000000,0,0;"gi|528993971|ref|XP_005219929.1|":0:311:318:4
-q51_p8_terms=E,F
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-q51_p9_terms=R,Q:R,Q
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-q51_p10_terms=P,F
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-q52_p4_terms=V,F
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-q52_p5_terms=V,F
-q52_p6=0,1526.659714,0.943544,6,QEQNGVNDDPSAPR,42,0000200000000000,1.16,0000002020000000000,0,0;"gi|528921180|ref|XP_005195747.1|":0:530:543:2
-q52_p6_terms=V,F
-q52_p7=0,1526.659714,0.943544,6,QEQNGVNDDPSAPR,42,0002000000000000,1.16,0000002020000000000,0,0;"gi|528921180|ref|XP_005195747.1|":0:530:543:2
-q52_p7_terms=V,F
-q52_p8=0,1527.643723,-0.040465,4,QEQNGVNDDPSAPR,66,0200000200000000,0.09,0000012010000000000,0,0;"gi|528921180|ref|XP_005195747.1|":0:530:543:2
-q52_p8_terms=V,F
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-q54_p1=1,1543.740555,1.970379,4,EILFEQSNSKGYK,8,000000202000000,18.27,0002000000000000000,0,0;"gi|529012038|ref|XP_005226889.1|":0:88:100:2
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-q54_p2_terms=R,Y
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-q54_p3_terms=R,D
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-q56_p1_terms=S,K
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-q60_p2_terms=K,L:K,L
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-q60_p3=0,1064.499435,0.003811,4,VLLSDMACR,18,00000000000,3.96,2001002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:1876:1884:51
-q60_p3_terms=M,T
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-q60_p4_terms=R,D
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-q60_p5_primary_nl=00000000010
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-q60_p7=0,1063.537201,0.966045,2,VIQFNAKPM,18,00020000040,1.95,2001000000000000000,0,0;"gi|528993973|ref|XP_005219930.1|":0:279:287:6,"gi|27806851|ref|NP_776358.1|":0:279:287:6
-q60_p7_terms=K,L:K,L
-q60_p7_primary_nl=00000000010
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-q60_p8_terms=K,E
-q60_p8_primary_nl=01000000000
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-q60_p9_terms=K,N
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-q60_p10_terms=V,S
-q61_p1=0,1064.538986,-0.029010,7,IVVTFQEAAS,40,000000200000,4.94,2000002000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1578:1587:48
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-q61_p2=0,1063.525970,0.984006,6,MQAFQPVLL,40,04200200000,1.88,2002000000000000000,0,0;"gi|528953234|ref|XP_005208080.1|":0:146:154:4
-q61_p2_terms=K,E
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-q62_p1=0,1065.437180,0.032488,2,IAMDHFCR,9,0004000000,7.83,1001002010000000000,0,0;"gi|528953246|ref|XP_005208086.1|":0:124:131:2
-q62_p1_terms=S,C
-q62_p1_primary_nl=0002000000
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-q62_p2_terms=V,S
-q62_p3=0,1065.480103,-0.010435,2,ALFQMDDVQ,18,00000000000,0.43,1002001010000000000,0,0;"gi|528968106|ref|XP_005212568.1|":0:181:189:5
-q62_p3_terms=R,I
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-q63_p1_terms=A,F
-q63_p1_primary_nl=00000000200
-q63_p2=1,1076.498566,1.978468,2,GNVLSKGSEEG,18,0020000000000,0.04,2001000000000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:85:95:7
-q63_p2_terms=R,R
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-q65_p1=-1
-q66_p1=-1
-q67_p1=-1
-q68_p1=-1
-q69_p1=0,1123.462921,0.947221,5,GTGQSDNSETK,50,0000000200000,5.62,2011000000000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:3191:3201:11
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-q71_p4_terms=K,A
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-q72_p1_terms=V,I
-q72_p2=0,1148.556061,0.032997,3,ASAVSISQEEK,10,0000000020000,1.67,0000002000000000000,0,0;"gi|528969819|ref|XP_005213230.1|":0:95:105:5
-q72_p2_terms=R,A
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-q73_p1_terms=V,S:V,S
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-q73_p2_terms=V,S:V,S
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-q78_p10=0,1160.501953,2.053971,2,QTEEKPGMDK,20,300000004000,0.46,1002000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4515:4524:40
-q78_p10_terms=R,V
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-q80_p2=0,1751.861740,1.020980,3,FLQNQGLLLAQYPSSA,10,000022000002000000,0.23,0002000010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7482:7497:59
-q80_p2_terms=R,G
-q80_p3=0,1750.877731,2.004989,3,FLQNQGLLLAQYPSSA,10,000202000000000000,0.23,0002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7482:7497:59
-q80_p3_terms=R,G
-q80_p4=0,1751.861740,1.020980,3,FLQNQGLLLAQYPSSA,10,000202000002000000,0.23,0002000010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7482:7497:59
-q80_p4_terms=R,G
-q80_p5=0,1750.877731,2.004989,3,FLQNQGLLLAQYPSSA,10,000220000000000000,0.23,0002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7482:7497:59
-q80_p5_terms=R,G
-q80_p6=0,1751.861740,1.020980,3,FLQNQGLLLAQYPSSA,10,000220000002000000,0.23,0002000010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7482:7497:59
-q80_p6_terms=R,G
-q81_p1=-1
-q82_p1=-1
-q83_p1=-1
-q84_p1=0,1192.597565,-0.034019,4,IVVTFQEAASQ,11,0000000000020,10.77,2001002010000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1578:1588:47
-q84_p1_terms=R,L
-q84_p2=0,1192.597565,-0.034019,4,IVVTFQEAASQ,11,0000002000000,9.42,2001002010000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1578:1588:47
-q84_p2_terms=R,L
-q84_p3=0,1192.572418,-0.008872,4,LVAGDQNFSDK,21,0000000000000,5.41,2001002010000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:990:1000:4,"gi|528966554|ref|XP_005211957.1|":0:990:1000:4
-q84_p3_terms=V,L:V,L
-q84_p4=0,1191.613556,0.949990,4,IVVTFQEAASQ,21,0000000000000,2.30,2002000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:1578:1588:47
-q84_p4_terms=R,L
-q84_p5=0,1192.610123,-0.046577,3,AIFAVNEHHR,21,000000000000,1.63,0002001000000000000,0,0;"gi|528908810|ref|XP_005199344.1|":0:232:241:14,"gi|528959655|ref|XP_005210515.1|":0:232:241:14
-q84_p5_terms=F,F:F,F
-q84_p6=0,1191.605698,0.957848,2,ILLGSCVTEVT,11,0000000000000,1.44,2010000000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:907:917:4,"gi|528966554|ref|XP_005211957.1|":0:907:917:4
-q84_p6_terms=K,G:K,G
-q84_p7=0,1190.524597,2.038949,2,LACMCLHLR,11,00004000000,1.29,1002000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:5564:5572:54
-q84_p7_terms=M,T
-q84_p7_primary_nl=00002000000
-q84_p8=0,1191.584549,0.978997,3,MQAFQPVLLE,38,042000000000,0.93,0002010000000000000,0,0;"gi|528953234|ref|XP_005208080.1|":0:146:155:7
-q84_p8_terms=K,E
-q84_p8_primary_nl=010000000000
-q84_p9=1,1190.530258,2.033288,2,LVQGEDSKQGE,11,0002000002000,0.76,2000000000000000000,0,0;"gi|528968108|ref|XP_005212569.1|":0:392:402:3
-q84_p9_terms=R,A
-q84_p10=0,1192.568558,-0.005012,3,MQAFQPVLLE,38,042002000000,0.44,0002000000000000000,0,0;"gi|528953234|ref|XP_005208080.1|":0:146:155:7
-q84_p10_terms=K,E
-q84_p10_primary_nl=010000000000
-q85_p1=0,1194.603302,-0.005900,4,VNAAEIQFFR,9,000000020000,9.58,2001002010000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:5096:5105:36
-q85_p1_terms=G,E
-q85_p2=0,1193.619293,0.978109,3,VNAAEIQFFR,26,000000000000,5.45,2001001010000000000,0,0;"gi|528944678|ref|XP_005204735.1|":0:5096:5105:36
-q85_p2_terms=G,E
-q86_p1=1,1207.608444,1.998062,4,LAKSDGIYASSP,9,00000000000000,5.29,2020000000000000000,0,0;"gi|528921180|ref|XP_005195747.1|":0:87:98:8
-q86_p1_terms=K,I
-q86_p2=0,1209.581192,0.025314,2,QDLIQQMYR,9,00000004000,2.72,1002001000000000000,0,0;"gi|358414198|ref|XP_002700672.2|":0:1072:1080:5,"gi|528966554|ref|XP_005211957.1|":0:1072:1080:5
-q86_p2_terms=I,R:I,R
-q86_p2_primary_nl=00000002000
-q86_p3=1,1209.639374,-0.032868,3,GLAFQTFGKQL,34,0000000000200,2.42,0001011020000000000,0,0;"gi|528921178|ref|XP_592304.7|":0:375:385:14
-q86_p3_terms=K,P
-q86_p4=1,1207.630920,1.975586,4,LRFQSESSVR,26,000000000000,1.95,2010000000000000000,0,0;"gi|528908802|ref|XP_005199340.1|":0:424:433:5,"gi|528908804|ref|XP_005199341.1|":0:424:433:5,"gi|528908806|ref|XP_005199342.1|":0:424:433:5,"gi|528959647|ref|XP_005210511.1|":0:424:433:5,"gi|528959649|ref|XP_005210512.1|":0:424:433:5,"gi|528959651|ref|XP_005210513.1|":0:424:433:5
-q86_p4_terms=Q,I:Q,I:Q,I:Q,I:Q,I:Q,I
-q87_p1=-1
-q88_p1=-1
-q89_p1=0,1218.518661,0.988633,3,QDNTPMDAKPS,10,0000004000000,8.94,2011000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:7309:7319:21
-q89_p1_terms=R,S
-q89_p1_primary_nl=0000002000000
-q89_p2=0,1219.521286,-0.013992,3,EMPCELGVER,10,000000000000,6.63,2000000000000000000,0,0;"gi|528993973|ref|XP_005219930.1|":0:659:668:5,"gi|27806851|ref|NP_776358.1|":0:659:668:5
-q89_p2_terms=V,S:V,S
-q90_p1=-1
-q91_p1=-1
-q92_p1=-1
-q93_p1=-1
-q94_p1=-1
-q95_p1=0,1864.767288,1.965546,4,GGFSPEMPQVQTQSEPQ,11,0000000402020200000,10.57,0000002010000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:6104:6120:28
-q95_p1_terms=K,V
-q95_p1_primary_nl=0000000100000000000
-q95_p2=0,1865.751297,0.981537,4,GGFSPEMPQVQTQSEPQ,22,0000000402020200020,3.05,0001002000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:6104:6120:28
-q95_p2_terms=K,V
-q95_p2_primary_nl=0000000200000000000
-q95_p3=1,1866.776428,-0.043594,3,QDETADAVFDMELRGMG,11,3000000000000000000,1.26,2000000000000000000,0,0;"gi|219804516|ref|NP_001137332.1|":0:4402:4418:12
-q95_p3_terms=K,A
-q96_p1=-1
-q97_p1=-1
-q98_p1=-1
-q99_p1=0,1331.656891,2.050103,3,QSGGGASLILVSSSS,12,30000000000000000,7.05,2010000000000000000,0,0;"gi|528944676|ref|XP_005204734.1|":0:3638:3652:72
-q99_p1_terms=R,H
-q100_p1=-1
-q101_p1=-1
-q102_p1=-1
-q103_p1=-1
-q104_p1=-1
-q105_p1=-1
-q106_p1=-1
-q107_p1=0,1626.687164,0.034692,3,QEQSPYQYMPSIR,12,300200020400000,0.76,0010002000000000000,0,0;"gi|528961845|ref|XP_005211304.1|":0:449:461:8,"gi|156523214|ref|NP_001096021.1|":0:449:461:8
-q107_p1_terms=I,A:I,A
-q107_p1_primary_nl=000000000200000
-q107_p2=0,1626.687164,0.034692,3,QEQSPYQYMPSIR,12,320000020400000,0.76,0010002000000000000,0,0;"gi|528961845|ref|XP_005211304.1|":0:449:461:8,"gi|156523214|ref|NP_001096021.1|":0:449:461:8
-q107_p2_terms=I,A:I,A
-q107_p2_primary_nl=000000000200000
-q108_p1=-1
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="proteins"
-
-"gi|28849951|ref|NP_788787.1|"=42402.25,"pregnancy-associated glycoprotein 2 precursor [Bos taurus]"
-"gi|156523214|ref|NP_001096021.1|"=75111.98,"protein KHNYN [Bos taurus]"
-"gi|529012038|ref|XP_005226889.1|"=37916.11,"PREDICTED: pregnancy-associated glycoprotein 2 isoform X1 [Bos taurus]"
-"gi|297479727|ref|XP_002690982.1|"=122273.28,"PREDICTED: solute carrier family 12 member 1 isoform X1 [Bos taurus]"
-"gi|528966554|ref|XP_005211957.1|"=122269.25,"PREDICTED: solute carrier family 12 member 1 isoform X3 [Bos taurus]"
-"gi|528966552|ref|XP_005211956.1|"=125413.01,"PREDICTED: solute carrier family 12 member 1 isoform X2 [Bos taurus]"
-"gi|528961845|ref|XP_005211304.1|"=75111.98,"PREDICTED: protein KHNYN isoform X2 [Bos taurus]"
-"gi|528961840|ref|XP_005211303.1|"=79807.30,"PREDICTED: protein KHNYN isoform X1 [Bos taurus]"
-"gi|119924469|ref|XP_001252524.1|"=42203.32,"PREDICTED: pregnancy-associated glycoprotein 2-like [Bos taurus]"
-"gi|358414198|ref|XP_002700672.2|"=122269.25,"PREDICTED: LOW QUALITY PROTEIN: solute carrier family 12 member 1 [Bos taurus]"
-"gi|27806851|ref|NP_776358.1|"=81519.24,"lactoperoxidase precursor [Bos taurus]"
-"gi|32880221|ref|NP_872593.1|"=61787.25,"glutamate dehydrogenase 1, mitochondrial precursor [Bos taurus]"
-"gi|27806963|ref|NP_776953.1|"=26176.28,"alpha-S2-casein precursor [Bos taurus]"
-"gi|165973958|ref|NP_001107199.1|"=26464.67,"cationic trypsin precursor [Bos taurus]"
-"gi|87196497|ref|NP_776354.2|"=20276.31,"beta-lactoglobulin precursor [Bos taurus]"
-"gi|30794280|ref|NP_851335.1|"=71308.64,"serum albumin precursor [Bos taurus]"
-"gi|219804516|ref|NP_001137332.1|"=621898.09,"microtubule-actin cross-linking factor 1 [Bos taurus]"
-"gi|28849955|ref|NP_788795.1|"=42193.27,"pregnancy-associated glycoprotein 12 precursor [Bos taurus]"
-"gi|115497338|ref|NP_001069884.1|"=73569.50,"exocyst complex component 6B [Bos taurus]"
-"gi|139948503|ref|NP_001077142.1|"=69007.23,"uncharacterized protein LOC512219 [Bos taurus]"
-"gi|529000951|ref|XP_005222651.1|"=96037.78,"PREDICTED: rab effector MyRIP isoform X2 [Bos taurus]"
-"gi|297488451|ref|XP_002696970.1|"=96037.78,"PREDICTED: rab effector MyRIP isoform X1 [Bos taurus]"
-"gi|528995523|ref|XP_002695913.2|"=149268.27,"PREDICTED: protein flightless-1 homolog [Bos taurus]"
-"gi|528993975|ref|XP_005219931.1|"=78365.30,"PREDICTED: lactoperoxidase isoform X3 [Bos taurus]"
-"gi|528993973|ref|XP_005219930.1|"=81519.24,"PREDICTED: lactoperoxidase isoform X2 [Bos taurus]"
-"gi|528993971|ref|XP_005219929.1|"=87651.28,"PREDICTED: lactoperoxidase isoform X1 [Bos taurus]"
-"gi|528969819|ref|XP_005213230.1|"=20304.34,"PREDICTED: beta-lactoglobulin isoform X1 [Bos taurus]"
-"gi|528968108|ref|XP_005212569.1|"=89776.36,"PREDICTED: exocyst complex component 6B isoform X3 [Bos taurus]"
-"gi|528968106|ref|XP_005212568.1|"=94915.23,"PREDICTED: exocyst complex component 6B isoform X2 [Bos taurus]"
-"gi|528968104|ref|XP_005212567.1|"=95400.49,"PREDICTED: exocyst complex component 6B isoform X1 [Bos taurus]"
-"gi|528959657|ref|XP_002689899.2|"=68463.94,"PREDICTED: zinc finger protein 169 isoform X1 [Bos taurus]"
-"gi|528959655|ref|XP_005210515.1|"=69330.37,"PREDICTED: zinc finger protein 169 isoform X6 [Bos taurus]"
-"gi|528959653|ref|XP_005210514.1|"=71618.60,"PREDICTED: zinc finger protein 169 isoform X5 [Bos taurus]"
-"gi|528959651|ref|XP_005210513.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X4 [Bos taurus]"
-"gi|528959649|ref|XP_005210512.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X3 [Bos taurus]"
-"gi|528959647|ref|XP_005210511.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X2 [Bos taurus]"
-"gi|528947854|ref|XP_002687054.3|"=26464.67,"PREDICTED: cationic trypsin isoform X1 [Bos taurus]"
-"gi|528944678|ref|XP_005204735.1|"=629529.96,"PREDICTED: microtubule-actin cross-linking factor 1 isoform X2 [Bos taurus]"
-"gi|528944676|ref|XP_005204734.1|"=864854.20,"PREDICTED: microtubule-actin cross-linking factor 1 isoform X1 [Bos taurus]"
-"gi|528928354|ref|XP_005193233.1|"=66478.61,"PREDICTED: fibrous sheath-interacting protein 2-like [Bos taurus]"
-"gi|528923273|ref|XP_005196452.1|"=96037.78,"PREDICTED: rab effector MyRIP isoform X1 [Bos taurus]"
-"gi|358418103|ref|XP_600387.4|"=96037.78,"PREDICTED: rab effector MyRIP isoform X2 [Bos taurus]"
-"gi|528921180|ref|XP_005195747.1|"=137814.29,"PREDICTED: protein flightless-1 homolog isoform X2 [Bos taurus]"
-"gi|528921178|ref|XP_592304.7|"=144054.68,"PREDICTED: protein flightless-1 homolog isoformX1 [Bos taurus]"
-"gi|528908812|ref|XP_609847.5|"=68463.94,"PREDICTED: zinc finger protein 169 isoform X6 [Bos taurus]"
-"gi|528908810|ref|XP_005199344.1|"=69330.37,"PREDICTED: zinc finger protein 169 isoform X5 [Bos taurus]"
-"gi|528908808|ref|XP_005199343.1|"=71618.60,"PREDICTED: zinc finger protein 169 isoform X4 [Bos taurus]"
-"gi|528908806|ref|XP_005199342.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X3 [Bos taurus]"
-"gi|528908804|ref|XP_005199341.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X2 [Bos taurus]"
-"gi|528908802|ref|XP_005199340.1|"=71689.63,"PREDICTED: zinc finger protein 169 isoform X1 [Bos taurus]"
-"gi|528903801|ref|XP_871686.4|"=26464.67,"PREDICTED: cationic trypsin isoformX1 [Bos taurus]"
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query1"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e9%2e9%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1191%20experiment%3d3%22
-rtinseconds=636.471
-charge=2+,3+
-mass_min=70.050003
-mass_max=701.271145
-int_min=1
-int_max=63
-num_vals=121
-num_used1=-1
-Ions1=155.089744:22,175.094603:11,336.629788:9,402.220302:63,490.242291:5,599.223386:2,672.288462:3,84.068946:7,183.099165:10,283.110021:8,404.201846:21,491.200779:3,613.203206:2,700.286497:2,86.085388:7,187.126996:8,284.190321:4,403.225708:17,497.699293:2,619.327561:2,701.271145:2,147.075607:6,262.083570:6,311.102645:4,384.203676:9,540.353974:2,654.244573:2,74.031353:3,185.117931:5,312.121036:4,385.186320:7,492.244408:1,617.251295:1,110.058369:3,176.090426:4,337.145299:4,373.125419:6,522.297255:1,648.278045:1,129.102053:3,217.096514:4,367.166908:4,391.153582:6,554.222966:1,133.082538:3,171.079971:3,339.616853:3,379.146670:3,156.102902:3,199.119779:3,350.658619:3,379.664175:3,159.075990:3,244.152171:3,360.131860:3,386.185137:3,70.050003:2,72.072027:2,130.061207:2,136.050005:2,144.053358:2,151.098088:2,157.100330:2,158.072301:2,166.024439:2,173.111428:2,188.073128:2,198.082116:2,201.095578:2,209.096318:1,210.118388:2,213.144131:1,216.079907:2,223.110174:2,225.064651:1,226.147813:2,227.176365:2,240.065478:1,245.101980:2,254.180827:3,254.616695:2,256.193769:2,282.191156:1,294.083647:1,297.124562:2,299.090508:1,300.181117:1,309.938897:2,312.697969:1,314.082090:2,315.078393:2,322.641864:2,325.114516:2,328.050161:2,334.654998:2,337.633309:2,338.205426:2,341.031219:2,344.079947:2,344.572948:1,350.147078:1,352.152747:2,353.122068:1,357.199154:1,359.138574:1,361.140944:3,361.617144:3,365.147878:3,366.193012:3,368.171228:1,369.162334:2,372.187579:2,372.685660:2,374.167216:2,382.227310:2,387.125503:2,392.235267:2,392.701452:2,393.137811:2,400.167699:3,449.655234:2
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query2"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e42%2e42%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1209%20experiment%3d5%22
-rtinseconds=715.808
-charge=2+,3+
-mass_min=70.062710
-mass_max=712.431557
-int_min=1
-int_max=55
-num_vals=123
-num_used1=-1
-Ions1=70.062710:12,183.129981:55,312.134447:4,395.230372:13,496.176335:3,597.181126:21,710.325946:9,86.078346:12,211.131919:16,288.151818:3,395.685553:7,477.601660:2,598.238953:6,711.297380:4,72.065583:4,175.104648:8,321.102950:3,403.195223:4,479.228792:2,597.515076:3,692.314372:3,84.068946:3,184.138065:7,340.120646:3,406.172960:4,488.244253:2,599.186223:3,693.293401:3,110.058369:3,173.071481:5,346.675672:3,407.213927:4,510.258426:2,579.176864:2,694.253121:2,120.079779:3,185.128259:5,291.084276:2,408.179541:4,481.691339:1,608.194582:2,675.322928:1,130.052550:3,195.102005:4,324.116123:2,388.126830:3,527.288041:1,632.278217:2,712.431557:1,129.119304:2,204.088411:4,339.141391:2,372.143647:2,544.225244:1,642.281134:1,136.058859:2,199.162628:3,341.143374:2,376.210995:2,552.615788:1,651.257893:1,138.058386:2,212.136832:3,342.097433:2,377.153887:2,553.204816:1,133.073781:1,144.071580:2,147.103226:2,158.100934:1,159.066417:2,168.035585:2,171.089900:2,179.033892:2,197.100445:2,201.095578:2,202.108719:2,207.114274:2,209.107295:2,217.074145:2,226.067912:2,227.153482:2,231.106144:2,233.106850:2,242.104513:2,243.097675:2,244.128449:2,249.087354:1,251.128181:1,272.144646:1,289.054517:1,290.139619:1,304.099917:1,309.084199:1,314.041732:1,319.160747:1,323.214788:1,333.129225:1,334.141395:1,335.196791:1,343.151249:1,347.156385:2,349.664298:1,352.166992:1,354.092721:1,355.193451:2,359.138574:2,360.088645:2,361.227503:1,362.136994:2,362.642761:1,370.198588:1,371.250919:1,378.230814:2,382.153110:2,383.147989:2,386.170220:2,387.244997:2,389.129450:2,398.120346:2,403.713630:2,407.918866:1,467.109152:1
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query3"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e67%2e67%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1216%20experiment%3d4%22
-rtinseconds=772.389
-charge=2+,3+
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-int_min=1
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-num_vals=206
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-Ions1=86.085388:42,245.042563:31,359.627848:8,396.652527:13,566.220575:26,651.374134:4,677.297019:3,84.068946:12,175.104648:19,322.151191:7,397.136456:11,562.257866:6,633.290258:3,678.146764:2,147.084813:9,199.044805:10,351.625882:7,409.177008:11,567.254798:5,580.145493:2,686.255854:2,70.056357:6,195.112609:7,352.166992:6,407.167974:10,549.325409:3,588.383893:2,680.263558:1,87.088403:5,244.128449:7,296.065646:5,408.164205:6,561.160425:3,629.246950:2,120.054825:5,227.096286:6,303.160788:5,397.666092:5,566.459584:3,636.120621:2,143.089233:5,171.089900:5,312.147859:5,371.053497:4,486.149868:2,647.273406:2,158.081845:4,201.117108:4,283.633931:4,388.201608:4,493.272285:2,650.270303:2,101.067920:3,173.111428:3,305.106791:4,405.209724:4,495.719902:2,667.180844:2,110.074297:3,181.091468:3,352.651496:4,448.207707:4,518.297517:2,574.236712:1,112.082365:2,113.064953:3,129.076179:3,130.095838:3,134.021186:3,136.041151:3,138.031630:2,144.035137:2,153.045149:2,155.061385:2,157.071788:3,159.075990:2,169.060503:3,176.090426:2,178.050026:2,182.011995:2,183.140254:3,184.065967:2,185.138587:3,190.087657:3,194.064303:3,200.074247:2,203.048681:2,204.077567:2,205.119924:3,207.092426:3,208.120542:2,209.096318:3,210.107384:2,212.114721:2,217.141254:2,219.046997:1,220.972351:1,222.068255:2,226.136398:2,228.149917:1,229.068104:2,233.187985:2,246.053634:3,248.105932:2,249.099335:2,250.130737:1,251.092094:2,252.115556:2,259.056991:1,260.133270:2,269.122615:1,272.132124:2,274.089110:1,276.040495:1,278.062088:2,280.167287:1,281.121035:3,281.643102:2,284.132734:3,291.978585:3,294.161758:2,295.178140:1,297.124562:2,298.028092:2,300.062762:2,301.115623:2,302.143938:1,302.632341:2,306.115330:1,307.085624:2,309.097544:2,310.152756:2,311.678635:2,312.630856:2,313.154525:2,313.544204:2,313.987926:2,314.647366:2,315.631079:2,316.157253:2,316.629834:2,318.632078:1,319.052267:1,323.146556:2,323.651642:3,324.198125:1,325.114516:3,326.141862:1,327.088451:2,328.132659:1,332.146259:2,337.173176:3,337.633309:2,339.141391:3,339.658821:1,342.083393:3,342.715475:1,343.151249:2,344.079947:3,346.181169:1,347.170528:1,348.161300:2,350.658619:1,351.198984:2,360.175078:3,361.227503:1,362.122548:2,363.134415:2,364.147694:2,365.205902:2,366.163960:2,367.123273:2,369.133165:2,374.196583:2,376.181549:2,377.139145:2,379.161451:2,381.159524:2,382.182789:2,385.245915:2,387.155375:1,389.249252:1,391.183609:3,392.220233:2,394.161949:2,409.668516:2,410.175692:3,430.153066:1,449.333360:2,450.283221:1,464.324289:1,469.195042:4,469.458161:2,489.116843:1,520.286807:1,537.323212:1,538.273812:1,540.706941:1,550.155981:2,593.162527:1,597.255329:1,605.221676:1,606.174457:1,623.661151:1,632.182784:1,635.374169:1
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query4"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e15%2e15%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1196%20experiment%3d2%22
-rtinseconds=651.787
-charge=2+,3+
-mass_min=84.068946
-mass_max=692.354319
-int_min=1
-int_max=33
-num_vals=135
-num_used1=-1
-Ions1=175.084559:33,262.120438:9,373.140082:12,391.153582:9,490.303926:6,603.225142:3,690.318500:5,86.085388:21,199.162628:8,374.123167:5,392.190167:9,491.234427:2,588.291832:1,691.296117:2,101.067920:19,201.117108:7,300.089061:4,411.206379:5,563.176216:2,642.108005:1,692.354319:1,173.101441:18,229.068108:6,345.165015:4,393.198018:3,580.163776:2,646.211655:1,84.068946:13,187.054315:4,379.161451:4,412.176712:3,492.261250:1,120.071461:7,202.108719:4,355.121923:3,384.218555:2,129.084804:7,203.091950:4,362.151439:3,385.186320:2,183.088894:7,213.077643:4,366.091336:3,413.256202:2,171.050186:6,216.079907:4,375.136949:3,445.207528:2,176.100500:6,185.148916:3,292.004524:2,102.054761:2,110.074297:4,112.082365:2,116.071158:3,130.069864:4,136.067714:2,143.116475:1,145.084717:2,147.112433:4,149.052260:1,154.023354:2,155.127560:4,157.100330:2,158.072301:5,159.095139:4,162.067461:2,165.106304:2,174.091588:4,181.091468:2,184.086565:2,189.052957:2,192.966094:3,198.071432:2,207.103350:3,209.140227:2,215.110217:2,223.144191:2,227.119161:2,235.057984:3,237.075686:2,243.097675:2,244.128449:2,245.137634:3,247.102582:2,253.008265:2,254.168725:1,255.077182:2,263.141484:2,271.018779:3,273.134830:1,277.151458:1,278.999569:2,283.148340:3,285.003490:1,294.122702:2,295.047736:1,296.130957:1,298.067407:2,301.168315:2,302.143938:1,305.093532:1,306.115330:1,309.097544:2,311.129423:2,312.174682:1,314.122450:2,315.132293:1,318.117387:2,322.096695:2,324.075126:1,325.141891:2,326.100737:2,327.074723:1,331.137119:2,332.367646:1,333.129225:2,335.099514:2,336.615860:2,337.117424:2,338.177506:1,341.213480:2,342.097433:2,343.151249:1,344.178519:2,350.104466:2,350.644405:2,351.170534:1,353.107804:1,356.152619:2,359.239280:1,365.162384:2,367.210546:1,369.176919:2,381.648741:2
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query5"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e7%2e7%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1189%20experiment%3d2%22
-rtinseconds=631.191
-charge=2+,3+
-mass_min=74.044416
-mass_max=748.267601
-int_min=1
-int_max=64
-num_vals=90
-num_used1=-1
-Ions1=101.060288:21,201.106343:8,345.658792:18,400.699351:64,490.272943:17,603.243786:7,690.298556:21,129.050308:17,262.120438:8,336.643715:16,412.261149:23,491.200779:4,604.213667:4,691.296117:9,155.089744:8,216.091066:6,311.116034:14,401.185742:21,566.351189:1,672.268780:3,692.274427:3,173.101441:8,183.109437:4,346.167045:9,391.153582:13,603.504831:2,748.267601:2,86.078346:4,198.071432:3,337.145299:8,401.687642:11,605.221676:1,147.084813:4,188.083539:2,283.161113:5,409.248676:9,623.206267:1,169.070373:4,199.066225:2,301.128796:5,411.237166:8,74.044416:2,202.097927:2,329.150986:5,413.703832:6,102.062429:2,210.999581:2,320.205826:4,413.163619:5,171.070042:2,244.164032:2,346.647405:4,374.108484:4,246.113173:1,246.971342:2,260.194489:2,260.770303:2,263.153797:1,264.102830:2,271.131261:2,282.114651:2,284.226579:3,297.085309:2,300.167965:2,302.130743:3,310.112652:2,312.134447:2,313.100795:2,315.132293:2,350.033453:2,351.142084:2,351.697057:2,365.220409:2,369.176919:1,372.172935:2,373.169409:4,375.181058:3,379.146670:3,379.634594:2,381.233628:1,383.237146:2,384.203676:2,385.275714:2,390.208334:2,392.175134:4,403.225708:3,412.839660:3,413.441399:2,414.198051:2,428.218774:2
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query6"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e80%2e80%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1220%20experiment%3d2%22
-rtinseconds=799.514
-charge=2+,3+
-mass_min=70.056357
-mass_max=754.384836
-int_min=1
-int_max=92
-num_vals=117
-num_used1=-1
-Ions1=86.092432:5,173.114251:92,331.137119:20,412.700859:89,532.285045:6,619.251999:50,754.384836:2,136.050005:4,201.117108:69,331.676058:11,413.194479:44,564.329719:4,620.272470:15,169.070373:3,174.101604:15,288.113163:5,385.233310:26,493.221709:2,661.272599:9,70.056357:2,202.108719:7,302.117551:4,411.729909:18,565.231714:2,662.268505:4,87.038822:2,175.094603:4,332.146259:4,413.703832:17,533.353889:1,589.249623:3,120.063143:2,227.107722:4,284.567945:3,409.177008:14,621.388390:3,143.098313:2,185.117931:3,297.120203:3,401.200946:12,602.293313:2,147.084813:2,207.092426:3,300.115362:3,401.702855:10,603.318364:1,157.119359:2,261.113643:3,310.112652:3,412.176712:10,637.289025:1,158.062757:2,172.273494:2,351.056743:3,409.699245:8,638.228356:1,177.099175:2,180.132519:2,189.084270:2,193.103200:2,198.103484:1,213.077643:1,219.035763:1,229.091082:2,233.141620:2,239.066799:1,241.219480:1,242.151760:1,259.081427:2,266.129839:2,270.157196:2,271.156260:2,282.140152:2,283.090868:2,285.131655:2,291.097227:2,298.067407:2,301.168315:2,301.603195:2,306.128611:2,311.182983:1,312.134447:1,322.164816:2,337.089549:2,343.123126:2,346.068189:1,349.139299:2,350.147078:2,352.181238:1,355.150533:2,357.744534:1,359.138574:2,366.149435:1,366.730676:1,367.196000:3,368.214925:2,369.045665:1,370.198588:1,370.943835:1,373.169409:1,375.048740:2,386.214973:7,388.306309:2,392.175134:2,393.122760:2,394.177020:2,395.157239:2,397.802341:2,400.122145:2,400.684156:1,402.189855:3,404.675087:4,417.247081:2,418.177941:2,435.253301:2,436.235732:2,437.187526:1
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query7"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e81%2e81%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1221%20experiment%3d2%22
-rtinseconds=802.149
-charge=2+,3+
-mass_min=70.056357
-mass_max=727.442338
-int_min=1
-int_max=81
-num_vals=149
-num_used1=-1
-Ions1=89.047379:72,177.089073:79,331.143941:81,416.224333:68,564.221528:9,661.272599:17,725.478202:3,133.073781:63,175.094603:14,331.662233:39,415.233776:55,566.224742:4,662.268505:7,692.414242:2,136.058859:23,221.130355:11,327.157098:10,371.192417:49,488.210707:3,654.361075:4,726.439478:1,86.085388:15,178.090544:7,332.132425:10,411.760715:31,546.192672:3,628.314254:3,727.442338:1,169.080244:11,203.135223:7,322.123942:8,412.269185:12,565.285857:3,644.264163:3,70.056357:8,233.118440:7,346.195293:8,414.213500:12,487.271899:2,655.390631:3,141.071500:7,199.098357:6,283.110021:6,391.071023:4,547.275382:2,663.245611:3,147.029582:5,171.079971:5,284.631975:6,435.237464:4,620.385908:2,87.038822:4,227.084843:5,332.699864:6,388.755187:3,621.407312:1,132.086113:4,265.140086:5,340.148646:5,397.136456:3,90.045842:3,117.095682:2,119.042254:2,120.071461:3,131.067360:3,143.107394:4,157.109844:3,158.062757:3,182.063204:1,183.140254:3,186.079686:2,187.095845:2,190.108589:1,195.133815:3,200.106460:2,201.095578:3,202.087136:3,204.142636:2,211.142949:3,215.121351:3,222.136132:2,239.125487:2,244.092869:1,245.149519:1,251.068038:2,254.168725:2,261.125909:4,263.166112:1,267.096624:3,268.152167:1,275.624458:1,276.128785:2,280.078353:2,281.133762:2,282.127402:4,283.621147:2,285.106019:2,285.503495:3,295.856701:2,296.666774:1,298.224693:2,300.128512:3,301.076107:2,305.080273:2,307.138835:2,309.150930:3,310.166125:3,310.660966:2,311.089256:2,313.127660:2,316.157253:2,319.120065:2,344.108109:2,344.671590:2,346.689806:5,347.170528:2,348.090484:2,353.193394:4,354.049870:2,361.083244:1,362.122548:1,365.191396:2,367.268733:1,369.191505:2,370.110961:2,370.636878:2,372.187579:2,373.110756:2,375.034039:1,376.107938:1,377.153887:2,378.201289:1,381.218807:2,382.182789:1,385.216117:2,387.200185:2,388.156740:2,389.264229:2,390.073392:2,392.671367:2,393.167914:2,396.184002:2,398.211228:2,399.150949:2,403.256195:3,404.171324:3,404.720899:3,410.283316:2,436.235732:2
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query8"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e56%2e56%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1213%20experiment%3d4%22
-rtinseconds=747.568
-charge=2+,3+
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-int_min=1
-int_max=45
-num_vals=152
-num_used1=-1
-Ions1=86.085388:28,175.094603:11,310.139387:6,417.216070:45,546.121712:7,600.208629:3,713.221965:8,169.099986:9,261.123681:11,289.106143:5,415.218307:15,484.277123:4,599.297716:2,714.256236:7,130.087180:6,185.159245:6,316.103266:5,417.696867:12,538.168149:4,648.297373:2,697.256524:2,148.034576:5,200.127936:5,291.064854:4,387.215122:8,485.296652:2,659.224564:2,715.291256:2,72.072027:4,268.127307:5,314.203177:3,416.193360:8,539.313392:2,650.367093:1,716.286393:1,84.068946:4,195.102005:4,324.676675:3,404.140803:5,540.265750:2,136.058859:4,201.117108:4,325.141891:3,413.194479:4,547.239866:2,147.084813:4,216.102224:4,327.010666:3,372.129003:3,475.215792:1,158.062757:4,229.091082:4,343.123126:3,382.182789:3,489.217577:1,157.109844:3,217.062961:3,344.164436:3,416.658073:3,508.750601:1,73.009484:2,87.081319:2,98.083532:2,120.088097:2,129.076179:2,143.089233:2,170.098438:3,182.032478:2,183.068352:2,184.148366:2,199.162628:2,203.102768:2,205.130796:2,209.129249:1,211.131919:2,215.110217:1,223.098836:2,227.142042:1,228.138452:2,231.048449:2,240.147815:2,243.156856:1,244.104729:1,244.603101:2,245.125749:2,247.150315:1,262.083570:2,268.388397:2,276.999832:2,279.189792:1,284.132734:1,286.106648:2,287.083305:1,288.126048:2,290.023261:1,292.160203:1,293.121136:1,295.060775:2,297.137647:2,298.054301:2,299.129893:2,300.062762:1,300.562641:1,301.102451:2,303.147571:2,304.192586:1,307.098927:1,308.150724:1,311.196374:1,312.094215:2,317.116286:1,330.157099:1,332.409164:1,334.113644:1,337.103486:1,342.153595:1,348.118809:1,350.104466:2,352.138503:2,353.136333:1,355.107618:2,356.682863:2,357.127425:3,357.644038:2,358.074834:2,358.620882:2,361.140944:2,361.660451:2,364.147694:1,365.786394:1,367.632509:1,368.214925:2,369.176919:2,369.658387:1,371.221668:2,373.125419:1,376.152104:2,381.189165:1,383.222286:2,388.231521:1,391.213637:2,392.175134:1,395.172329:2,397.242355:2,398.650637:2,399.166115:2,400.182884:2,405.148605:2,405.652977:1,406.111769:2,406.708586:2,418.224511:2
---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query9"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e2%2e2%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1183%20experiment%3d2%22
-rtinseconds=617.506
-charge=2+,3+
-mass_min=70.056357
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-int_min=1
-int_max=44
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query10"
-
-title=201208%2d378803%2dABRR%2dAUG%2d1%2e28%2e28%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1202%20experiment%3d3%22
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query11"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e6%2e6%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1188%20experiment%3d3%22
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query12"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e11%2e11%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1192%20experiment%3d3%22
-rtinseconds=641.231
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query13"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e8%2e8%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1191%20experiment%3d2%22
-rtinseconds=634.351
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query14"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e17%2e17%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1198%20experiment%3d2%22
-rtinseconds=657.097
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query15"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e24%2e24%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1201%20experiment%3d2%22
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---gc0p4Jq0M2Yt08jU534c0p
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e4%2e4%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1187%20experiment%3d2%22
-rtinseconds=623.806
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---gc0p4Jq0M2Yt08jU534c0p
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e46%2e46%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1211%20experiment%3d2%22
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e22%2e22%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1200%20experiment%3d3%22
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query20"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e14%2e14%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1194%20experiment%3d2%22
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query22"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e101%2e101%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1238%20experiment%3d2%22
-rtinseconds=853.56
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---gc0p4Jq0M2Yt08jU534c0p
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e12%2e12%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1193%20experiment%3d2%22
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query24"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e44%2e44%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1210%20experiment%3d3%22
-rtinseconds=720.588
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query25"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e33%2e33%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1204%20experiment%3d4%22
-rtinseconds=694.152
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query26"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e65%2e65%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1216%20experiment%3d2%22
-rtinseconds=768.164
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---gc0p4Jq0M2Yt08jU534c0p
-Content-Type: application/x-Mascot; name="query27"
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e36%2e36%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1207%20experiment%3d3%22
-rtinseconds=702.072
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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-title=201208%2d378803%2dABRR%2dAUG%2d1%2e85%2e85%2e%20File%3a%22201208%2d378803%2ewiff%22%2c%20NativeID%3a%22sample%3d1%20period%3d1%20cycle%3d1223%20experiment%3d3%22
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p
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---gc0p4Jq0M2Yt08jU534c0p--
diff -r d239e445e2e6 -r f962717ca1db test-data/input/cow.protein.PRG2012-subset.fasta
diff -r d239e445e2e6 -r f962717ca1db tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 05 11:54:46 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bumbershoot" version="3.0.8789">
-    <repository changeset_revision="d9c7584f69f6" name="package_bumbershoot_3_0_8789" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>