# HG changeset patch
# User galaxyp
# Date 1507316411 14400
# Node ID aec819a9068b2caa0642fa7aed578be7bcac2396
# Parent  feebe32c3a52818b0ca46d563687ef355af741e6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64

diff -r feebe32c3a52 -r aec819a9068b COPYING
--- a/COPYING	Fri Sep 22 10:46:42 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-Creative Commons Legal Code
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-of the License, and in such case Affirmer hereby affirms that he or she
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diff -r feebe32c3a52 -r aec819a9068b README.md
--- a/README.md	Fri Sep 22 10:46:42 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-GalaxyP - idpQonvert
-====================
-
-* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
-* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/idpqonvert>
-* Tool ID: `idpqonvert`
-
-
-Description
------------
-
-Bumbershoot idpQonvert, a part of Bumbershoot IDPicker.
-
-See:
-
-* <http://idpicker.org/>
-
-
-GalaxyP Community
------------------
-
-Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
-
-<https://github.com/galaxyproteomics>
-
-
-License
--------
-
-Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
-
-To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
-
-You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
-
-You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
-
-
-Contributing
-------------
-
-Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/>
-
-
-Authors
--------
-
-Authors and contributors:
-
-* Matt Chambers <matt.chambers42@gmail.com>
-
-* John Chilton <jmchilton@gmail.com>
-  Minnesota Supercomputing Institute, University of Minnesota
diff -r feebe32c3a52 -r aec819a9068b idpQonvertEmbedder.xml
--- a/idpQonvertEmbedder.xml	Fri Sep 22 10:46:42 2017 -0400
+++ b/idpQonvertEmbedder.xml	Fri Oct 06 15:00:11 2017 -0400
@@ -60,17 +60,17 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="input/201208-378803.idpDB" />
+            <param name="input" value="201208-378803.idpDB" />
             <param name="EmbedGeneMetadata" value="false" />
-            <output name="output" file="input/201208-378803.idpDB" compare="sim_size" delta="500000" />
+            <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803.idpDB" />
+            <param name="input" value="201208-378803.idpDB" />
             <param name="EmbedGeneMetadata" value="true" />
             <output name="output" file="201208-378803-embeddedGenes.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803.idpDB" />
+            <param name="input" value="201208-378803.idpDB" />
             <param name="EmbedGeneMetadata" value="true" />
             <param name="use_raw_data" value="true" /> 
             <param name="input_raw" value="input/201208-378803.mzML" />
@@ -80,7 +80,7 @@
             <output name="output" file="201208-378803-embeddedGenesAndScanTimes.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803.idpDB" />
+            <param name="input" value="201208-378803.idpDB" />
             <param name="EmbedGeneMetadata" value="true" />
             <param name="use_raw_data" value="true" /> 
             <param name="input_raw" value="input/201208-378803.mzML" />
@@ -90,7 +90,7 @@
             <output name="output" file="201208-378803-embeddedGenesAndSpectra.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803.idpDB" />
+            <param name="input" value="201208-378803.idpDB" />
             <param name="EmbedGeneMetadata" value="true" />
             <param name="use_raw_data" value="true" /> 
             <param name="input_raw" value="input/201208-378803.mzML" />
diff -r feebe32c3a52 -r aec819a9068b idpqonvert.xml
--- a/idpqonvert.xml	Fri Sep 22 10:46:42 2017 -0400
+++ b/idpqonvert.xml	Fri Oct 06 15:00:11 2017 -0400
@@ -174,19 +174,19 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="input/201208-378803-myrimatch.pepXML" />
+            <param name="input" value="201208-378803-mm.pepXML" />
             <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
             <param name="MaxFDR" value="0.05" />
-            <output name="output" file="201208-378803-myrimatch.idpDB" compare="sim_size" delta="500000" />
+            <output name="output" file="201208-378803-mm.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803-cm.pep.xml" />
+            <param name="input" value="201208-378803-cm.pep.xml" />
             <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
             <param name="MaxFDR" value="0.05" />
             <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
-            <param name="input" value="input/201208-378803-msgf.mzid" />
+            <param name="input" value="201208-378803-msgf.mzid" />
             <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
             <param name="MaxFDR" value="0.05" />
             <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
diff -r feebe32c3a52 -r aec819a9068b test-data/201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,20 @@
+GeneId	Accession	DistinctPeptides
+Unmapped_gi|165973958|ref|NP_001107199.1|	gi|165973958|ref|NP_001107199.1|	2
+Unmapped_gi|27806851|ref|NP_776358.1|	gi|27806851|ref|NP_776358.1|	21
+Unmapped_gi|27806963|ref|NP_776953.1|	gi|27806963|ref|NP_776953.1|	2
+Unmapped_gi|27807109|ref|NP_777040.1|	gi|27807109|ref|NP_777040.1|	7
+Unmapped_gi|30466252|ref|NP_848667.1|	gi|30466252|ref|NP_848667.1|	16
+Unmapped_gi|30794280|ref|NP_851335.1|	gi|30794280|ref|NP_851335.1|	29
+Unmapped_gi|30794348|ref|NP_851372.1|	gi|30794348|ref|NP_851372.1|	13
+Unmapped_gi|32880221|ref|NP_872593.1|	gi|32880221|ref|NP_872593.1|	21
+Unmapped_gi|528903801|ref|XP_871686.4|	gi|528903801|ref|XP_871686.4|	2
+Unmapped_gi|528935739|ref|XP_005201142.1|	gi|528935739|ref|XP_005201142.1|	7
+Unmapped_gi|528947854|ref|XP_002687054.3|	gi|528947854|ref|XP_002687054.3|	2
+Unmapped_gi|528953234|ref|XP_005208080.1|	gi|528953234|ref|XP_005208080.1|	13
+Unmapped_gi|528953238|ref|XP_005208082.1|	gi|528953238|ref|XP_005208082.1|	13
+Unmapped_gi|528953240|ref|XP_005208083.1|	gi|528953240|ref|XP_005208083.1|	13
+Unmapped_gi|528969819|ref|XP_005213230.1|	gi|528969819|ref|XP_005213230.1|	18
+Unmapped_gi|528993971|ref|XP_005219929.1|	gi|528993971|ref|XP_005219929.1|	21
+Unmapped_gi|528993973|ref|XP_005219930.1|	gi|528993973|ref|XP_005219930.1|	21
+Unmapped_gi|528993975|ref|XP_005219931.1|	gi|528993975|ref|XP_005219931.1|	21
+Unmapped_gi|87196497|ref|NP_776354.2|	gi|87196497|ref|NP_776354.2|	18
diff -r feebe32c3a52 -r aec819a9068b test-data/201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,10 @@
+GeneGroup	GeneId	DistinctMatches
+1	Unmapped_gi|27806963|ref|NP_776953.1|	2
+2	Unmapped_gi|30466252|ref|NP_848667.1|	29
+3	Unmapped_gi|30794280|ref|NP_851335.1|	43
+4	Unmapped_gi|32880221|ref|NP_872593.1|	27
+5	Unmapped_gi|528935739|ref|XP_005201142.1|;Unmapped_gi|27807109|ref|NP_777040.1|	9
+6	Unmapped_gi|528903801|ref|XP_871686.4|;Unmapped_gi|528947854|ref|XP_002687054.3|;Unmapped_gi|165973958|ref|NP_001107199.1|	4
+7	Unmapped_gi|528953234|ref|XP_005208080.1|;Unmapped_gi|528953238|ref|XP_005208082.1|;Unmapped_gi|528953240|ref|XP_005208083.1|;Unmapped_gi|30794348|ref|NP_851372.1|	17
+8	Unmapped_gi|528993971|ref|XP_005219929.1|;Unmapped_gi|528993973|ref|XP_005219930.1|;Unmapped_gi|528993975|ref|XP_005219931.1|;Unmapped_gi|27806851|ref|NP_776358.1|	27
+9	Unmapped_gi|528969819|ref|XP_005213230.1|;Unmapped_gi|87196497|ref|NP_776354.2|	33
diff -r feebe32c3a52 -r aec819a9068b test-data/201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,20 @@
+Accession	FilteredSpectra	Description
+gi|528903801|ref|XP_871686.4|	4	PREDICTED: cationic trypsin isoformX1 [Bos taurus]
+gi|528935739|ref|XP_005201142.1|	10	PREDICTED: superoxide dismutase [Cu-Zn] isoform X1 [Bos taurus]
+gi|528947854|ref|XP_002687054.3|	4	PREDICTED: cationic trypsin isoform X1 [Bos taurus]
+gi|528953234|ref|XP_005208080.1|	20	PREDICTED: alpha-S1-casein isoform X1 [Bos taurus]
+gi|528953238|ref|XP_005208082.1|	20	PREDICTED: alpha-S1-casein isoform X3 [Bos taurus]
+gi|528953240|ref|XP_005208083.1|	20	PREDICTED: alpha-S1-casein isoform X4 [Bos taurus]
+gi|528969819|ref|XP_005213230.1|	36	PREDICTED: beta-lactoglobulin isoform X1 [Bos taurus]
+gi|528993971|ref|XP_005219929.1|	29	PREDICTED: lactoperoxidase isoform X1 [Bos taurus]
+gi|528993973|ref|XP_005219930.1|	29	PREDICTED: lactoperoxidase isoform X2 [Bos taurus]
+gi|528993975|ref|XP_005219931.1|	29	PREDICTED: lactoperoxidase isoform X3 [Bos taurus]
+gi|30794280|ref|NP_851335.1|	43	serum albumin precursor [Bos taurus]
+gi|30794348|ref|NP_851372.1|	20	alpha-S1-casein precursor [Bos taurus]
+gi|87196497|ref|NP_776354.2|	36	beta-lactoglobulin precursor [Bos taurus]
+gi|165973958|ref|NP_001107199.1|	4	cationic trypsin precursor [Bos taurus]
+gi|27807109|ref|NP_777040.1|	10	superoxide dismutase [Cu-Zn] [Bos taurus]
+gi|27806963|ref|NP_776953.1|	2	alpha-S2-casein precursor [Bos taurus]
+gi|30466252|ref|NP_848667.1|	31	carbonic anhydrase 2 [Bos taurus]
+gi|32880221|ref|NP_872593.1|	32	glutamate dehydrogenase 1, mitochondrial precursor [Bos taurus]
+gi|27806851|ref|NP_776358.1|	29	lactoperoxidase precursor [Bos taurus]
diff -r feebe32c3a52 -r aec819a9068b test-data/201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,10 @@
+ProteinGroup	Accession	PercentCoverage
+1	gi|30794280|ref|NP_851335.1|	42.01
+2	gi|30466252|ref|NP_848667.1|	39.23
+3	gi|32880221|ref|NP_872593.1|	35.84
+4	gi|27806963|ref|NP_776953.1|	7.21
+5	gi|528969819|ref|XP_005213230.1|;gi|87196497|ref|NP_776354.2|	56.18
+6	gi|528993971|ref|XP_005219929.1|;gi|528993973|ref|XP_005219930.1|;gi|528993975|ref|XP_005219931.1|;gi|27806851|ref|NP_776358.1|	28.09
+7	gi|528903801|ref|XP_871686.4|;gi|528947854|ref|XP_002687054.3|;gi|165973958|ref|NP_001107199.1|	12.6
+8	gi|528953234|ref|XP_005208080.1|;gi|528953238|ref|XP_005208082.1|;gi|528953240|ref|XP_005208083.1|;gi|30794348|ref|NP_851372.1|	41.59
+9	gi|528935739|ref|XP_005201142.1|;gi|27807109|ref|NP_777040.1|	33.55
diff -r feebe32c3a52 -r aec819a9068b test-data/201203-624176-12-mm-gui-test.idpDB
Binary file test-data/201203-624176-12-mm-gui-test.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-cm-filtered.idpDB
Binary file test-data/201208-378803-cm-filtered.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-cm.pep.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-cm.pep.xml	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +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"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="MMSASSYNEDL" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="40" calc_neutral_pep_mass="1246.484589" massdiff="-1.011644" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="54">
+    <search_score name="xcorr" value="0.163"/>
+    <search_score name="deltacn" value="0.284"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.7"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="4.75E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="PYDDDAEYMK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" num_matched_ions="1" tot_num_ions="36" calc_neutral_pep_mass="1245.485970" massdiff="-0.013025" num_tol_term="2" num_missed_cleavages="0" num_matched_peptides="54">
+    <search_score name="xcorr" value="0.117"/>
+    <search_score name="deltacn" value="0.002"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.4"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="1.05E+002"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="CHEVFKQHC" peptide_prev_aa="K" peptide_next_aa="M" protein="XXX_gi|358418103|ref|XP_600387.4|" num_tot_proteins="4" num_matched_ions="1" tot_num_ions="32" calc_neutral_pep_mass="1246.474695" massdiff="-1.001750" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="54">
+    <modification_info modified_peptide="CHEVFKQ[129]HC">
+     <mod_aminoacid_mass position="1" mass="161.014665"/>
+     <mod_aminoacid_mass position="7" mass="129.042594"/>
+     <mod_aminoacid_mass position="9" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.116"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.5"/>
+    <search_score name="sprank" value="4"/>
+    <search_score name="expect" value="1.05E+002"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00003.00003.3" spectrumNativeID="sample=1 period=1 cycle=1186 experiment=2" start_scan="3" end_scan="3" precursor_neutral_mass="1575.554503" assumed_charge="3" index="5" retention_time_sec="621.2">
+  <search_result>
+   <search_hit hit_rank="1" peptide="SSSSASQSNHSCTSM" peptide_prev_aa="R" peptide_next_aa="P" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="56" calc_neutral_pep_mass="1574.546067" massdiff="1.008437" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="100">
+    <modification_info modified_peptide="SSSSASQ[129]SNHSCTSM[147]">
+     <mod_aminoacid_mass position="7" mass="129.042594"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+     <mod_aminoacid_mass position="15" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.197"/>
+    <search_score name="deltacn" value="0.185"/>
+    <search_score name="deltacnstar" value="0.003"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="3.11E+001"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="SSSSASQSNHSCTSM" peptide_prev_aa="R" peptide_next_aa="P" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="56" calc_neutral_pep_mass="1574.546067" massdiff="1.008437" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="100">
+    <modification_info modified_peptide="SSSSASQSN[115]HSCTSM[147]">
+     <mod_aminoacid_mass position="9" mass="115.026943"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+     <mod_aminoacid_mass position="15" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.196"/>
+    <search_score name="deltacn" value="0.183"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="3.14E+001"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="FNRGCEPCVHHC" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|528908812|ref|XP_609847.5|" num_tot_proteins="12" num_matched_ions="0" tot_num_ions="44" calc_neutral_pep_mass="1574.570069" massdiff="0.984434" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="100">
+    <modification_info modified_peptide="FNRGCEPCVHHC">
+     <mod_aminoacid_mass position="5" mass="161.014665"/>
+     <mod_aminoacid_mass position="8" mass="161.014665"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.160"/>
+    <search_score name="deltacn" value="0.268"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="5.73E+001"/>
+   </search_hit>
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+ <spectrum_query spectrum="201208-378803.00108.00108.3" spectrumNativeID="sample=1 period=1 cycle=1627 experiment=2" start_scan="108" end_scan="108" precursor_neutral_mass="1743.773361" assumed_charge="3" index="215" retention_time_sec="1070.9">
+  <search_result>
+   <search_hit hit_rank="1" peptide="MGPTQGGYFPENVKAM" peptide_prev_aa="-" peptide_next_aa="T" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="60" calc_neutral_pep_mass="1742.764379" massdiff="1.008982" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="882">
+    <modification_info modified_peptide="MGPTQ[129]GGYFPENVKAM[147]">
+     <mod_aminoacid_mass position="5" mass="129.042594"/>
+     <mod_aminoacid_mass position="16" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.557"/>
+    <search_score name="deltacn" value="0.165"/>
+    <search_score name="deltacnstar" value="0.141"/>
+    <search_score name="spscore" value="0.6"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="4.67E+000"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="MGPTQGGYFPENVKAM" peptide_prev_aa="-" peptide_next_aa="T" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="60" calc_neutral_pep_mass="1741.780363" massdiff="1.992998" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="882">
+    <modification_info modified_peptide="MGPTQGGYFPENVKAM[147]">
+     <mod_aminoacid_mass position="16" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.479"/>
+    <search_score name="deltacn" value="0.028"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.6"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="1.02E+001"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="TTSECLTVTNSSWEK" peptide_prev_aa="V" peptide_next_aa="K" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" num_matched_ions="2" tot_num_ions="56" calc_neutral_pep_mass="1743.750912" massdiff="0.022449" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="882">
+    <modification_info modified_peptide="TTSECLTVTN[115]SSWEK">
+     <mod_aminoacid_mass position="5" mass="161.014665"/>
+     <mod_aminoacid_mass position="10" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.465"/>
+    <search_score name="deltacn" value="0.148"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="2.5"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.17E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="VLDSKQCFNRGCEK" peptide_prev_aa="P" peptide_next_aa="H" protein="XXX_gi|528908812|ref|XP_609847.5|" num_tot_proteins="12" num_matched_ions="1" tot_num_ions="52" calc_neutral_pep_mass="1743.744388" massdiff="0.028973" num_tol_term="1" num_missed_cleavages="2" num_matched_peptides="882">
+    <modification_info modified_peptide="VLDSKQ[129]CFN[115]RGCEK">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+     <mod_aminoacid_mass position="7" mass="161.014665"/>
+     <mod_aminoacid_mass position="9" mass="115.026943"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.396"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="1.3"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="2.32E+001"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="VLDSKQCFNRGCEK" peptide_prev_aa="P" peptide_next_aa="H" protein="XXX_gi|528908812|ref|XP_609847.5|" num_tot_proteins="12" num_matched_ions="1" tot_num_ions="52" calc_neutral_pep_mass="1742.760372" massdiff="1.012989" num_tol_term="1" num_missed_cleavages="2" num_matched_peptides="882">
+    <modification_info modified_peptide="VLDSKQ[129]CFNRGCEK">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+     <mod_aminoacid_mass position="7" mass="161.014665"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.396"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="1.3"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="2.32E+001"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00108.00108.2" spectrumNativeID="sample=1 period=1 cycle=1627 experiment=2" start_scan="108" end_scan="108" precursor_neutral_mass="1162.515574" assumed_charge="2" index="216" retention_time_sec="1070.9">
+  <search_result>
+   <search_hit hit_rank="1" 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="ISDMN[115]QNIGAT">
+     <mod_aminoacid_mass position="5" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.721"/>
+    <search_score name="deltacn" value="0.290"/>
+    <search_score name="deltacnstar" value="0.063"/>
+    <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="2" 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="ISDMNQ[129]NIGAT">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+    </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="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 feebe32c3a52 -r aec819a9068b test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,499 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<msms_pipeline_analysis date="2015-09-03T17:55:14" summary_xml="201208-378803.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">
+  <analysis_summary analysis="MyriMatch" version="2.2.8634" time="2015-09-03T17:55:14"/>
+  <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data="">
+    <sample_enzyme name="Trypsin" independent="false" fidelity="specific">
+      <specificity sense="C" cut="KR" no_cut="P" min_spacing="1"/>
+    </sample_enzyme>
+    <search_summary base_name="201208-378803" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">
+      <search_database local_path="cow.protein.PRG2012-subset.fasta" database_name="SDB" type="AA"/>
+      <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="4" min_number_termini="2"/>
+      <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/>
+      <parameter name="Config: ClassSizeMultiplier" value="2"/>
+      <parameter name="Config: CleavageRules" value="Trypsin"/>
+      <parameter name="Config: ComputeXCorr" value="1"/>
+      <parameter name="Config: DecoyPrefix" value="XXX_"/>
+      <parameter name="Config: DynamicMods" value=""/>
+      <parameter name="Config: EstimateSearchTimeOnly" value="0"/>
+      <parameter name="Config: FragmentMzTolerance" value="0.5mz"/>
+      <parameter name="Config: FragmentationAutoRule" value="1"/>
+      <parameter name="Config: FragmentationRule" value="cid"/>
+      <parameter name="Config: KeepUnadjustedPrecursorMz" value="0"/>
+      <parameter name="Config: MaxDynamicMods" value="4"/>
+      <parameter name="Config: MaxFragmentChargeState" value="0"/>
+      <parameter name="Config: MaxMissedCleavages" value="4"/>
+      <parameter name="Config: MaxPeakCount" value="300"/>
+      <parameter name="Config: MaxPeptideLength" value="75"/>
+      <parameter name="Config: MaxPeptideMass" value="10000"/>
+      <parameter name="Config: MaxPeptideVariants" value="1000000"/>
+      <parameter name="Config: MaxResultRank" value="1"/>
+      <parameter name="Config: MinMatchedFragments" value="5"/>
+      <parameter name="Config: MinPeptideLength" value="5"/>
+      <parameter name="Config: MinPeptideMass" value="0"/>
+      <parameter name="Config: MinResultScore" value="9.9999999999999995e-08"/>
+      <parameter name="Config: MinTerminiCleavages" value="2"/>
+      <parameter name="Config: MonoPrecursorMzTolerance" value="15ppm"/>
+      <parameter name="Config: MonoisotopeAdjustmentSet" value="[0,0] "/>
+      <parameter name="Config: NumBatches" value="50"/>
+      <parameter name="Config: NumChargeStates" value="3"/>
+      <parameter name="Config: NumIntensityClasses" value="3"/>
+      <parameter name="Config: NumMzFidelityClasses" value="3"/>
+      <parameter name="Config: OutputFormat" value="pepXML"/>
+      <parameter name="Config: OutputSuffix" value=""/>
+      <parameter name="Config: PrecursorMzToleranceRule" value="mono"/>
+      <parameter name="Config: PreferIntenseComplements" value="1"/>
+      <parameter name="Config: ProteinDatabase" value="cow.protein.PRG2012-subset.fasta"/>
+      <parameter name="Config: ProteinListFilters" value=""/>
+      <parameter name="Config: ProteinSamplingTime" value="15"/>
+      <parameter name="Config: ResultsPerBatch" value="200000"/>
+      <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/>
+      <parameter name="Config: StaticMods" value=""/>
+      <parameter name="Config: StatusUpdateFrequency" value="5"/>
+      <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/>
+      <parameter name="Config: UseMultipleProcessors" value="1"/>
+      <parameter name="Config: UseSmartPlusThreeModel" value="1"/>
+      <parameter name="Config: WorkingDirectory" value="/galaxy-central"/>
+      <parameter name="PeakCounts: 1stQuartile: Filtered" value="116"/>
+      <parameter name="PeakCounts: 1stQuartile: Original" value="120"/>
+      <parameter name="PeakCounts: 2ndQuartile: Filtered" value="146"/>
+      <parameter name="PeakCounts: 2ndQuartile: Original" value="154"/>
+      <parameter name="PeakCounts: 3rdQuartile: Filtered" value="178"/>
+      <parameter name="PeakCounts: 3rdQuartile: Original" value="180"/>
+      <parameter name="PeakCounts: Mean: Filtered" value="151"/>
+      <parameter name="PeakCounts: Mean: Original" value="157"/>
+      <parameter name="PeakCounts: Min/Max: Filtered" value="41 / 298"/>
+      <parameter name="PeakCounts: Min/Max: Original" value="42 / 471"/>
+      <parameter name="SearchEngine: Name" value="MyriMatch"/>
+      <parameter name="SearchEngine: Version" value="2.2.8634"/>
+      <parameter name="SearchStats: Nodes" value="1"/>
+      <parameter name="SearchStats: Overall" value="144 proteins; 49480 peptides; 27944 variants; 401 comparisons"/>
+      <parameter name="SearchTime: Duration" value="0.342288971 seconds"/>
+      <parameter name="SearchTime: Started" value="17:55:14 on 09/03/2015"/>
+      <parameter name="SearchTime: Stopped" value="17:55:14 on 09/03/2015"/>
+    </search_summary>
+    <spectrum_query spectrum="201208-378803.1.1.3" spectrumNativeID="sample=1 period=1 cycle=1192 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1326.694182167619" assumed_charge="3" index="1" retention_time_sec="639.111">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="GDRADKQLVVAR" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1326.7367964476" massdiff="0.042614279981" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="7" tot_num_ions="23">
+          <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="9.156783954627"/>
+          <search_score name="mzFidelity" value="25.381087340985"/>
+          <search_score name="xcorr" value="1.1044896737935341"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="TKPQIWPKMAK" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|27806963|ref|NP_776953.1|" num_tot_proteins="1" calc_neutral_pep_mass="1326.7482127568" massdiff="0.054030589181" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="22">
+          <search_score name="mvh" value="5.65200821354"/>
+          <search_score name="mzFidelity" value="16.183265741347"/>
+          <search_score name="xcorr" value="0.19536201572501194"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.2.2.3" spectrumNativeID="sample=1 period=1 cycle=1192 experiment=3" start_scan="2" end_scan="2" precursor_neutral_mass="1296.540613339326" assumed_charge="3" index="2" retention_time_sec="641.23099999998">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="GEIFGTCGEEQK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1296.5656165233" massdiff="0.025003183974" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="23">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="4.73735499523"/>
+          <search_score name="mzFidelity" value="20.706193451615"/>
+          <search_score name="xcorr" value="-0.027179517265532343"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.3.3.2" spectrumNativeID="sample=1 period=1 cycle=1193 experiment=2" start_scan="3" end_scan="3" precursor_neutral_mass="915.392372425296" assumed_charge="2" index="3" retention_time_sec="643.866">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="4">
+        <search_hit hit_rank="1" peptide="KQYSCCGK" peptide_prev_aa="R" peptide_next_aa="C" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" calc_neutral_pep_mass="915.3942578605" massdiff="0.001885435204" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="15">
+          <alternative_protein protein="XXX_gi|358418103|ref|XP_600387.4|"/>
+          <alternative_protein protein="XXX_gi|528923273|ref|XP_005196452.1|"/>
+          <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/>
+          <search_score name="mvh" value="7.006737263411"/>
+          <search_score name="mzFidelity" value="20.083610152632"/>
+          <search_score name="xcorr" value="0.10145246835947037"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.4.4.3" spectrumNativeID="sample=1 period=1 cycle=1202 experiment=2" start_scan="4" end_scan="4" precursor_neutral_mass="1464.686590506963" assumed_charge="3" index="4" retention_time_sec="680.352">
+      <search_result num_target_comparisons="8" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="LMLLSRDDSGSGSK" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1464.7242424303" massdiff="0.037651923337" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="28">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="9.626642757254"/>
+          <search_score name="mzFidelity" value="17.69444115758"/>
+          <search_score name="xcorr" value="0.63278641261563584"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.5.5.2" spectrumNativeID="sample=1 period=1 cycle=1203 experiment=2" start_scan="5" end_scan="5" precursor_neutral_mass="1065.469667444928" assumed_charge="2" index="5" retention_time_sec="685.11700000002">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="1">
+        <search_hit hit_rank="1" peptide="FAVSAEAEDK" peptide_prev_aa="R" peptide_next_aa="V" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1065.4978545341" massdiff="0.028187089172" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="19">
+          <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="7.875817776738"/>
+          <search_score name="mzFidelity" value="25.766451627541"/>
+          <search_score name="xcorr" value="0.25966326437518"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.6.6.3" spectrumNativeID="sample=1 period=1 cycle=1204 experiment=3" start_scan="6" end_scan="6" precursor_neutral_mass="2165.295835942044" assumed_charge="3" index="6" retention_time_sec="692.03200000002">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="VIPSTGSKLKRPTPAFHSSR" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="1" calc_neutral_pep_mass="2165.2069200887" massdiff="-0.088915853344" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="7" tot_num_ions="40">
+          <search_score name="mvh" value="5.152631021794"/>
+          <search_score name="mzFidelity" value="13.354233874427"/>
+          <search_score name="xcorr" value="1.5719721875880248"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
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+        <search_hit hit_rank="1" peptide="SQVNSEGLHSYGL" peptide_prev_aa="K" peptide_next_aa="-" protein="gi|528953246|ref|XP_005208086.1|" num_tot_proteins="1" calc_neutral_pep_mass="1389.6524576957" massdiff="0.028482066272" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="26">
+          <search_score name="mvh" value="4.718035090273"/>
+          <search_score name="mzFidelity" value="19.580751896886"/>
+          <search_score name="xcorr" value="0.61395449436268368"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.22.22.2" spectrumNativeID="sample=1 period=1 cycle=1216 experiment=5" start_scan="22" end_scan="22" precursor_neutral_mass="1149.594918445548" assumed_charge="2" index="25" retention_time_sec="774.177">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="AWTLVEEFR" peptide_prev_aa="K" peptide_next_aa="A" protein="XXX_gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1149.581858935" massdiff="-0.013059510548" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="XXX_gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="8.617394604809"/>
+          <search_score name="mzFidelity" value="41.257129700066"/>
+          <search_score name="xcorr" value="0.50047582628726961"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.23.23.2" spectrumNativeID="sample=1 period=1 cycle=1217 experiment=2" start_scan="23" end_scan="23" precursor_neutral_mass="1001.473988799636" assumed_charge="2" index="26" retention_time_sec="776.78599999998">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="0">
+        <search_hit hit_rank="1" peptide="QSPVDIDTK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|30466252|ref|NP_848667.1|" num_tot_proteins="1" calc_neutral_pep_mass="1001.502939912" massdiff="0.028951112364" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="17">
+          <search_score name="mvh" value="6.736171527742"/>
+          <search_score name="mzFidelity" value="25.329090035405"/>
+          <search_score name="xcorr" value="0.18480664704442024"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.24.24.2" spectrumNativeID="sample=1 period=1 cycle=1217 experiment=4" start_scan="24" end_scan="24" precursor_neutral_mass="1141.631807949586" assumed_charge="2" index="27" retention_time_sec="780.153">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="2">
+        <search_hit hit_rank="1" peptide="LPREKGRMR" peptide_prev_aa="K" peptide_next_aa="F" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="1141.6502300467" massdiff="0.018422097114" num_tol_term="2" num_missed_cleavages="3" num_matched_ions="7" tot_num_ions="17">
+          <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
+          <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
+          <search_score name="mvh" value="7.929069617921"/>
+          <search_score name="mzFidelity" value="29.580519925012"/>
+          <search_score name="xcorr" value="0.21898586032688619"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.25.25.2" spectrumNativeID="sample=1 period=1 cycle=1218 experiment=2" start_scan="25" end_scan="25" precursor_neutral_mass="1153.526999083812" assumed_charge="2" index="28" retention_time_sec="784.929">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="CFHAWSTFR" peptide_prev_aa="R" peptide_next_aa="Q" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="1153.5127335123" massdiff="-0.014265571512" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="6" tot_num_ions="17">
+          <alternative_protein protein="gi|528921180|ref|XP_005195747.1|"/>
+          <alternative_protein protein="gi|528995523|ref|XP_002695913.2|"/>
+          <search_score name="mvh" value="6.610627314763"/>
+          <search_score name="mzFidelity" value="25.103994445626"/>
+          <search_score name="xcorr" value="0.63611245342344047"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.26.26.2" spectrumNativeID="sample=1 period=1 cycle=1219 experiment=3" start_scan="26" end_scan="26" precursor_neutral_mass="1016.499381574794" assumed_charge="2" index="29" retention_time_sec="794.75899999998">
+      <search_result num_target_comparisons="4" num_decoy_comparisons="4">
+        <search_hit hit_rank="1" peptide="DARDGRDGR" peptide_prev_aa="K" peptide_next_aa="D" protein="XXX_gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1016.4747681016" massdiff="-0.024613473194" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="6" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="XXX_gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="8.674293346576"/>
+          <search_score name="mzFidelity" value="26.395843983313"/>
+          <search_score name="xcorr" value="0.25083901307377965"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="DAENTVRGR" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1016.4999202196" massdiff="5.386448059426e-04" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="17">
+          <search_score name="mvh" value="6.018930162713"/>
+          <search_score name="mzFidelity" value="21.495483219677"/>
+          <search_score name="xcorr" value="0.48560360629353672"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.27.27.3" spectrumNativeID="sample=1 period=1 cycle=1220 experiment=2" start_scan="27" end_scan="27" precursor_neutral_mass="1227.620988215667" assumed_charge="3" index="30" retention_time_sec="799.51399999998">
+      <search_result num_target_comparisons="3" num_decoy_comparisons="10">
+        <search_hit hit_rank="1" peptide="VQALGISDNRR" peptide_prev_aa="-" peptide_next_aa="D" protein="XXX_gi|28849955|ref|NP_788795.1|" num_tot_proteins="1" calc_neutral_pep_mass="1227.6683825314" massdiff="0.047394315733" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="22">
+          <search_score name="mvh" value="10.596869413746"/>
+          <search_score name="mzFidelity" value="16.943900632366"/>
+          <search_score name="xcorr" value="0.80438670446588878"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="QRKLNDALDR" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="1227.6683825314" massdiff="0.047394315733" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="5" tot_num_ions="20">
+          <search_score name="mvh" value="8.043398295653"/>
+          <search_score name="mzFidelity" value="22.280698819327"/>
+          <search_score name="xcorr" value="1.1322035509574475"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.28.28.3" spectrumNativeID="sample=1 period=1 cycle=1222 experiment=2" start_scan="28" end_scan="28" precursor_neutral_mass="1743.833885215164" assumed_charge="3" index="31" retention_time_sec="806.97400000002">
+      <search_result num_target_comparisons="16" num_decoy_comparisons="19">
+        <search_hit hit_rank="1" peptide="GAAQLNFNVDLEGQLR" peptide_prev_aa="R" peptide_next_aa="M" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" calc_neutral_pep_mass="1743.8903965562" massdiff="0.056511341036" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="9" tot_num_ions="31">
+          <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="8.703745165284"/>
+          <search_score name="mzFidelity" value="27.499216944034"/>
+          <search_score name="xcorr" value="0.88904612235733371"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="LQGELDVNFNLQAAGR" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|358418103|ref|XP_600387.4|" num_tot_proteins="1" calc_neutral_pep_mass="1743.8903965562" massdiff="0.056511341036" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="7" tot_num_ions="32">
+          <search_score name="mvh" value="7.396562819256"/>
+          <search_score name="mzFidelity" value="16.597930481493"/>
+          <search_score name="xcorr" value="0.85658302524349561"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.29.29.3" spectrumNativeID="sample=1 period=1 cycle=1224 experiment=2" start_scan="29" end_scan="29" precursor_neutral_mass="1725.858220325283" assumed_charge="3" index="32" retention_time_sec="814.37500000002">
+      <search_result num_target_comparisons="5" num_decoy_comparisons="5">
+        <search_hit hit_rank="1" peptide="IHGFDLAAINLQRCR" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1725.9096922103" massdiff="0.051471885017" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="12" tot_num_ions="30">
+          <alternative_protein protein="gi|528993971|ref|XP_005219929.1|"/>
+          <alternative_protein protein="gi|528993973|ref|XP_005219930.1|"/>
+          <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/>
+          <search_score name="mvh" value="12.259750257107"/>
+          <search_score name="mzFidelity" value="34.970325461964"/>
+          <search_score name="xcorr" value="1.9202226581428345"/>
+        </search_hit>
+        <search_hit hit_rank="2" peptide="ISELFDKLDSMSVDK" peptide_prev_aa="R" peptide_next_aa="I" protein="XXX_gi|528968108|ref|XP_005212569.1|" num_tot_proteins="1" calc_neutral_pep_mass="1725.8495025234" massdiff="-0.008717801883" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="11" tot_num_ions="30">
+          <search_score name="mvh" value="11.323857836871"/>
+          <search_score name="mzFidelity" value="36.756835575306"/>
+          <search_score name="xcorr" value="0.93184037338923231"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.30.30.3" spectrumNativeID="sample=1 period=1 cycle=1231 experiment=2" start_scan="30" end_scan="30" precursor_neutral_mass="1467.72458061501" assumed_charge="3" index="33" retention_time_sec="839.28400000002">
+      <search_result num_target_comparisons="8" num_decoy_comparisons="2">
+        <search_hit hit_rank="1" peptide="GVTEHSNQQQGRK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1467.7178519195" massdiff="-0.00672869551" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="25">
+          <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>
+          <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>
+          <search_score name="mvh" value="6.653798251586"/>
+          <search_score name="mzFidelity" value="14.932769947598"/>
+          <search_score name="xcorr" value="0.028206144867315191"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.31.31.2" spectrumNativeID="sample=1 period=1 cycle=1234 experiment=2" start_scan="31" end_scan="31" precursor_neutral_mass="1030.473954852586" assumed_charge="2" index="34" retention_time_sec="842.98000000002">
+      <search_result num_target_comparisons="0" num_decoy_comparisons="3">
+        <search_hit hit_rank="1" peptide="TFAHQENGK" peptide_prev_aa="R" peptide_next_aa="R" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="1030.4832075229" massdiff="0.009252670314" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="17">
+          <alternative_protein protein="XXX_gi|528921180|ref|XP_005195747.1|"/>
+          <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/>
+          <search_score name="mvh" value="6.979786912131"/>
+          <search_score name="mzFidelity" value="21.605021401289"/>
+          <search_score name="xcorr" value="0.49320911207199097"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="201208-378803.32.32.3" spectrumNativeID="sample=1 period=1 cycle=1283 experiment=2" start_scan="32" end_scan="32" precursor_neutral_mass="1770.954827198736" assumed_charge="3" index="35" retention_time_sec="883.49500000002">
+      <search_result num_target_comparisons="1" num_decoy_comparisons="9">
+        <search_hit hit_rank="1" peptide="TEPHSFQRLSLTEVK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1770.9264477115" massdiff="-0.028379487236" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="30">
+          <search_score name="mvh" value="6.109846868339"/>
+          <search_score name="mzFidelity" value="13.900987096911"/>
+          <search_score name="xcorr" value="0.73578462478668327"/>
+        </search_hit>
+      </search_result>
+    </spectrum_query>
+  </msms_run_summary>
+</msms_pipeline_analysis>
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-mm-filtered.idpDB
Binary file test-data/201208-378803-mm-filtered.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-mm.idpDB
Binary file test-data/201208-378803-mm.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-mm.pepXML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-mm.pepXML	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,20531 @@
+<?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">
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+        <search_hit hit_rank="4" peptide="KLANSEPVGTQTAKIQQQIIR" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2324.2699746859" massdiff="0.247491610852" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="10" tot_num_ions="112">
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+          <search_score name="xcorr" value="0.61379451555985531"/>
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+        <search_hit hit_rank="5" peptide="AMTVETAREWRSNLEEQMK" peptide_prev_aa="R" peptide_next_aa="K" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2324.0889000998" massdiff="0.066417024752" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="10" tot_num_ions="100">
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+          <search_score name="mvh" value="8.044847874038"/>
+          <search_score name="mzFidelity" value="11.334993594303"/>
+          <search_score name="xcorr" value="1.64827341749171"/>
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+    <spectrum_query spectrum="201208-378803.107.107.5" spectrumNativeID="sample=1 period=1 cycle=1627 experiment=2" start_scan="107" end_scan="107" precursor_neutral_mass="2906.28893498831" assumed_charge="5" index="405" retention_time_sec="1070.93800000002">
+      <search_result num_target_comparisons="5707" num_decoy_comparisons="5567">
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+        <search_hit hit_rank="2" peptide="EMLIAHSQPAEMSCGKGESEKLSQIE" peptide_prev_aa="K" peptide_next_aa="N" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="2905.3143452141" massdiff="0.03407514139" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="21" tot_num_ions="180">
+          <modification_info>
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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|"/>
+          <alternative_protein protein="XXX_gi|528968108|ref|XP_005212569.1|"/>
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+          <search_score name="xcorr" value="2.564456180282789"/>
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+        <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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+            <mod_aminoacid_mass position="1" mass="129.0425935114"/>
+            <mod_aminoacid_mass position="24" mass="115.0269434472"/>
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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>
+            <mod_aminoacid_mass position="7" mass="129.0425935114"/>
+            <mod_aminoacid_mass position="10" mass="129.0425935114"/>
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+          <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 feebe32c3a52 -r aec819a9068b test-data/201208-378803-msgf-filtered.idpDB
Binary file test-data/201208-378803-msgf-filtered.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-msgf.mzid
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-msgf.mzid	Fri Oct 06 15:00:11 2017 -0400
@@ -0,0 +1,4631 @@
+<?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>
+<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>
+<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"/>
+    </DBSequence>
+    <DBSequence accession="gi|528993971|ref|XP_005219929.1|" searchDatabase_ref="SearchDB_1" length="768" id="DBSeq31093">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528993971|ref|XP_005219929.1| PREDICTED: lactoperoxidase isoform X1 [Bos taurus]" name="protein description"/>
+    </DBSequence>
+    <DBSequence accession="gi|528993973|ref|XP_005219930.1|" searchDatabase_ref="SearchDB_1" length="712" id="DBSeq31862">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528993973|ref|XP_005219930.1| PREDICTED: lactoperoxidase isoform X2 [Bos taurus]" name="protein description"/>
+    </DBSequence>
+    <DBSequence accession="gi|528993975|ref|XP_005219931.1|" searchDatabase_ref="SearchDB_1" length="685" id="DBSeq32575">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528993975|ref|XP_005219931.1| PREDICTED: lactoperoxidase isoform X3 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|27806851|ref|NP_776358.1| lactoperoxidase precursor [Bos taurus]" name="protein description"/>
+    </DBSequence>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|27806963|ref|NP_776953.1| alpha-S2-casein precursor [Bos taurus]" name="protein description"/>
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+    <DBSequence accession="XXX_gi|528944676|ref|XP_005204734.1|" searchDatabase_ref="SearchDB_1" length="7610" id="DBSeq65480"/>
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+    <DBSequence accession="gi|528944678|ref|XP_005204735.1|" searchDatabase_ref="SearchDB_1" length="5498" id="DBSeq17116">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528944678|ref|XP_005204735.1| PREDICTED: microtubule-actin cross-linking factor 1 isoform X2 [Bos taurus]" name="protein description"/>
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+    <DBSequence accession="gi|219804516|ref|NP_001137332.1|" searchDatabase_ref="SearchDB_1" length="5422" id="DBSeq38514">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|219804516|ref|NP_001137332.1| microtubule-actin cross-linking factor 1 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|32880221|ref|NP_872593.1| glutamate dehydrogenase 1, mitochondrial precursor [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968104|ref|XP_005212567.1| PREDICTED: exocyst complex component 6B isoform X1 [Bos taurus]" name="protein description"/>
+    </DBSequence>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968106|ref|XP_005212568.1| PREDICTED: exocyst complex component 6B isoform X2 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968108|ref|XP_005212569.1| PREDICTED: exocyst complex component 6B isoform X3 [Bos taurus]" name="protein description"/>
+    </DBSequence>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528935739|ref|XP_005201142.1| PREDICTED: superoxide dismutase [Cu-Zn] isoform X1 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|27807109|ref|NP_777040.1| superoxide dismutase [Cu-Zn] [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|30466252|ref|NP_848667.1| carbonic anhydrase 2 [Bos taurus]" name="protein description"/>
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+    <DBSequence accession="XXX_gi|297479727|ref|XP_002690982.1|" searchDatabase_ref="SearchDB_1" length="1099" id="DBSeq109459"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|358418103|ref|XP_600387.4| PREDICTED: rab effector MyRIP isoform X2 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528923273|ref|XP_005196452.1| PREDICTED: rab effector MyRIP isoform X1 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|297488451|ref|XP_002696970.1| PREDICTED: rab effector MyRIP isoform X1 [Bos taurus]" name="protein description"/>
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+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|529000951|ref|XP_005222651.1| PREDICTED: rab effector MyRIP isoform X2 [Bos taurus]" name="protein description"/>
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+    <DBSequence accession="XXX_gi|30794280|ref|NP_851335.1|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq99912"/>
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+    <DBSequence accession="XXX_gi|528953234|ref|XP_005208080.1|" searchDatabase_ref="SearchDB_1" length="213" id="DBSeq78837"/>
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+    <DBSequence accession="XXX_gi|30794348|ref|NP_851372.1|" searchDatabase_ref="SearchDB_1" length="214" id="DBSeq100983"/>
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+    <DBSequence accession="XXX_gi|87196497|ref|NP_776354.2|" searchDatabase_ref="SearchDB_1" length="178" id="DBSeq101198"/>
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+        <PeptideSequence>YICDNQDTISSK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep2">
+        <PeptideSequence>LVNELTEFAK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep3">
+        <PeptideSequence>CCTESLVNR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="1">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="2">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep4">
+        <PeptideSequence>CDENSPYR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="1">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep5">
+        <PeptideSequence>NAVPITPTLNR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep6">
+        <PeptideSequence>TITGDCNNR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep7">
+        <PeptideSequence>TITGDCNNR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep8">
+        <PeptideSequence>ISELFDKLDSMSVDK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep9">
+        <PeptideSequence>NEMFQQLK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep10">
+        <PeptideSequence>KQTALVELLK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep11">
+        <PeptideSequence>GFCGLSQPK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep12">
+        <PeptideSequence>EFENWLERSEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep13">
+        <PeptideSequence>SVQESLER</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep14">
+        <PeptideSequence>KLYGTTTFKDAR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep15">
+        <PeptideSequence>LQDRWHR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep16">
+        <PeptideSequence>ELQEYQNLVR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep17">
+        <PeptideSequence>PKNDPKLKTQGK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep18">
+        <PeptideSequence>PKNDPKLKTQGK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep19">
+        <PeptideSequence>HVGDLGNVTADK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep20">
+        <PeptideSequence>QLQTGGIIDTVTGR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep21">
+        <PeptideSequence>QLQTGGIIDTVTGR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep22">
+        <PeptideSequence>NVFTRQLCLEHDEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="8">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep23">
+        <PeptideSequence>EQKWHVVSSKMEER</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="11">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep24">
+        <PeptideSequence>NVFTRQLCLEHDEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="8">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep25">
+        <PeptideSequence>DFPIANGER</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep26">
+        <PeptideSequence>ALAQRFTSWAHFCR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="13">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep27">
+        <PeptideSequence>LGRQFQQIR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep28">
+        <PeptideSequence>EEVMQGEEPNLEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep29">
+        <PeptideSequence>PTAEFQDR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep30">
+        <PeptideSequence>EPISVSSQQMLK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep31">
+        <PeptideSequence>VICQPRFNK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep32">
+        <PeptideSequence>NEGIQEVQ</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep33">
+        <PeptideSequence>RRCGDCK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep34">
+        <PeptideSequence>RMMESR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="3">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep35">
+        <PeptideSequence>TSDATEMFQTVMDR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="7">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="12">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep36">
+        <PeptideSequence>YNNSVDPR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep37">
+        <PeptideSequence>FEDLAMWGGGVR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="6">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep38">
+        <PeptideSequence>QLEGRLQDLR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep39">
+        <PeptideSequence>VWVCCVCQQARVLR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="4">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="5">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="7">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="9">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep40">
+        <PeptideSequence>LIGSDQESK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep41">
+        <PeptideSequence>LAEAEKEGR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep42">
+        <PeptideSequence>GLKEFQDCNQK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="8">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="9">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="10">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep43">
+        <PeptideSequence>KVQDWPN</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep44">
+        <PeptideSequence>MMEQQATTE</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="1">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="2">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep45">
+        <PeptideSequence>DYELQLMTYK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep46">
+        <PeptideSequence>SSDEETLSER</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep47">
+        <PeptideSequence>EVEDEGFLR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep48">
+        <PeptideSequence>HSFLEDMSDK</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="7">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep49">
+        <PeptideSequence>DLPFLSNEYK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep50">
+        <PeptideSequence>PYDDDAEYMK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep51">
+        <PeptideSequence>NDQPHFDK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep52">
+        <PeptideSequence>FSDHQAHIEK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep53">
+        <PeptideSequence>LMHDPSR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="2">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep54">
+        <PeptideSequence>AEMFEHLSEK</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep55">
+        <PeptideSequence>AAQGALQPSL</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep56">
+        <PeptideSequence>LETQYCK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep57">
+        <PeptideSequence>QQSEVFAK</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep58">
+        <PeptideSequence>QRSEMMRK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep59">
+        <PeptideSequence>QSIDIEDDKKENK</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep60">
+        <PeptideSequence>YNCDKMICRK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="8">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep61">
+        <PeptideSequence>LQDSMAQDEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="5">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep62">
+        <PeptideSequence>EGSHTRQHRIL</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep63">
+        <PeptideSequence>QSHAILMEKR</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="7">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep64">
+        <PeptideSequence>FCKVMVDNIPKLR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="2">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="5">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep65">
+        <PeptideSequence>DKNSCISIFQ</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="5">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="10">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep66">
+        <PeptideSequence>ARWQEYQSR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep67">
+        <PeptideSequence>ARWQEYQSR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep68">
+        <PeptideSequence>GGVYIRLKCDKWKK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="9">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep69">
+        <PeptideSequence>DFHPQDNK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep70">
+        <PeptideSequence>LDGIKTRYAD</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep71">
+        <PeptideSequence>EAQCCEQFVGNYK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="4">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="5">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="11">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep72">
+        <PeptideSequence>LQSYLEM</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="7">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep73">
+        <PeptideSequence>DAMETASR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep74">
+        <PeptideSequence>EQIGENK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep75">
+        <PeptideSequence>LMLCLPVLEMYSK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="4">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep76">
+        <PeptideSequence>YINDKCL</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep77">
+        <PeptideSequence>ALELTTVEDHVKNFR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="13">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep78">
+        <PeptideSequence>QQEEMR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep79">
+        <PeptideSequence>LEECEQ</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="4">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep80">
+        <PeptideSequence>SPDHMLKSTISVK</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="5">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep81">
+        <PeptideSequence>VVRMTQQQENPK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="10">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep82">
+        <PeptideSequence>QFMENK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep83">
+        <PeptideSequence>VVILPLKKMKTLR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="9">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep84">
+        <PeptideSequence>EMKDTSR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep85">
+        <PeptideSequence>STDKMER</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep86">
+        <PeptideSequence>NLLNNFLEEQAYR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="10">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep87">
+        <PeptideSequence>NLLNNFLEEQAYR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="10">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep88">
+        <PeptideSequence>VDFILQREPYCR</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="11">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep89">
+        <PeptideSequence>VDFILQREPYCR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="11">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep90">
+        <PeptideSequence>KAETCNAQDADEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="5">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep91">
+        <PeptideSequence>QVAQCKCAK</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="5">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="7">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep92">
+        <PeptideSequence>RHYSEAAADR</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep93">
+        <PeptideSequence>ARHQELLSQQ</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="9">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep94">
+        <PeptideSequence>QDVFRSLQDT</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep95">
+        <PeptideSequence>EMNSGMAK</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="2">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep96">
+        <PeptideSequence>WVDFDFNAFEK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep97">
+        <PeptideSequence>RCIMKDCNYKQ</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="2">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="7">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="8">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep98">
+        <PeptideSequence>DLGEEHF</PeptideSequence>
+    </Peptide>
+    <Peptide id="Pep99">
+        <PeptideSequence>MDGFTGCR</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="1">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="7">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep100">
+        <PeptideSequence>LDQMVFFWED</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="4">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep101">
+        <PeptideSequence>RIYLDQMGR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep102">
+        <PeptideSequence>CESCVYPK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="1">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="4">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep103">
+        <PeptideSequence>QPWEPEDEAR</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep104">
+        <PeptideSequence>YEGLKEFQDCNQK</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="10">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="11">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="12">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep105">
+        <PeptideSequence>FNCMKEIER</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="4">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep106">
+        <PeptideSequence>QPEQNFSK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep107">
+        <PeptideSequence>ACQVYIQH</PeptideSequence>
+        <Modification monoisotopicMassDelta="58.00548" location="2">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="7">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep108">
+        <PeptideSequence>QRNQVQT</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="4">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep109">
+        <PeptideSequence>YESGQHR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep110">
+        <PeptideSequence>DLQYFQR</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="3">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="6">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep111">
+        <PeptideSequence>MPCTEDYLSLILN</PeptideSequence>
+        <Modification monoisotopicMassDelta="15.9949" location="1">
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+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep112">
+        <PeptideSequence>QQQENPK</PeptideSequence>
+        <Modification monoisotopicMassDelta="-17.026" location="0">
+            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="0.984016" location="5">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep113">
+        <PeptideSequence>SNLEEQMK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="2">
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+        </Modification>
+        <Modification monoisotopicMassDelta="15.9949" location="7">
+            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep114">
+        <PeptideSequence>DEMNNAWENLNK</PeptideSequence>
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+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+    </Peptide>
+    <Peptide id="Pep115">
+        <PeptideSequence>QACEGNEWK</PeptideSequence>
+        <Modification monoisotopicMassDelta="0.984016" location="1">
+            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="3">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
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+        <Modification monoisotopicMassDelta="15.9949" location="1">
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+        </Modification>
+    </Peptide>
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+        </Modification>
+    </Peptide>
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+        </Modification>
+    </Peptide>
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+    </Peptide>
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+        <PeptideSequence>CLFVYCD</PeptideSequence>
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+        </Modification>
+        <Modification monoisotopicMassDelta="58.00548" location="6">
+            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
+        </Modification>
+    </Peptide>
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+        <Modification monoisotopicMassDelta="15.9949" location="6">
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+        </Modification>
+    </Peptide>
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+        </Modification>
+    </Peptide>
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+        </Modification>
+    </Peptide>
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+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="sample=1 period=1 cycle=1238 experiment=2" id="SIR_101">
+                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep119" calculatedMassToCharge="455.3005065917969" experimentalMassToCharge="455.6540832519531" chargeState="3" id="SII_101_1">
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+                    <userParam value="1" name="IsotopeError"/>
+                    <userParam value="HCD" name="AssumedDissociationMethod"/>
+                    <userParam value="0.0" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.0" name="CTermIonCurrentRatio"/>
+                    <userParam value="352.0" name="MS2IonCurrent"/>
+                </SpectrumIdentificationItem>
+            </SpectrumIdentificationResult>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="sample=1 period=1 cycle=1188 experiment=2" id="SIR_5">
+                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep120" calculatedMassToCharge="489.68280029296875" experimentalMassToCharge="489.1662292480469" chargeState="2" id="SII_5_1">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_60905_120_331"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_62158_120_331"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_90178_120_331"/>
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+                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.5125" name="MS-GF:QValue"/>
+                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.51898736" name="MS-GF:PepQValue"/>
+                    <userParam value="-1" name="IsotopeError"/>
+                    <userParam value="HCD" name="AssumedDissociationMethod"/>
+                    <userParam value="0.0" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0" name="NTermIonCurrentRatio"/>
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+                    <userParam value="352.0" name="MS2IonCurrent"/>
+                </SpectrumIdentificationItem>
+            </SpectrumIdentificationResult>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="sample=1 period=1 cycle=1211 experiment=4" id="SIR_48">
+                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep121" calculatedMassToCharge="677.2850341796875" experimentalMassToCharge="677.2626342773438" chargeState="2" id="SII_48_1">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_66843_121_1364"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_74384_121_1294"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_95782_121_1294"/>
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+                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="1.0" name="MS-GF:PepQValue"/>
+                    <userParam value="0" name="IsotopeError"/>
+                    <userParam value="HCD" name="AssumedDissociationMethod"/>
+                    <userParam value="0.02173913" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.02173913" name="CTermIonCurrentRatio"/>
+                    <userParam value="138.0" name="MS2IonCurrent"/>
+                    <userParam value="1" name="NumMatchedMainIons"/>
+                    <userParam value="5.6731687" name="MeanErrorAll"/>
+                    <userParam value="0.0" name="StdevErrorAll"/>
+                    <userParam value="5.6731687" name="MeanErrorTop7"/>
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+                    <userParam value="-5.6731687" name="MeanRelErrorAll"/>
+                    <userParam value="0.0" name="StdevRelErrorAll"/>
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+                    <userParam value="0.0" name="StdevRelErrorTop7"/>
+                </SpectrumIdentificationItem>
+                <SpectrumIdentificationItem passThreshold="true" rank="2" peptide_ref="Pep122" calculatedMassToCharge="676.79296875" experimentalMassToCharge="677.2626342773438" chargeState="2" id="SII_48_2">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_66843_122_1364"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_74384_122_1294"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_95782_122_1294"/>
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+                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="1.0" name="MS-GF:PepQValue"/>
+                    <userParam value="1" name="IsotopeError"/>
+                    <userParam value="HCD" name="AssumedDissociationMethod"/>
+                    <userParam value="0.02173913" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.02173913" name="CTermIonCurrentRatio"/>
+                    <userParam value="138.0" name="MS2IonCurrent"/>
+                    <userParam value="1" name="NumMatchedMainIons"/>
+                    <userParam value="5.6731687" name="MeanErrorAll"/>
+                    <userParam value="0.0" name="StdevErrorAll"/>
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+                    <userParam value="0.0" name="StdevErrorTop7"/>
+                    <userParam value="-5.6731687" name="MeanRelErrorAll"/>
+                    <userParam value="0.0" name="StdevRelErrorAll"/>
+                    <userParam value="-5.6731687" name="MeanRelErrorTop7"/>
+                    <userParam value="0.0" name="StdevRelErrorTop7"/>
+                </SpectrumIdentificationItem>
+                <SpectrumIdentificationItem passThreshold="true" rank="3" peptide_ref="Pep123" calculatedMassToCharge="677.2850341796875" experimentalMassToCharge="677.2626342773438" chargeState="2" id="SII_48_3">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_66843_123_1364"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_74384_123_1294"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_95782_123_1294"/>
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+                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="40" name="MS-GF:DeNovoScore"/>
+                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.0031106102" name="MS-GF:SpecEValue"/>
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+                    <cvParam accession="MS:1002054" cvRef="PSI-MS" value="1.0" name="MS-GF:QValue"/>
+                    <cvParam accession="MS:1002055" cvRef="PSI-MS" value="1.0" name="MS-GF:PepQValue"/>
+                    <userParam value="0" name="IsotopeError"/>
+                    <userParam value="HCD" name="AssumedDissociationMethod"/>
+                    <userParam value="0.02173913" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.02173913" name="CTermIonCurrentRatio"/>
+                    <userParam value="138.0" name="MS2IonCurrent"/>
+                    <userParam value="1" name="NumMatchedMainIons"/>
+                    <userParam value="5.6731687" name="MeanErrorAll"/>
+                    <userParam value="0.0" name="StdevErrorAll"/>
+                    <userParam value="5.6731687" name="MeanErrorTop7"/>
+                    <userParam value="0.0" name="StdevErrorTop7"/>
+                    <userParam value="-5.6731687" name="MeanRelErrorAll"/>
+                    <userParam value="0.0" name="StdevRelErrorAll"/>
+                    <userParam value="-5.6731687" name="MeanRelErrorTop7"/>
+                    <userParam value="0.0" name="StdevRelErrorTop7"/>
+                </SpectrumIdentificationItem>
+            </SpectrumIdentificationResult>
+        </SpectrumIdentificationList>
+    </AnalysisData>
+</DataCollection>
+</MzIdentML>
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803-myrimatch.idpDB
Binary file test-data/201208-378803-myrimatch.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/201208-378803.idpDB
Binary file test-data/201208-378803.idpDB has changed
diff -r feebe32c3a52 -r aec819a9068b test-data/input/201208-378803-cm.pep.xml
--- a/test-data/input/201208-378803-cm.pep.xml	Fri Sep 22 10:46:42 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10303 +0,0 @@
-<?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>
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- </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"/>
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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>
diff -r feebe32c3a52 -r aec819a9068b test-data/input/201208-378803-msgf.mzid
--- a/test-data/input/201208-378803-msgf.mzid	Fri Sep 22 10:46:42 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4631 +0,0 @@
-<?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"/>
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep7">
-        <PeptideSequence>TITGDCNNR</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="6">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep8">
-        <PeptideSequence>ISELFDKLDSMSVDK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep9">
-        <PeptideSequence>NEMFQQLK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="1">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep10">
-        <PeptideSequence>KQTALVELLK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="2">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep11">
-        <PeptideSequence>GFCGLSQPK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="3">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep12">
-        <PeptideSequence>EFENWLERSEK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="4">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep13">
-        <PeptideSequence>SVQESLER</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="3">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep14">
-        <PeptideSequence>KLYGTTTFKDAR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep15">
-        <PeptideSequence>LQDRWHR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="2">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep16">
-        <PeptideSequence>ELQEYQNLVR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="6">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep17">
-        <PeptideSequence>PKNDPKLKTQGK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep18">
-        <PeptideSequence>PKNDPKLKTQGK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="3">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep19">
-        <PeptideSequence>HVGDLGNVTADK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep20">
-        <PeptideSequence>QLQTGGIIDTVTGR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="1">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep21">
-        <PeptideSequence>QLQTGGIIDTVTGR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="3">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep22">
-        <PeptideSequence>NVFTRQLCLEHDEK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="6">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="8">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep23">
-        <PeptideSequence>EQKWHVVSSKMEER</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="11">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep24">
-        <PeptideSequence>NVFTRQLCLEHDEK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="8">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep25">
-        <PeptideSequence>DFPIANGER</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep26">
-        <PeptideSequence>ALAQRFTSWAHFCR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="4">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="13">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep27">
-        <PeptideSequence>LGRQFQQIR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="4">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="6">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep28">
-        <PeptideSequence>EEVMQGEEPNLEK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="5">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep29">
-        <PeptideSequence>PTAEFQDR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep30">
-        <PeptideSequence>EPISVSSQQMLK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep31">
-        <PeptideSequence>VICQPRFNK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="3">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="4">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="8">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep32">
-        <PeptideSequence>NEGIQEVQ</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="8">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep33">
-        <PeptideSequence>RRCGDCK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="3">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="6">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep34">
-        <PeptideSequence>RMMESR</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="3">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep35">
-        <PeptideSequence>TSDATEMFQTVMDR</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="7">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="15.9949" location="12">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep36">
-        <PeptideSequence>YNNSVDPR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep37">
-        <PeptideSequence>FEDLAMWGGGVR</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="6">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep38">
-        <PeptideSequence>QLEGRLQDLR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep39">
-        <PeptideSequence>VWVCCVCQQARVLR</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="4">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="5">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="7">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="8">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="9">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep40">
-        <PeptideSequence>LIGSDQESK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="6">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep41">
-        <PeptideSequence>LAEAEKEGR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep42">
-        <PeptideSequence>GLKEFQDCNQK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="8">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="9">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="10">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep43">
-        <PeptideSequence>KVQDWPN</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep44">
-        <PeptideSequence>MMEQQATTE</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="1">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="15.9949" location="2">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep45">
-        <PeptideSequence>DYELQLMTYK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep46">
-        <PeptideSequence>SSDEETLSER</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep47">
-        <PeptideSequence>EVEDEGFLR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep48">
-        <PeptideSequence>HSFLEDMSDK</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="7">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep49">
-        <PeptideSequence>DLPFLSNEYK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep50">
-        <PeptideSequence>PYDDDAEYMK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep51">
-        <PeptideSequence>NDQPHFDK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="1">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep52">
-        <PeptideSequence>FSDHQAHIEK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep53">
-        <PeptideSequence>LMHDPSR</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="2">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep54">
-        <PeptideSequence>AEMFEHLSEK</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep55">
-        <PeptideSequence>AAQGALQPSL</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep56">
-        <PeptideSequence>LETQYCK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="6">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep57">
-        <PeptideSequence>QQSEVFAK</PeptideSequence>
-        <Modification monoisotopicMassDelta="-17.026" location="0">
-            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="2">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep58">
-        <PeptideSequence>QRSEMMRK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="1">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep59">
-        <PeptideSequence>QSIDIEDDKKENK</PeptideSequence>
-        <Modification monoisotopicMassDelta="-17.026" location="0">
-            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep60">
-        <PeptideSequence>YNCDKMICRK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="3">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="8">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep61">
-        <PeptideSequence>LQDSMAQDEK</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="5">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep62">
-        <PeptideSequence>EGSHTRQHRIL</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep63">
-        <PeptideSequence>QSHAILMEKR</PeptideSequence>
-        <Modification monoisotopicMassDelta="-17.026" location="0">
-            <cvParam accession="UNIMOD:28" cvRef="UNIMOD" name="Gln-&gt;pyro-Glu"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="15.9949" location="7">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep64">
-        <PeptideSequence>FCKVMVDNIPKLR</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="2">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="15.9949" location="5">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="8">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep65">
-        <PeptideSequence>DKNSCISIFQ</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="5">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="10">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep66">
-        <PeptideSequence>ARWQEYQSR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="4">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep67">
-        <PeptideSequence>ARWQEYQSR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep68">
-        <PeptideSequence>GGVYIRLKCDKWKK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="9">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep69">
-        <PeptideSequence>DFHPQDNK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep70">
-        <PeptideSequence>LDGIKTRYAD</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep71">
-        <PeptideSequence>EAQCCEQFVGNYK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="4">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="5">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="7">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="11">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep72">
-        <PeptideSequence>LQSYLEM</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="7">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep73">
-        <PeptideSequence>DAMETASR</PeptideSequence>
-    </Peptide>
-    <Peptide id="Pep74">
-        <PeptideSequence>EQIGENK</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="2">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="6">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep75">
-        <PeptideSequence>LMLCLPVLEMYSK</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="4">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep76">
-        <PeptideSequence>YINDKCL</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="3">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="6">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep77">
-        <PeptideSequence>ALELTTVEDHVKNFR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="13">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep78">
-        <PeptideSequence>QQEEMR</PeptideSequence>
-        <Modification monoisotopicMassDelta="0.984016" location="1">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="2">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep79">
-        <PeptideSequence>LEECEQ</PeptideSequence>
-        <Modification monoisotopicMassDelta="58.00548" location="4">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep80">
-        <PeptideSequence>SPDHMLKSTISVK</PeptideSequence>
-        <Modification monoisotopicMassDelta="15.9949" location="5">
-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep81">
-        <PeptideSequence>VVRMTQQQENPK</PeptideSequence>
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-        </Modification>
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-        </Modification>
-    </Peptide>
-    <Peptide id="Pep82">
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
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-        </Modification>
-    </Peptide>
-    <Peptide id="Pep83">
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-        </Modification>
-    </Peptide>
-    <Peptide id="Pep84">
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-    </Peptide>
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-    </Peptide>
-    <Peptide id="Pep86">
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="10">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep87">
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep88">
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-        </Modification>
-    </Peptide>
-    <Peptide id="Pep89">
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="11">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
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-        </Modification>
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="8">
-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep91">
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-        </Modification>
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-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-        <Modification monoisotopicMassDelta="58.00548" location="7">
-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
-    </Peptide>
-    <Peptide id="Pep92">
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-    </Peptide>
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-        </Modification>
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-            <cvParam accession="UNIMOD:7" cvRef="UNIMOD" name="Deamidated"/>
-        </Modification>
-    </Peptide>
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-        </Modification>
-    </Peptide>
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-        </Modification>
-        <Modification monoisotopicMassDelta="0.984016" location="3">
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-        </Modification>
-    </Peptide>
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-        </Modification>
-    </Peptide>
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-        </Modification>
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-            <cvParam accession="MS:1001460" cvRef="UNIMOD" name="unknown modification"/>
-        </Modification>
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-        </Modification>
-    </Peptide>
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-    </Peptide>
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-        </Modification>
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-        </Modification>
-    </Peptide>
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-        </Modification>
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-            <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
-        </Modification>
-    </Peptide>
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-        </Modification>
-    </Peptide>
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-        </Modification>
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-        </Modification>
-    </Peptide>
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-        </Modification>
-    </Peptide>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
-    </Peptide>
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-        </Modification>
-    </Peptide>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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-        </Modification>
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diff -r feebe32c3a52 -r aec819a9068b test-data/input/201208-378803-myrimatch.pepXML
--- a/test-data/input/201208-378803-myrimatch.pepXML	Fri Sep 22 10:46:42 2017 -0400
+++ /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>
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diff -r feebe32c3a52 -r aec819a9068b test-data/input/201208-378803.idpDB
Binary file test-data/input/201208-378803.idpDB has changed