Mercurial > repos > galaxyp > myrimatch
changeset 2:8240d0714a97 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
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--- a/COPYING Wed Feb 01 20:53:23 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -Creative Commons Legal Code - -CC0 1.0 Universal - - CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE - LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN - ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS - INFORMATION ON AN "AS-IS" BASIS. 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--- a/README.md Wed Feb 01 20:53:23 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -GalaxyP - MyriMatch -=================== - -* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> -* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/myrimatch> -* Tool ID: `myrimatch` - - -Description ------------ - -Bumbershoot MyriMatch. - -See: - -* <http://fenchurch.mc.vanderbilt.edu/> - - -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> - Vanderbilt University Medical Center - -* John Chilton <jmchilton@gmail.com> - Minnesota Supercomputing Institute, Univeristy of Minnesota
--- a/macros.xml Wed Feb 01 20:53:23 2017 -0500 +++ b/macros.xml Fri Oct 06 15:00:29 2017 -0400 @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">3.0.10246</token> + <token name="@VERSION@">3.0.11392</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3_0_10246">bumbershoot</requirement> + <requirement type="package" version="3_0_11392">bumbershoot</requirement> <yield/> </requirements> </xml>
--- /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 15:00:29 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
--- /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 15:00:29 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
--- /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 15:00:29 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]
--- /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 15:00:29 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-cm.pep.xml Fri Oct 06 15:00:29 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" 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<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->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->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->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" 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</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 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<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"> 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