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comparison IDFilter.xml @ 16:093a52644633 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:42:57 +0000
parents a5d785af0ad8
children
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15:a5d785af0ad8 16:093a52644633
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
4 <tool id="IDFilter" name="IDFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IDFilter" name="IDFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Filters results from protein or peptide identification engines based on different criteria.</description> 4 <description>Filters results from protein or peptide identification engines based on different criteria</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDFilter</token> 6 <token name="@EXECUTABLE@">IDFilter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $whitelist.proteins: 19 #if $whitelist.proteins:
21 mkdir whitelist.proteins && 20 mkdir whitelist.proteins &&
22 ln -s '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' && 21 cp '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' &&
23 #end if 22 #end if
24 #if $whitelist.peptides: 23 #if $whitelist.peptides:
25 mkdir whitelist.peptides && 24 mkdir whitelist.peptides &&
26 ln -s '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' && 25 cp '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' &&
27 #end if 26 #end if
28 #if $blacklist.proteins: 27 #if $blacklist.proteins:
29 mkdir blacklist.proteins && 28 mkdir blacklist.proteins &&
30 ln -s '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' && 29 cp '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' &&
31 #end if 30 #end if
32 #if $blacklist.peptides: 31 #if $blacklist.peptides:
33 mkdir blacklist.peptides && 32 mkdir blacklist.peptides &&
34 ln -s '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' && 33 cp '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' &&
35 #end if 34 #end if
36 #if $in_silico_digestion.fasta: 35 #if $in_silico_digestion.fasta:
37 mkdir in_silico_digestion.fasta && 36 mkdir in_silico_digestion.fasta &&
38 ln -s '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' && 37 cp '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' &&
39 #end if 38 #end if
40 39
41 ## Main program call 40 ## Main program call
42 41
43 set -o pipefail && 42 set -o pipefail &&
77 <configfiles> 76 <configfiles>
78 <inputs name="args_json" data_style="paths"/> 77 <inputs name="args_json" data_style="paths"/>
79 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 78 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
80 </configfiles> 79 </configfiles>
81 <inputs> 80 <inputs>
82 <param argument="-in" type="data" format="consensusxml,idxml" optional="false" label="input file" help=" select consensusxml,idxml data sets(s)"/> 81 <param argument="-in" type="data" format="consensusxml,idxml" label="input file" help=" select consensusxml,idxml data sets(s)"/>
83 <param argument="-var_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)" help=""/> 82 <param argument="-var_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)" help=""/>
84 <param argument="-remove_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only peptides matching exactly one protein are kept" help="Remember that isoforms count as different proteins!"/> 83 <param argument="-remove_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only peptides matching exactly one protein are kept" help="Remember that isoforms count as different proteins!"/>
85 <param argument="-keep_unreferenced_protein_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Proteins not referenced by a peptide are retained in the IDs" help=""/> 84 <param argument="-keep_unreferenced_protein_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Proteins not referenced by a peptide are retained in the IDs" help=""/>
86 <param argument="-remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove proteins according to the information in the user parameters" help="Usually used in combination with 'delete_unreferenced_peptide_hits'"/> 85 <param argument="-remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove proteins according to the information in the user parameters" help="Usually used in combination with 'delete_unreferenced_peptide_hits'"/>
87 <param argument="-delete_unreferenced_peptide_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Peptides not referenced by any protein are deleted in the IDs" help="Usually used in combination with 'score:prot' or 'thresh:prot'"/> 86 <param argument="-delete_unreferenced_peptide_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Peptides not referenced by any protein are deleted in the IDs" help="Usually used in combination with 'score:prot' or 'thresh:prot'"/>
88 <section name="precursor" title="Filtering by precursor attributes (RT, m/z, charge, length)" help="" expanded="false"> 87 <section name="precursor" title="Filtering by precursor attributes (RT, m/z, charge, length)" help="" expanded="false">
89 <param name="rt" argument="-precursor:rt" type="text" optional="true" value=":" label="Retention time range to extract" help=""> 88 <param name="rt" argument="-precursor:rt" type="text" value=":" label="Retention time range to extract" help="">
90 <expand macro="list_string_san" name="rt"/> 89 <expand macro="list_string_san" name="rt"/>
91 </param> 90 </param>
92 <param name="mz" argument="-precursor:mz" type="text" optional="true" value=":" label="Mass-to-charge range to extract" help=""> 91 <param name="mz" argument="-precursor:mz" type="text" value=":" label="Mass-to-charge range to extract" help="">
93 <expand macro="list_string_san" name="mz"/> 92 <expand macro="list_string_san" name="mz"/>
94 </param> 93 </param>
95 <param name="length" argument="-precursor:length" type="text" optional="true" value=":" label="Keep only peptide hits with a sequence length in this range" help=""> 94 <param name="length" argument="-precursor:length" type="text" value=":" label="Keep only peptide hits with a sequence length in this range" help="">
96 <expand macro="list_string_san" name="length"/> 95 <expand macro="list_string_san" name="length"/>
97 </param> 96 </param>
98 <param name="charge" argument="-precursor:charge" type="text" optional="true" value=":" label="Keep only peptide hits with charge states in this range" help=""> 97 <param name="charge" argument="-precursor:charge" type="text" value=":" label="Keep only peptide hits with charge states in this range" help="">
99 <expand macro="list_string_san" name="charge"/> 98 <expand macro="list_string_san" name="charge"/>
100 </param> 99 </param>
101 </section> 100 </section>
102 <section name="score" title="Filtering by peptide/protein score" help="" expanded="false"> 101 <section name="score" title="Filtering by peptide/protein score" help="" expanded="false">
103 <param name="pep" argument="-score:pep" type="float" optional="true" value="0.0" label="The score which should be reached by a peptide hit to be kept" help=""/> 102 <param name="pep" argument="-score:pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help=""/>
104 <param name="prot" argument="-score:prot" type="float" optional="true" value="0.0" label="The score which should be reached by a protein hit to be kept" help="All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/> 103 <param name="prot" argument="-score:prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
105 <param name="protgroup" argument="-score:protgroup" type="float" optional="true" value="0.0" label="The score which should be reached by a protein group to be kept" help="Performs group level score filtering (including groups of single proteins). Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/> 104 <param name="protgroup" argument="-score:protgroup" type="float" value="0.0" label="The score which should be reached by a protein group to be kept" help="Performs group level score filtering (including groups of single proteins). Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
106 </section> 105 </section>
107 <section name="whitelist" title="Filtering by whitelisting (only peptides/proteins from a given set can pass)" help="" expanded="false"> 106 <section name="whitelist" title="Filtering by whitelisting (only peptides/proteins from a given set can pass)" help="" expanded="false">
108 <param name="proteins" argument="-whitelist:proteins" type="data" format="fasta" optional="true" label="Filename of a FASTA file containing protein sequences" help="All peptides that are not referencing a protein in this file are removed.. All proteins whose accessions are not present in this file are removed select fasta data sets(s)"/> 107 <param name="proteins" argument="-whitelist:proteins" type="data" format="fasta" optional="true" label="Filename of a FASTA file containing protein sequences" help="All peptides that are not referencing a protein in this file are removed.. All proteins whose accessions are not present in this file are removed select fasta data sets(s)"/>
109 <param name="protein_accessions" argument="-whitelist:protein_accessions" type="text" optional="true" value="" label="All peptides that do not reference at least one of the provided protein accession are removed" help="Only proteins of the provided list are retained (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 108 <param name="protein_accessions" argument="-whitelist:protein_accessions" type="text" optional="true" value="" label="All peptides that do not reference at least one of the provided protein accession are removed" help="Only proteins of the provided list are retained (space separated list, in order to allow for spaces in list items surround them by single quotes)">
110 <expand macro="list_string_val" name="protein_accessions"/> 109 <expand macro="list_string_val" name="protein_accessions"/>
111 <expand macro="list_string_san" name="protein_accessions"/> 110 <expand macro="list_string_san" name="protein_accessions"/>
112 </param> 111 </param>
113 <param name="peptides" argument="-whitelist:peptides" type="data" format="idxml" optional="true" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="Use with 'whitelist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/> 112 <param name="peptides" argument="-whitelist:peptides" type="data" format="idxml" optional="true" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="Use with 'whitelist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/>
114 <param name="ignore_modifications" argument="-whitelist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare whitelisted peptides by sequence only" help=""/> 113 <param name="ignore_modifications" argument="-whitelist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare whitelisted peptides by sequence only" help=""/>
115 <param name="modifications" argument="-whitelist:modifications" multiple="true" type="select" optional="true" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help=""> 114 <param name="modifications" argument="-whitelist:modifications" type="select" multiple="true" optional="true" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="">
116 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 115 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
117 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 116 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
118 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 117 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
119 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 118 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
120 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 119 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
121 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 120 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
122 <option value="2-succinyl (C)">2-succinyl (C)</option> 121 <option value="2-succinyl (C)">2-succinyl (C)</option>
123 <option value="2HPG (R)">2HPG (R)</option> 122 <option value="2HPG (R)">2HPG (R)</option>
124 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 123 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
124 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
125 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
126 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
127 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
125 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 128 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
126 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 129 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
127 <option value="4-ONE (C)">4-ONE (C)</option> 130 <option value="4-ONE (C)">4-ONE (C)</option>
128 <option value="4-ONE (H)">4-ONE (H)</option> 131 <option value="4-ONE (H)">4-ONE (H)</option>
129 <option value="4-ONE (K)">4-ONE (K)</option> 132 <option value="4-ONE (K)">4-ONE (K)</option>
209 <option value="Ammonium (D)">Ammonium (D)</option> 212 <option value="Ammonium (D)">Ammonium (D)</option>
210 <option value="Ammonium (E)">Ammonium (E)</option> 213 <option value="Ammonium (E)">Ammonium (E)</option>
211 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 214 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
212 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 215 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
213 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 216 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
217 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
214 <option value="Archaeol (C)">Archaeol (C)</option> 218 <option value="Archaeol (C)">Archaeol (C)</option>
215 <option value="Arg (N-term)">Arg (N-term)</option> 219 <option value="Arg (N-term)">Arg (N-term)</option>
216 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 220 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
217 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 221 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
218 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 222 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
312 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 316 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
313 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 317 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
314 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 318 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
315 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 319 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
316 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 320 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
321 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
317 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 322 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
318 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 323 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
319 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 324 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
320 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 325 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
321 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 326 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
344 <option value="BITC (C)">BITC (C)</option> 349 <option value="BITC (C)">BITC (C)</option>
345 <option value="BITC (K)">BITC (K)</option> 350 <option value="BITC (K)">BITC (K)</option>
346 <option value="BITC (N-term)">BITC (N-term)</option> 351 <option value="BITC (N-term)">BITC (N-term)</option>
347 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 352 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
348 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 353 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
349 <option value="Bodipy (C)">Bodipy (C)</option>
350 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 354 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
351 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 355 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
352 <option value="Bromo (F)">Bromo (F)</option> 356 <option value="Bromo (F)">Bromo (F)</option>
353 <option value="Bromo (H)">Bromo (H)</option> 357 <option value="Bromo (H)">Bromo (H)</option>
354 <option value="Bromo (W)">Bromo (W)</option> 358 <option value="Bromo (W)">Bromo (W)</option>
776 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 780 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
777 <option value="Dehydrated (S)">Dehydrated (S)</option> 781 <option value="Dehydrated (S)">Dehydrated (S)</option>
778 <option value="Dehydrated (T)">Dehydrated (T)</option> 782 <option value="Dehydrated (T)">Dehydrated (T)</option>
779 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 783 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
780 <option value="Dehydro (C)">Dehydro (C)</option> 784 <option value="Dehydro (C)">Dehydro (C)</option>
785 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
781 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 786 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
782 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 787 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
783 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
784 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 788 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
785 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 789 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
786 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 790 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
787 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 791 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
788 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 792 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
789 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 793 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
790 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 794 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
791 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 795 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
792 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 796 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
793 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
794 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 797 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
795 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 798 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
796 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 799 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
797 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 800 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
798 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 801 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
800 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 803 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
801 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 804 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
802 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 805 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
803 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 806 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
804 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 807 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
808 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
805 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 809 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
806 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 810 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
807 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 811 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
808 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 812 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
809 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 813 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
1372 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 1376 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
1373 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 1377 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
1374 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 1378 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
1375 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 1379 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
1376 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 1380 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
1377 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
1378 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 1381 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
1379 <option value="Ethyl (D)">Ethyl (D)</option> 1382 <option value="Ethyl (D)">Ethyl (D)</option>
1380 <option value="Ethyl (E)">Ethyl (E)</option> 1383 <option value="Ethyl (E)">Ethyl (E)</option>
1381 <option value="Ethyl (K)">Ethyl (K)</option> 1384 <option value="Ethyl (K)">Ethyl (K)</option>
1382 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 1385 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
1466 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 1469 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
1467 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 1470 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
1468 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 1471 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
1469 <option value="Glu (E)">Glu (E)</option> 1472 <option value="Glu (E)">Glu (E)</option>
1470 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 1473 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
1474 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
1471 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 1475 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
1472 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 1476 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
1473 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 1477 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
1474 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 1478 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
1475 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 1479 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
1480 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1484 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1481 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1485 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1482 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1486 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1483 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1487 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1484 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1488 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1485 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
1486 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 1489 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
1487 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1490 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1488 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1491 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
1489 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 1492 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
1490 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 1493 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
1504 <option value="Gluratylation (K)">Gluratylation (K)</option> 1507 <option value="Gluratylation (K)">Gluratylation (K)</option>
1505 <option value="Glutathione (C)">Glutathione (C)</option> 1508 <option value="Glutathione (C)">Glutathione (C)</option>
1506 <option value="Gly (K)">Gly (K)</option> 1509 <option value="Gly (K)">Gly (K)</option>
1507 <option value="Gly (S)">Gly (S)</option> 1510 <option value="Gly (S)">Gly (S)</option>
1508 <option value="Gly (T)">Gly (T)</option> 1511 <option value="Gly (T)">Gly (T)</option>
1512 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
1509 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 1513 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
1510 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 1514 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
1511 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 1515 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
1512 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 1516 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
1513 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 1517 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
1894 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 1898 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
1895 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 1899 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
1896 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 1900 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
1897 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 1901 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
1898 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 1902 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
1903 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
1899 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 1904 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
1900 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 1905 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
1901 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 1906 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
1902 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 1907 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
1903 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 1908 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
1905 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 1910 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
1906 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 1911 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
1907 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 1912 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
1908 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 1913 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
1909 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 1914 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
1915 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
1916 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
1917 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
1910 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 1918 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
1911 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 1919 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
1912 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 1920 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
1913 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 1921 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
1914 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 1922 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
1960 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 1968 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
1961 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 1969 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
1962 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 1970 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
1963 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 1971 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
1964 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 1972 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
1973 <option value="His+O(2) (H)">His+O(2) (H)</option>
1965 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 1974 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
1966 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 1975 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
1967 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 1976 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
1968 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 1977 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
1969 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 1978 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
2097 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 2106 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
2098 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 2107 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
2099 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 2108 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
2100 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 2109 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
2101 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 2110 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
2111 <option value="Kdo (S)">Kdo (S)</option>
2112 <option value="Kdo (T)">Kdo (T)</option>
2102 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 2113 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
2103 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 2114 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
2104 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 2115 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
2105 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 2116 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
2106 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 2117 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
2118 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
2107 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 2119 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
2108 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 2120 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
2109 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 2121 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
2110 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 2122 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
2111 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 2123 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
2186 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 2198 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
2187 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 2199 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
2188 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 2200 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
2189 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 2201 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
2190 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 2202 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
2203 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
2191 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 2204 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
2192 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 2205 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
2193 <option value="Lipoyl (K)">Lipoyl (K)</option> 2206 <option value="Lipoyl (K)">Lipoyl (K)</option>
2194 <option value="LRGG (K)">LRGG (K)</option> 2207 <option value="LRGG (K)">LRGG (K)</option>
2195 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 2208 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
2196 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 2209 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
2210 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
2197 <option value="Lys (N-term)">Lys (N-term)</option> 2211 <option value="Lys (N-term)">Lys (N-term)</option>
2212 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
2198 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 2213 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
2199 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 2214 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
2200 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 2215 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
2201 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 2216 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
2202 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 2217 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
2227 <option value="maleimide5 (C)">maleimide5 (C)</option> 2242 <option value="maleimide5 (C)">maleimide5 (C)</option>
2228 <option value="maleimide5 (K)">maleimide5 (K)</option> 2243 <option value="maleimide5 (K)">maleimide5 (K)</option>
2229 <option value="Malonyl (C)">Malonyl (C)</option> 2244 <option value="Malonyl (C)">Malonyl (C)</option>
2230 <option value="Malonyl (K)">Malonyl (K)</option> 2245 <option value="Malonyl (K)">Malonyl (K)</option>
2231 <option value="Malonyl (S)">Malonyl (S)</option> 2246 <option value="Malonyl (S)">Malonyl (S)</option>
2247 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
2232 <option value="MDCC (C)">MDCC (C)</option> 2248 <option value="MDCC (C)">MDCC (C)</option>
2233 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 2249 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
2234 <option value="Menadione (C)">Menadione (C)</option> 2250 <option value="Menadione (C)">Menadione (C)</option>
2235 <option value="Menadione (K)">Menadione (K)</option> 2251 <option value="Menadione (K)">Menadione (K)</option>
2236 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 2252 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
2238 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 2254 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
2239 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 2255 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
2240 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 2256 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
2241 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 2257 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
2242 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 2258 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
2259 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
2243 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 2260 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
2244 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 2261 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
2245 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 2262 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
2246 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 2263 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
2247 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 2264 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
2421 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 2438 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
2422 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 2439 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
2423 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 2440 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
2424 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 2441 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
2425 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 2442 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
2426 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
2427 <option value="NP40 (N-term)">NP40 (N-term)</option> 2443 <option value="NP40 (N-term)">NP40 (N-term)</option>
2428 <option value="NQIGG (K)">NQIGG (K)</option> 2444 <option value="NQIGG (K)">NQIGG (K)</option>
2429 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 2445 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
2430 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 2446 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
2431 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 2447 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
2509 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 2525 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
2510 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 2526 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
2511 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 2527 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
2512 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 2528 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
2513 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 2529 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
2530 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
2531 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
2532 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
2533 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
2514 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 2534 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
2515 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 2535 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
2516 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 2536 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
2517 <option value="Phospho (C)">Phospho (C)</option> 2537 <option value="Phospho (C)">Phospho (C)</option>
2518 <option value="Phospho (D)">Phospho (D)</option> 2538 <option value="Phospho (D)">Phospho (D)</option>
2523 <option value="Phospho (S)">Phospho (S)</option> 2543 <option value="Phospho (S)">Phospho (S)</option>
2524 <option value="Phospho (T)">Phospho (T)</option> 2544 <option value="Phospho (T)">Phospho (T)</option>
2525 <option value="Phospho (Y)">Phospho (Y)</option> 2545 <option value="Phospho (Y)">Phospho (Y)</option>
2526 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 2546 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
2527 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 2547 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
2548 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
2528 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 2549 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
2529 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 2550 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
2530 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 2551 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
2531 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 2552 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
2532 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 2553 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
2554 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 2575 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
2555 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 2576 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
2556 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 2577 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
2557 <option value="Piperidine (K)">Piperidine (K)</option> 2578 <option value="Piperidine (K)">Piperidine (K)</option>
2558 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 2579 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
2580 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
2559 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 2581 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
2560 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 2582 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
2561 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 2583 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
2562 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 2584 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
2563 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 2585 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
2631 <option value="QEQTGG (K)">QEQTGG (K)</option> 2653 <option value="QEQTGG (K)">QEQTGG (K)</option>
2632 <option value="QQQTGG (K)">QQQTGG (K)</option> 2654 <option value="QQQTGG (K)">QQQTGG (K)</option>
2633 <option value="QTGG (K)">QTGG (K)</option> 2655 <option value="QTGG (K)">QTGG (K)</option>
2634 <option value="Quinone (W)">Quinone (W)</option> 2656 <option value="Quinone (W)">Quinone (W)</option>
2635 <option value="Quinone (Y)">Quinone (Y)</option> 2657 <option value="Quinone (Y)">Quinone (Y)</option>
2658 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
2659 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
2660 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
2661 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
2662 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
2663 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
2664 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
2665 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
2666 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
2667 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
2668 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
2669 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
2670 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
2671 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
2672 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
2673 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
2674 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
2675 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
2676 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
2677 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
2636 <option value="Retinylidene (K)">Retinylidene (K)</option> 2678 <option value="Retinylidene (K)">Retinylidene (K)</option>
2637 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 2679 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
2638 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 2680 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
2639 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 2681 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
2640 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
2641 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
2642 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
2643 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
2644 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
2645 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
2646 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
2647 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
2648 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 2682 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
2649 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 2683 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
2650 <option value="Saligenin (H)">Saligenin (H)</option> 2684 <option value="Saligenin (H)">Saligenin (H)</option>
2651 <option value="Saligenin (K)">Saligenin (K)</option> 2685 <option value="Saligenin (K)">Saligenin (K)</option>
2652 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 2686 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
2670 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 2704 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
2671 <option value="serotonylation (Q)">serotonylation (Q)</option> 2705 <option value="serotonylation (Q)">serotonylation (Q)</option>
2672 <option value="shTMT (K)">shTMT (K)</option> 2706 <option value="shTMT (K)">shTMT (K)</option>
2673 <option value="shTMT (N-term)">shTMT (N-term)</option> 2707 <option value="shTMT (N-term)">shTMT (N-term)</option>
2674 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 2708 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
2709 <option value="shTMTpro (K)">shTMTpro (K)</option>
2710 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
2711 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
2675 <option value="SMA (K)">SMA (K)</option> 2712 <option value="SMA (K)">SMA (K)</option>
2676 <option value="SMA (N-term)">SMA (N-term)</option> 2713 <option value="SMA (N-term)">SMA (N-term)</option>
2677 <option value="spermidine (Q)">spermidine (Q)</option> 2714 <option value="spermidine (Q)">spermidine (Q)</option>
2678 <option value="spermine (Q)">spermine (Q)</option> 2715 <option value="spermine (Q)">spermine (Q)</option>
2679 <option value="SPITC (K)">SPITC (K)</option> 2716 <option value="SPITC (K)">SPITC (K)</option>
2845 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 2882 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
2846 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 2883 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
2847 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 2884 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
2848 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 2885 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
2849 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 2886 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
2850 <option value="Ub-amide (C)">Ub-amide (C)</option>
2851 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 2887 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
2852 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 2888 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
2853 <option value="Ub-VME (C)">Ub-VME (C)</option> 2889 <option value="Ub-VME (C)">Ub-VME (C)</option>
2854 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 2890 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
2855 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 2891 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
3049 <expand macro="list_string_val" name="protein_accessions"/> 3085 <expand macro="list_string_val" name="protein_accessions"/>
3050 <expand macro="list_string_san" name="protein_accessions"/> 3086 <expand macro="list_string_san" name="protein_accessions"/>
3051 </param> 3087 </param>
3052 <param name="peptides" argument="-blacklist:peptides" type="data" format="idxml" optional="true" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="Use with 'blacklist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/> 3088 <param name="peptides" argument="-blacklist:peptides" type="data" format="idxml" optional="true" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="Use with 'blacklist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/>
3053 <param name="ignore_modifications" argument="-blacklist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare blacklisted peptides by sequence only" help=""/> 3089 <param name="ignore_modifications" argument="-blacklist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare blacklisted peptides by sequence only" help=""/>
3054 <param name="modifications" argument="-blacklist:modifications" multiple="true" type="select" optional="true" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help=""> 3090 <param name="modifications" argument="-blacklist:modifications" type="select" multiple="true" optional="true" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="">
3055 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3091 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3056 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3092 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3057 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3093 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3058 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3094 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3059 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3095 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
3060 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 3096 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
3061 <option value="2-succinyl (C)">2-succinyl (C)</option> 3097 <option value="2-succinyl (C)">2-succinyl (C)</option>
3062 <option value="2HPG (R)">2HPG (R)</option> 3098 <option value="2HPG (R)">2HPG (R)</option>
3063 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 3099 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
3100 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
3101 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
3102 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
3103 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
3064 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 3104 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
3065 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 3105 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
3066 <option value="4-ONE (C)">4-ONE (C)</option> 3106 <option value="4-ONE (C)">4-ONE (C)</option>
3067 <option value="4-ONE (H)">4-ONE (H)</option> 3107 <option value="4-ONE (H)">4-ONE (H)</option>
3068 <option value="4-ONE (K)">4-ONE (K)</option> 3108 <option value="4-ONE (K)">4-ONE (K)</option>
3148 <option value="Ammonium (D)">Ammonium (D)</option> 3188 <option value="Ammonium (D)">Ammonium (D)</option>
3149 <option value="Ammonium (E)">Ammonium (E)</option> 3189 <option value="Ammonium (E)">Ammonium (E)</option>
3150 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 3190 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
3151 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 3191 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
3152 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 3192 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
3193 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
3153 <option value="Archaeol (C)">Archaeol (C)</option> 3194 <option value="Archaeol (C)">Archaeol (C)</option>
3154 <option value="Arg (N-term)">Arg (N-term)</option> 3195 <option value="Arg (N-term)">Arg (N-term)</option>
3155 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 3196 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
3156 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 3197 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
3157 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 3198 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
3251 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 3292 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
3252 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 3293 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
3253 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 3294 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
3254 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 3295 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
3255 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 3296 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
3297 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
3256 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 3298 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
3257 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 3299 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
3258 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 3300 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
3259 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 3301 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
3260 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 3302 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
3283 <option value="BITC (C)">BITC (C)</option> 3325 <option value="BITC (C)">BITC (C)</option>
3284 <option value="BITC (K)">BITC (K)</option> 3326 <option value="BITC (K)">BITC (K)</option>
3285 <option value="BITC (N-term)">BITC (N-term)</option> 3327 <option value="BITC (N-term)">BITC (N-term)</option>
3286 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 3328 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
3287 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 3329 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
3288 <option value="Bodipy (C)">Bodipy (C)</option>
3289 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 3330 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
3290 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 3331 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
3291 <option value="Bromo (F)">Bromo (F)</option> 3332 <option value="Bromo (F)">Bromo (F)</option>
3292 <option value="Bromo (H)">Bromo (H)</option> 3333 <option value="Bromo (H)">Bromo (H)</option>
3293 <option value="Bromo (W)">Bromo (W)</option> 3334 <option value="Bromo (W)">Bromo (W)</option>
3715 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 3756 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
3716 <option value="Dehydrated (S)">Dehydrated (S)</option> 3757 <option value="Dehydrated (S)">Dehydrated (S)</option>
3717 <option value="Dehydrated (T)">Dehydrated (T)</option> 3758 <option value="Dehydrated (T)">Dehydrated (T)</option>
3718 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 3759 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
3719 <option value="Dehydro (C)">Dehydro (C)</option> 3760 <option value="Dehydro (C)">Dehydro (C)</option>
3761 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
3720 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 3762 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
3721 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 3763 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
3722 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
3723 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 3764 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
3724 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 3765 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
3725 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 3766 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
3726 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 3767 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
3727 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 3768 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
3728 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 3769 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
3729 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 3770 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
3730 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 3771 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
3731 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 3772 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
3732 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
3733 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 3773 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
3734 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 3774 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
3735 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 3775 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
3736 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 3776 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
3737 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 3777 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
3739 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 3779 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
3740 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 3780 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
3741 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 3781 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
3742 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 3782 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
3743 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 3783 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
3784 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
3744 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 3785 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
3745 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 3786 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
3746 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 3787 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
3747 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 3788 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
3748 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 3789 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
4311 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 4352 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
4312 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 4353 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
4313 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 4354 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
4314 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 4355 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
4315 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 4356 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
4316 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
4317 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 4357 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
4318 <option value="Ethyl (D)">Ethyl (D)</option> 4358 <option value="Ethyl (D)">Ethyl (D)</option>
4319 <option value="Ethyl (E)">Ethyl (E)</option> 4359 <option value="Ethyl (E)">Ethyl (E)</option>
4320 <option value="Ethyl (K)">Ethyl (K)</option> 4360 <option value="Ethyl (K)">Ethyl (K)</option>
4321 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 4361 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
4405 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 4445 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
4406 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 4446 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
4407 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 4447 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
4408 <option value="Glu (E)">Glu (E)</option> 4448 <option value="Glu (E)">Glu (E)</option>
4409 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 4449 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
4450 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
4410 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 4451 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
4411 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 4452 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
4412 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 4453 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
4413 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 4454 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
4414 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 4455 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
4419 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4460 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4420 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4461 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4421 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4462 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4422 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4463 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4423 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4464 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4424 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
4425 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 4465 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
4426 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4466 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4427 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4467 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
4428 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 4468 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
4429 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 4469 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
4443 <option value="Gluratylation (K)">Gluratylation (K)</option> 4483 <option value="Gluratylation (K)">Gluratylation (K)</option>
4444 <option value="Glutathione (C)">Glutathione (C)</option> 4484 <option value="Glutathione (C)">Glutathione (C)</option>
4445 <option value="Gly (K)">Gly (K)</option> 4485 <option value="Gly (K)">Gly (K)</option>
4446 <option value="Gly (S)">Gly (S)</option> 4486 <option value="Gly (S)">Gly (S)</option>
4447 <option value="Gly (T)">Gly (T)</option> 4487 <option value="Gly (T)">Gly (T)</option>
4488 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
4448 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 4489 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
4449 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 4490 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
4450 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 4491 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
4451 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 4492 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
4452 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 4493 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
4833 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 4874 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
4834 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 4875 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
4835 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 4876 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
4836 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 4877 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
4837 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 4878 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
4879 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
4838 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 4880 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
4839 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 4881 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
4840 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 4882 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
4841 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 4883 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
4842 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 4884 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
4844 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 4886 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
4845 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 4887 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
4846 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 4888 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
4847 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 4889 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
4848 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 4890 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
4891 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
4892 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
4893 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
4849 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 4894 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
4850 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 4895 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
4851 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 4896 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
4852 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 4897 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
4853 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 4898 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
4899 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 4944 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
4900 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 4945 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
4901 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 4946 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
4902 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 4947 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
4903 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 4948 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
4949 <option value="His+O(2) (H)">His+O(2) (H)</option>
4904 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 4950 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
4905 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 4951 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
4906 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 4952 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
4907 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 4953 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
4908 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 4954 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
5036 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 5082 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
5037 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 5083 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
5038 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 5084 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
5039 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 5085 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
5040 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 5086 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
5087 <option value="Kdo (S)">Kdo (S)</option>
5088 <option value="Kdo (T)">Kdo (T)</option>
5041 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 5089 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
5042 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 5090 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
5043 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 5091 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
5044 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 5092 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
5045 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 5093 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
5094 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
5046 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 5095 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
5047 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 5096 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
5048 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 5097 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
5049 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 5098 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
5050 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 5099 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
5125 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 5174 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
5126 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 5175 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
5127 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 5176 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
5128 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 5177 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
5129 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 5178 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
5179 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
5130 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 5180 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
5131 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 5181 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
5132 <option value="Lipoyl (K)">Lipoyl (K)</option> 5182 <option value="Lipoyl (K)">Lipoyl (K)</option>
5133 <option value="LRGG (K)">LRGG (K)</option> 5183 <option value="LRGG (K)">LRGG (K)</option>
5134 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 5184 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
5135 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 5185 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
5186 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
5136 <option value="Lys (N-term)">Lys (N-term)</option> 5187 <option value="Lys (N-term)">Lys (N-term)</option>
5188 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
5137 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 5189 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
5138 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 5190 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
5139 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 5191 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
5140 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 5192 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
5141 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 5193 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
5166 <option value="maleimide5 (C)">maleimide5 (C)</option> 5218 <option value="maleimide5 (C)">maleimide5 (C)</option>
5167 <option value="maleimide5 (K)">maleimide5 (K)</option> 5219 <option value="maleimide5 (K)">maleimide5 (K)</option>
5168 <option value="Malonyl (C)">Malonyl (C)</option> 5220 <option value="Malonyl (C)">Malonyl (C)</option>
5169 <option value="Malonyl (K)">Malonyl (K)</option> 5221 <option value="Malonyl (K)">Malonyl (K)</option>
5170 <option value="Malonyl (S)">Malonyl (S)</option> 5222 <option value="Malonyl (S)">Malonyl (S)</option>
5223 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
5171 <option value="MDCC (C)">MDCC (C)</option> 5224 <option value="MDCC (C)">MDCC (C)</option>
5172 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 5225 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
5173 <option value="Menadione (C)">Menadione (C)</option> 5226 <option value="Menadione (C)">Menadione (C)</option>
5174 <option value="Menadione (K)">Menadione (K)</option> 5227 <option value="Menadione (K)">Menadione (K)</option>
5175 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 5228 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
5177 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 5230 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
5178 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 5231 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
5179 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 5232 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
5180 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 5233 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
5181 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 5234 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
5235 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
5182 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 5236 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
5183 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 5237 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
5184 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 5238 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
5185 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 5239 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
5186 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 5240 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
5360 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 5414 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
5361 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 5415 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
5362 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 5416 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
5363 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 5417 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
5364 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 5418 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
5365 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
5366 <option value="NP40 (N-term)">NP40 (N-term)</option> 5419 <option value="NP40 (N-term)">NP40 (N-term)</option>
5367 <option value="NQIGG (K)">NQIGG (K)</option> 5420 <option value="NQIGG (K)">NQIGG (K)</option>
5368 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 5421 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
5369 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 5422 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
5370 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 5423 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
5448 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 5501 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
5449 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 5502 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
5450 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 5503 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
5451 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 5504 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
5452 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 5505 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
5506 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
5507 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
5508 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
5509 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
5453 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 5510 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
5454 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 5511 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
5455 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 5512 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
5456 <option value="Phospho (C)">Phospho (C)</option> 5513 <option value="Phospho (C)">Phospho (C)</option>
5457 <option value="Phospho (D)">Phospho (D)</option> 5514 <option value="Phospho (D)">Phospho (D)</option>
5462 <option value="Phospho (S)">Phospho (S)</option> 5519 <option value="Phospho (S)">Phospho (S)</option>
5463 <option value="Phospho (T)">Phospho (T)</option> 5520 <option value="Phospho (T)">Phospho (T)</option>
5464 <option value="Phospho (Y)">Phospho (Y)</option> 5521 <option value="Phospho (Y)">Phospho (Y)</option>
5465 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 5522 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
5466 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 5523 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
5524 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
5467 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 5525 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
5468 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 5526 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
5469 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 5527 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
5470 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 5528 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
5471 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 5529 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
5493 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 5551 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
5494 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 5552 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
5495 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 5553 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
5496 <option value="Piperidine (K)">Piperidine (K)</option> 5554 <option value="Piperidine (K)">Piperidine (K)</option>
5497 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 5555 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
5556 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
5498 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 5557 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
5499 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 5558 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
5500 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 5559 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
5501 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 5560 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
5502 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 5561 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
5570 <option value="QEQTGG (K)">QEQTGG (K)</option> 5629 <option value="QEQTGG (K)">QEQTGG (K)</option>
5571 <option value="QQQTGG (K)">QQQTGG (K)</option> 5630 <option value="QQQTGG (K)">QQQTGG (K)</option>
5572 <option value="QTGG (K)">QTGG (K)</option> 5631 <option value="QTGG (K)">QTGG (K)</option>
5573 <option value="Quinone (W)">Quinone (W)</option> 5632 <option value="Quinone (W)">Quinone (W)</option>
5574 <option value="Quinone (Y)">Quinone (Y)</option> 5633 <option value="Quinone (Y)">Quinone (Y)</option>
5634 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
5635 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
5636 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
5637 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
5638 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
5639 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
5640 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
5641 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
5642 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
5643 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
5644 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
5645 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
5646 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
5647 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
5648 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
5649 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
5650 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
5651 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
5652 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
5653 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
5575 <option value="Retinylidene (K)">Retinylidene (K)</option> 5654 <option value="Retinylidene (K)">Retinylidene (K)</option>
5576 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 5655 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
5577 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 5656 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
5578 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 5657 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
5579 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
5580 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
5581 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
5582 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
5583 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
5584 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
5585 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
5586 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
5587 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 5658 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
5588 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 5659 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
5589 <option value="Saligenin (H)">Saligenin (H)</option> 5660 <option value="Saligenin (H)">Saligenin (H)</option>
5590 <option value="Saligenin (K)">Saligenin (K)</option> 5661 <option value="Saligenin (K)">Saligenin (K)</option>
5591 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 5662 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
5609 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 5680 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
5610 <option value="serotonylation (Q)">serotonylation (Q)</option> 5681 <option value="serotonylation (Q)">serotonylation (Q)</option>
5611 <option value="shTMT (K)">shTMT (K)</option> 5682 <option value="shTMT (K)">shTMT (K)</option>
5612 <option value="shTMT (N-term)">shTMT (N-term)</option> 5683 <option value="shTMT (N-term)">shTMT (N-term)</option>
5613 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 5684 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
5685 <option value="shTMTpro (K)">shTMTpro (K)</option>
5686 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
5687 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
5614 <option value="SMA (K)">SMA (K)</option> 5688 <option value="SMA (K)">SMA (K)</option>
5615 <option value="SMA (N-term)">SMA (N-term)</option> 5689 <option value="SMA (N-term)">SMA (N-term)</option>
5616 <option value="spermidine (Q)">spermidine (Q)</option> 5690 <option value="spermidine (Q)">spermidine (Q)</option>
5617 <option value="spermine (Q)">spermine (Q)</option> 5691 <option value="spermine (Q)">spermine (Q)</option>
5618 <option value="SPITC (K)">SPITC (K)</option> 5692 <option value="SPITC (K)">SPITC (K)</option>
5784 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 5858 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
5785 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 5859 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
5786 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 5860 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
5787 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 5861 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
5788 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 5862 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
5789 <option value="Ub-amide (C)">Ub-amide (C)</option>
5790 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 5863 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
5791 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 5864 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
5792 <option value="Ub-VME (C)">Ub-VME (C)</option> 5865 <option value="Ub-VME (C)">Ub-VME (C)</option>
5793 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 5866 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
5794 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 5867 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
5985 <expand macro="list_string_san" name="RegEx"/> 6058 <expand macro="list_string_san" name="RegEx"/>
5986 </param> 6059 </param>
5987 </section> 6060 </section>
5988 <section name="in_silico_digestion" title="This filter option removes peptide hits which are not in the list of in silico peptides generated by the rules specified below" help="" expanded="false"> 6061 <section name="in_silico_digestion" title="This filter option removes peptide hits which are not in the list of in silico peptides generated by the rules specified below" help="" expanded="false">
5989 <param name="fasta" argument="-in_silico_digestion:fasta" type="data" format="fasta" optional="true" label="fasta protein sequence database" help=" select fasta data sets(s)"/> 6062 <param name="fasta" argument="-in_silico_digestion:fasta" type="data" format="fasta" optional="true" label="fasta protein sequence database" help=" select fasta data sets(s)"/>
5990 <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help=""> 6063 <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" label="enzyme used for the digestion of the sample" help="">
5991 <option value="Trypsin" selected="true">Trypsin</option>
5992 <option value="cyanogen-bromide">cyanogen-bromide</option>
5993 <option value="Clostripain/P">Clostripain/P</option>
5994 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
5995 <option value="no cleavage">no cleavage</option>
5996 <option value="unspecific cleavage">unspecific cleavage</option>
5997 <option value="Arg-C/P">Arg-C/P</option>
5998 <option value="Formic_acid">Formic_acid</option>
5999 <option value="Lys-C">Lys-C</option> 6064 <option value="Lys-C">Lys-C</option>
6000 <option value="Lys-N">Lys-N</option> 6065 <option value="Lys-N">Lys-N</option>
6001 <option value="leukocyte elastase">leukocyte elastase</option>
6002 <option value="proline endopeptidase">proline endopeptidase</option>
6003 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6004 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6005 <option value="Lys-C/P">Lys-C/P</option> 6066 <option value="Lys-C/P">Lys-C/P</option>
6006 <option value="PepsinA">PepsinA</option> 6067 <option value="PepsinA">PepsinA</option>
6007 <option value="TrypChymo">TrypChymo</option> 6068 <option value="TrypChymo">TrypChymo</option>
6008 <option value="Trypsin/P">Trypsin/P</option> 6069 <option value="Trypsin/P">Trypsin/P</option>
6009 <option value="V8-DE">V8-DE</option> 6070 <option value="V8-DE">V8-DE</option>
6010 <option value="V8-E">V8-E</option> 6071 <option value="V8-E">V8-E</option>
6072 <option value="leukocyte elastase">leukocyte elastase</option>
6073 <option value="Chymotrypsin">Chymotrypsin</option>
6074 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6075 <option value="CNBr">CNBr</option>
6076 <option value="Formic_acid">Formic_acid</option>
6077 <option value="Arg-C">Arg-C</option>
6078 <option value="Arg-C/P">Arg-C/P</option>
6079 <option value="Asp-N">Asp-N</option>
6080 <option value="Asp-N/B">Asp-N/B</option>
6011 <option value="Asp-N_ambic">Asp-N_ambic</option> 6081 <option value="Asp-N_ambic">Asp-N_ambic</option>
6012 <option value="Chymotrypsin">Chymotrypsin</option> 6082 <option value="Trypsin" selected="true">Trypsin</option>
6083 <option value="proline endopeptidase">proline endopeptidase</option>
6084 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6085 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6013 <option value="2-iodobenzoate">2-iodobenzoate</option> 6086 <option value="2-iodobenzoate">2-iodobenzoate</option>
6014 <option value="iodosobenzoate">iodosobenzoate</option> 6087 <option value="iodosobenzoate">iodosobenzoate</option>
6015 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 6088 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6016 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 6089 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6017 <option value="Glu-C+P">Glu-C+P</option> 6090 <option value="Glu-C+P">Glu-C+P</option>
6018 <option value="PepsinA + P">PepsinA + P</option> 6091 <option value="PepsinA + P">PepsinA + P</option>
6019 <option value="Arg-C">Arg-C</option> 6092 <option value="cyanogen-bromide">cyanogen-bromide</option>
6020 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 6093 <option value="Clostripain/P">Clostripain/P</option>
6021 <option value="CNBr">CNBr</option> 6094 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6022 <option value="Asp-N">Asp-N</option> 6095 <option value="no cleavage">no cleavage</option>
6023 <option value="Asp-N/B">Asp-N/B</option> 6096 <option value="unspecific cleavage">unspecific cleavage</option>
6024 <expand macro="list_string_san" name="enzyme"/> 6097 <expand macro="list_string_san" name="enzyme"/>
6025 </param> 6098 </param>
6026 <param name="specificity" argument="-in_silico_digestion:specificity" type="select" optional="true" label="Specificity of the filte" help=""> 6099 <param name="specificity" argument="-in_silico_digestion:specificity" type="select" label="Specificity of the filte" help="">
6027 <option value="none">none</option> 6100 <option value="none">none</option>
6028 <option value="semi">semi</option> 6101 <option value="semi">semi</option>
6029 <option value="full" selected="true">full</option> 6102 <option value="full" selected="true">full</option>
6030 <expand macro="list_string_san" name="specificity"/> 6103 <expand macro="list_string_san" name="specificity"/>
6031 </param> 6104 </param>
6032 <param name="missed_cleavages" argument="-in_silico_digestion:missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="range of allowed missed cleavages in the peptide sequences" help="By default missed cleavages are ignored"/> 6105 <param name="missed_cleavages" argument="-in_silico_digestion:missed_cleavages" type="integer" min="-1" value="-1" label="range of allowed missed cleavages in the peptide sequences" help="By default missed cleavages are ignored"/>
6033 <param name="methionine_cleavage" argument="-in_silico_digestion:methionine_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow methionine cleavage at the N-terminus of the protein" help=""/> 6106 <param name="methionine_cleavage" argument="-in_silico_digestion:methionine_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow methionine cleavage at the N-terminus of the protein" help=""/>
6034 </section> 6107 </section>
6035 <section name="missed_cleavages" title="This filter option removes peptide hits which do not confirm with the allowed missed cleavages specified below" help="" expanded="false"> 6108 <section name="missed_cleavages" title="This filter option removes peptide hits which do not confirm with the allowed missed cleavages specified below" help="" expanded="false">
6036 <param name="number_of_missed_cleavages" argument="-missed_cleavages:number_of_missed_cleavages" type="text" optional="true" value=":" label="range of allowed missed cleavages in the peptide sequences" help="For example: 0:1 -&gt; peptides with two or more missed cleavages will be removed,. 0:0 -&gt; peptides with any missed cleavages will be removed"> 6109 <param name="number_of_missed_cleavages" argument="-missed_cleavages:number_of_missed_cleavages" type="text" value=":" label="range of allowed missed cleavages in the peptide sequences" help="For example: 0:1 -&gt; peptides with two or more missed cleavages will be removed,. 0:0 -&gt; peptides with any missed cleavages will be removed">
6037 <expand macro="list_string_san" name="number_of_missed_cleavages"/> 6110 <expand macro="list_string_san" name="number_of_missed_cleavages"/>
6038 </param> 6111 </param>
6039 <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help=""> 6112 <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" label="enzyme used for the digestion of the sample" help="">
6040 <option value="Trypsin" selected="true">Trypsin</option>
6041 <option value="cyanogen-bromide">cyanogen-bromide</option>
6042 <option value="Clostripain/P">Clostripain/P</option>
6043 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6044 <option value="no cleavage">no cleavage</option>
6045 <option value="unspecific cleavage">unspecific cleavage</option>
6046 <option value="Arg-C/P">Arg-C/P</option>
6047 <option value="Formic_acid">Formic_acid</option>
6048 <option value="Lys-C">Lys-C</option> 6113 <option value="Lys-C">Lys-C</option>
6049 <option value="Lys-N">Lys-N</option> 6114 <option value="Lys-N">Lys-N</option>
6050 <option value="leukocyte elastase">leukocyte elastase</option>
6051 <option value="proline endopeptidase">proline endopeptidase</option>
6052 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6053 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6054 <option value="Lys-C/P">Lys-C/P</option> 6115 <option value="Lys-C/P">Lys-C/P</option>
6055 <option value="PepsinA">PepsinA</option> 6116 <option value="PepsinA">PepsinA</option>
6056 <option value="TrypChymo">TrypChymo</option> 6117 <option value="TrypChymo">TrypChymo</option>
6057 <option value="Trypsin/P">Trypsin/P</option> 6118 <option value="Trypsin/P">Trypsin/P</option>
6058 <option value="V8-DE">V8-DE</option> 6119 <option value="V8-DE">V8-DE</option>
6059 <option value="V8-E">V8-E</option> 6120 <option value="V8-E">V8-E</option>
6121 <option value="leukocyte elastase">leukocyte elastase</option>
6122 <option value="Chymotrypsin">Chymotrypsin</option>
6123 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6124 <option value="CNBr">CNBr</option>
6125 <option value="Formic_acid">Formic_acid</option>
6126 <option value="Arg-C">Arg-C</option>
6127 <option value="Arg-C/P">Arg-C/P</option>
6128 <option value="Asp-N">Asp-N</option>
6129 <option value="Asp-N/B">Asp-N/B</option>
6060 <option value="Asp-N_ambic">Asp-N_ambic</option> 6130 <option value="Asp-N_ambic">Asp-N_ambic</option>
6061 <option value="Chymotrypsin">Chymotrypsin</option> 6131 <option value="Trypsin" selected="true">Trypsin</option>
6132 <option value="proline endopeptidase">proline endopeptidase</option>
6133 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6134 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6062 <option value="2-iodobenzoate">2-iodobenzoate</option> 6135 <option value="2-iodobenzoate">2-iodobenzoate</option>
6063 <option value="iodosobenzoate">iodosobenzoate</option> 6136 <option value="iodosobenzoate">iodosobenzoate</option>
6064 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 6137 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6065 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 6138 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6066 <option value="Glu-C+P">Glu-C+P</option> 6139 <option value="Glu-C+P">Glu-C+P</option>
6067 <option value="PepsinA + P">PepsinA + P</option> 6140 <option value="PepsinA + P">PepsinA + P</option>
6068 <option value="Arg-C">Arg-C</option> 6141 <option value="cyanogen-bromide">cyanogen-bromide</option>
6069 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 6142 <option value="Clostripain/P">Clostripain/P</option>
6070 <option value="CNBr">CNBr</option> 6143 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6071 <option value="Asp-N">Asp-N</option> 6144 <option value="no cleavage">no cleavage</option>
6072 <option value="Asp-N/B">Asp-N/B</option> 6145 <option value="unspecific cleavage">unspecific cleavage</option>
6073 <expand macro="list_string_san" name="enzyme"/> 6146 <expand macro="list_string_san" name="enzyme"/>
6074 </param> 6147 </param>
6075 </section> 6148 </section>
6076 <section name="rt" title="Filtering by RT predicted by 'RTPredict'" help="" expanded="false"> 6149 <section name="rt" title="Filtering by RT predicted by 'RTPredict'" help="" expanded="false">
6077 <param name="p_value" argument="-rt:p_value" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help=""/> 6150 <param name="p_value" argument="-rt:p_value" type="float" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help=""/>
6078 <param name="p_value_1st_dim" argument="-rt:p_value_1st_dim" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help=""/> 6151 <param name="p_value_1st_dim" argument="-rt:p_value_1st_dim" type="float" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help=""/>
6079 </section> 6152 </section>
6080 <section name="mz" title="Filtering by mass erro" help="" expanded="false"> 6153 <section name="mz" title="Filtering by mass erro" help="" expanded="false">
6081 <param name="error" argument="-mz:error" type="float" optional="true" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/> 6154 <param name="error" argument="-mz:error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/>
6082 <param name="unit" argument="-mz:unit" type="select" optional="true" label="Absolute or relative erro" help=""> 6155 <param name="unit" argument="-mz:unit" type="select" label="Absolute or relative erro" help="">
6083 <option value="Da">Da</option> 6156 <option value="Da">Da</option>
6084 <option value="ppm" selected="true">ppm</option> 6157 <option value="ppm" selected="true">ppm</option>
6085 <expand macro="list_string_san" name="unit"/> 6158 <expand macro="list_string_san" name="unit"/>
6086 </param> 6159 </param>
6087 </section> 6160 </section>
6088 <section name="best" title="Filtering best hits per spectrum (for peptides) or from proteins" help="" expanded="false"> 6161 <section name="best" title="Filtering best hits per spectrum (for peptides) or from proteins" help="" expanded="false">
6089 <param name="n_spectra" argument="-best:n_spectra" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' best spectra" help="(i.e., PeptideIdentifications) (for n &gt; 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum"/> 6162 <param name="n_spectra" argument="-best:n_spectra" type="integer" min="0" value="0" label="Keep only the 'n' best spectra" help="(i.e., PeptideIdentifications) (for n &gt; 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum"/>
6090 <param name="n_peptide_hits" argument="-best:n_peptide_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n &gt; 0)" help=""/> 6163 <param name="n_peptide_hits" argument="-best:n_peptide_hits" type="integer" min="0" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n &gt; 0)" help=""/>
6091 <param name="n_protein_hits" argument="-best:n_protein_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring protein hits (for n &gt; 0)" help=""/> 6164 <param name="spectrum_per_peptide" argument="-best:spectrum_per_peptide" type="select" label="Keep one spectrum per peptide" help="Value determines if same sequence but different charges or modifications are treated as separate peptides or the same peptide. (default: false = filter disabled)">
6165 <option value="false" selected="true">false</option>
6166 <option value="sequence">sequence</option>
6167 <option value="sequence+charge">sequence+charge</option>
6168 <option value="sequence+modification">sequence+modification</option>
6169 <option value="sequence+charge+modification">sequence+charge+modification</option>
6170 <expand macro="list_string_san" name="spectrum_per_peptide"/>
6171 </param>
6172 <param name="n_protein_hits" argument="-best:n_protein_hits" type="integer" min="0" value="0" label="Keep only the 'n' highest scoring protein hits (for n &gt; 0)" help=""/>
6092 <param name="strict" argument="-best:strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only the highest scoring peptide hit" help="Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept"/> 6173 <param name="strict" argument="-best:strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only the highest scoring peptide hit" help="Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept"/>
6093 <param name="n_to_m_peptide_hits" argument="-best:n_to_m_peptide_hits" type="text" optional="true" value=":" label="Peptide hit rank range to extracts" help=""> 6174 <param name="n_to_m_peptide_hits" argument="-best:n_to_m_peptide_hits" type="text" value=":" label="Peptide hit rank range to extracts" help="">
6094 <expand macro="list_string_san" name="n_to_m_peptide_hits"/> 6175 <expand macro="list_string_san" name="n_to_m_peptide_hits"/>
6095 </param> 6176 </param>
6096 </section> 6177 </section>
6097 <expand macro="adv_opts_macro"> 6178 <expand macro="adv_opts_macro">
6098 <param argument="-remove_duplicate_psm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes duplicated PSMs per spectrum and retains the one with the higher score" help=""/> 6179 <param argument="-remove_duplicate_psm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes duplicated PSMs per spectrum and retains the one with the higher score" help=""/>
6099 <param argument="-remove_peptide_hits_by_metavalue" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. &lt;name&gt; 'lt|eq|gt|ne' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less, greater, not equal) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6180 <param argument="-remove_peptide_hits_by_metavalue" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. &lt;name&gt; 'lt|eq|gt|ne' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less, greater, not equal) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6100 <expand macro="list_string_val" name="remove_peptide_hits_by_metavalue"/> 6181 <expand macro="list_string_val" name="remove_peptide_hits_by_metavalue"/>
6101 <expand macro="list_string_san" name="remove_peptide_hits_by_metavalue"/> 6182 <expand macro="list_string_san" name="remove_peptide_hits_by_metavalue"/>
6102 </param> 6183 </param>
6103 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6184 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6104 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6185 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
6105 <expand macro="list_string_san" name="test"/> 6186 <expand macro="list_string_san" name="test"/>
6106 </param> 6187 </param>
6107 </expand> 6188 </expand>
6108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6189 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 6190 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
6113 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 6194 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
6114 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6195 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6115 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6196 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6116 </data> 6197 </data>
6117 </outputs> 6198 </outputs>
6118 <tests><!-- TOPP_IDFilter_1 --> 6199 <tests>
6200 <!-- TOPP_IDFilter_1 -->
6119 <test expect_num_outputs="2"> 6201 <test expect_num_outputs="2">
6120 <section name="adv_opts"> 6202 <section name="adv_opts">
6121 <param name="remove_duplicate_psm" value="false"/> 6203 <param name="remove_duplicate_psm" value="false"/>
6122 <param name="remove_peptide_hits_by_metavalue" value=""/>
6123 <param name="force" value="false"/> 6204 <param name="force" value="false"/>
6124 <param name="test" value="true"/> 6205 <param name="test" value="true"/>
6125 </section> 6206 </section>
6126 <param name="in" value="IDFilter_1_input.idXML"/> 6207 <param name="in" value="IDFilter_1_input.idXML"/>
6127 <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6208 <output name="out" value="IDFilter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6128 <param name="var_mods" value="false"/> 6209 <param name="var_mods" value="false"/>
6129 <param name="remove_shared_peptides" value="false"/> 6210 <param name="remove_shared_peptides" value="false"/>
6130 <param name="keep_unreferenced_protein_hits" value="false"/> 6211 <param name="keep_unreferenced_protein_hits" value="false"/>
6131 <param name="remove_decoys" value="false"/> 6212 <param name="remove_decoys" value="false"/>
6132 <param name="delete_unreferenced_peptide_hits" value="false"/> 6213 <param name="delete_unreferenced_peptide_hits" value="false"/>
6141 <param name="prot" value="0.0"/> 6222 <param name="prot" value="0.0"/>
6142 <param name="protgroup" value="0.0"/> 6223 <param name="protgroup" value="0.0"/>
6143 </section> 6224 </section>
6144 <section name="whitelist"> 6225 <section name="whitelist">
6145 <param name="proteins" value="IDFilter_1_input.fas"/> 6226 <param name="proteins" value="IDFilter_1_input.fas"/>
6146 <param name="protein_accessions" value=""/>
6147 <param name="ignore_modifications" value="false"/> 6227 <param name="ignore_modifications" value="false"/>
6148 <param name="modifications"/>
6149 </section> 6228 </section>
6150 <section name="blacklist"> 6229 <section name="blacklist">
6151 <param name="protein_accessions" value=""/>
6152 <param name="ignore_modifications" value="false"/> 6230 <param name="ignore_modifications" value="false"/>
6153 <param name="modifications"/>
6154 <param name="RegEx" value=""/> 6231 <param name="RegEx" value=""/>
6155 </section> 6232 </section>
6156 <section name="in_silico_digestion"> 6233 <section name="in_silico_digestion">
6157 <param name="enzyme" value="Trypsin"/> 6234 <param name="enzyme" value="Trypsin"/>
6158 <param name="specificity" value="full"/> 6235 <param name="specificity" value="full"/>
6172 <param name="unit" value="ppm"/> 6249 <param name="unit" value="ppm"/>
6173 </section> 6250 </section>
6174 <section name="best"> 6251 <section name="best">
6175 <param name="n_spectra" value="0"/> 6252 <param name="n_spectra" value="0"/>
6176 <param name="n_peptide_hits" value="0"/> 6253 <param name="n_peptide_hits" value="0"/>
6254 <param name="spectrum_per_peptide" value="false"/>
6177 <param name="n_protein_hits" value="0"/> 6255 <param name="n_protein_hits" value="0"/>
6178 <param name="strict" value="false"/> 6256 <param name="strict" value="false"/>
6179 <param name="n_to_m_peptide_hits" value=":"/> 6257 <param name="n_to_m_peptide_hits" value=":"/>
6180 </section> 6258 </section>
6181 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6259 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6182 <output name="ctd_out" ftype="xml"> 6260 <output name="ctd_out" ftype="xml">
6183 <assert_contents> 6261 <assert_contents>
6184 <is_valid_xml/> 6262 <is_valid_xml/>
6185 </assert_contents> 6263 </assert_contents>
6186 </output> 6264 </output>
6265 <assert_stdout>
6266 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6267 </assert_stdout>
6187 </test> 6268 </test>
6188 <!-- TOPP_IDFilter_3 --> 6269 <!-- TOPP_IDFilter_3 -->
6189 <test expect_num_outputs="2"> 6270 <test expect_num_outputs="2">
6190 <section name="adv_opts"> 6271 <section name="adv_opts">
6191 <param name="remove_duplicate_psm" value="false"/> 6272 <param name="remove_duplicate_psm" value="false"/>
6192 <param name="remove_peptide_hits_by_metavalue" value=""/>
6193 <param name="force" value="false"/> 6273 <param name="force" value="false"/>
6194 <param name="test" value="true"/> 6274 <param name="test" value="true"/>
6195 </section> 6275 </section>
6196 <param name="in" value="IDFilter_3_input.idXML"/> 6276 <param name="in" value="IDFilter_3_input.idXML"/>
6197 <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6277 <output name="out" value="IDFilter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6198 <param name="var_mods" value="false"/> 6278 <param name="var_mods" value="false"/>
6199 <param name="remove_shared_peptides" value="false"/> 6279 <param name="remove_shared_peptides" value="false"/>
6200 <param name="keep_unreferenced_protein_hits" value="false"/> 6280 <param name="keep_unreferenced_protein_hits" value="false"/>
6201 <param name="remove_decoys" value="false"/> 6281 <param name="remove_decoys" value="false"/>
6202 <param name="delete_unreferenced_peptide_hits" value="false"/> 6282 <param name="delete_unreferenced_peptide_hits" value="false"/>
6210 <param name="pep" value="0.0"/> 6290 <param name="pep" value="0.0"/>
6211 <param name="prot" value="0.0"/> 6291 <param name="prot" value="0.0"/>
6212 <param name="protgroup" value="0.0"/> 6292 <param name="protgroup" value="0.0"/>
6213 </section> 6293 </section>
6214 <section name="whitelist"> 6294 <section name="whitelist">
6215 <param name="protein_accessions" value=""/>
6216 <param name="ignore_modifications" value="false"/> 6295 <param name="ignore_modifications" value="false"/>
6217 <param name="modifications"/>
6218 </section> 6296 </section>
6219 <section name="blacklist"> 6297 <section name="blacklist">
6220 <param name="protein_accessions" value=""/>
6221 <param name="peptides" value="IDFilter_3_2_input.idXML"/> 6298 <param name="peptides" value="IDFilter_3_2_input.idXML"/>
6222 <param name="ignore_modifications" value="false"/> 6299 <param name="ignore_modifications" value="false"/>
6223 <param name="modifications"/>
6224 <param name="RegEx" value=""/> 6300 <param name="RegEx" value=""/>
6225 </section> 6301 </section>
6226 <section name="in_silico_digestion"> 6302 <section name="in_silico_digestion">
6227 <param name="enzyme" value="Trypsin"/> 6303 <param name="enzyme" value="Trypsin"/>
6228 <param name="specificity" value="full"/> 6304 <param name="specificity" value="full"/>
6242 <param name="unit" value="ppm"/> 6318 <param name="unit" value="ppm"/>
6243 </section> 6319 </section>
6244 <section name="best"> 6320 <section name="best">
6245 <param name="n_spectra" value="0"/> 6321 <param name="n_spectra" value="0"/>
6246 <param name="n_peptide_hits" value="0"/> 6322 <param name="n_peptide_hits" value="0"/>
6323 <param name="spectrum_per_peptide" value="false"/>
6247 <param name="n_protein_hits" value="0"/> 6324 <param name="n_protein_hits" value="0"/>
6248 <param name="strict" value="false"/> 6325 <param name="strict" value="false"/>
6249 <param name="n_to_m_peptide_hits" value=":"/> 6326 <param name="n_to_m_peptide_hits" value=":"/>
6250 </section> 6327 </section>
6251 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6252 <output name="ctd_out" ftype="xml"> 6329 <output name="ctd_out" ftype="xml">
6253 <assert_contents> 6330 <assert_contents>
6254 <is_valid_xml/> 6331 <is_valid_xml/>
6255 </assert_contents> 6332 </assert_contents>
6256 </output> 6333 </output>
6334 <assert_stdout>
6335 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6336 </assert_stdout>
6257 </test> 6337 </test>
6258 <!-- TOPP_IDFilter_4 --> 6338 <!-- TOPP_IDFilter_4 -->
6259 <test expect_num_outputs="2"> 6339 <test expect_num_outputs="2">
6260 <section name="adv_opts"> 6340 <section name="adv_opts">
6261 <param name="remove_duplicate_psm" value="false"/> 6341 <param name="remove_duplicate_psm" value="false"/>
6262 <param name="remove_peptide_hits_by_metavalue" value=""/>
6263 <param name="force" value="false"/> 6342 <param name="force" value="false"/>
6264 <param name="test" value="true"/> 6343 <param name="test" value="true"/>
6265 </section> 6344 </section>
6266 <param name="in" value="IDFilter_4_input.idXML"/> 6345 <param name="in" value="IDFilter_4_input.idXML"/>
6267 <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6346 <output name="out" value="IDFilter_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6268 <param name="var_mods" value="false"/> 6347 <param name="var_mods" value="false"/>
6269 <param name="remove_shared_peptides" value="false"/> 6348 <param name="remove_shared_peptides" value="false"/>
6270 <param name="keep_unreferenced_protein_hits" value="false"/> 6349 <param name="keep_unreferenced_protein_hits" value="false"/>
6271 <param name="remove_decoys" value="false"/> 6350 <param name="remove_decoys" value="false"/>
6272 <param name="delete_unreferenced_peptide_hits" value="false"/> 6351 <param name="delete_unreferenced_peptide_hits" value="false"/>
6280 <param name="pep" value="0.0"/> 6359 <param name="pep" value="0.0"/>
6281 <param name="prot" value="0.0"/> 6360 <param name="prot" value="0.0"/>
6282 <param name="protgroup" value="0.0"/> 6361 <param name="protgroup" value="0.0"/>
6283 </section> 6362 </section>
6284 <section name="whitelist"> 6363 <section name="whitelist">
6285 <param name="protein_accessions" value=""/>
6286 <param name="ignore_modifications" value="false"/> 6364 <param name="ignore_modifications" value="false"/>
6287 <param name="modifications"/>
6288 </section> 6365 </section>
6289 <section name="blacklist"> 6366 <section name="blacklist">
6290 <param name="protein_accessions" value=""/>
6291 <param name="ignore_modifications" value="false"/> 6367 <param name="ignore_modifications" value="false"/>
6292 <param name="modifications"/>
6293 <param name="RegEx" value=""/> 6368 <param name="RegEx" value=""/>
6294 </section> 6369 </section>
6295 <section name="in_silico_digestion"> 6370 <section name="in_silico_digestion">
6296 <param name="enzyme" value="Trypsin"/> 6371 <param name="enzyme" value="Trypsin"/>
6297 <param name="specificity" value="full"/> 6372 <param name="specificity" value="full"/>
6311 <param name="unit" value="ppm"/> 6386 <param name="unit" value="ppm"/>
6312 </section> 6387 </section>
6313 <section name="best"> 6388 <section name="best">
6314 <param name="n_spectra" value="0"/> 6389 <param name="n_spectra" value="0"/>
6315 <param name="n_peptide_hits" value="0"/> 6390 <param name="n_peptide_hits" value="0"/>
6391 <param name="spectrum_per_peptide" value="false"/>
6316 <param name="n_protein_hits" value="0"/> 6392 <param name="n_protein_hits" value="0"/>
6317 <param name="strict" value="false"/> 6393 <param name="strict" value="false"/>
6318 <param name="n_to_m_peptide_hits" value=":"/> 6394 <param name="n_to_m_peptide_hits" value=":"/>
6319 </section> 6395 </section>
6320 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6396 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6321 <output name="ctd_out" ftype="xml"> 6397 <output name="ctd_out" ftype="xml">
6322 <assert_contents> 6398 <assert_contents>
6323 <is_valid_xml/> 6399 <is_valid_xml/>
6324 </assert_contents> 6400 </assert_contents>
6325 </output> 6401 </output>
6402 <assert_stdout>
6403 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6404 </assert_stdout>
6326 </test> 6405 </test>
6327 <!-- TOPP_IDFilter_5 --> 6406 <!-- TOPP_IDFilter_5 -->
6328 <test expect_num_outputs="2"> 6407 <test expect_num_outputs="2">
6329 <section name="adv_opts"> 6408 <section name="adv_opts">
6330 <param name="remove_duplicate_psm" value="false"/> 6409 <param name="remove_duplicate_psm" value="false"/>
6331 <param name="remove_peptide_hits_by_metavalue" value=""/>
6332 <param name="force" value="false"/> 6410 <param name="force" value="false"/>
6333 <param name="test" value="true"/> 6411 <param name="test" value="true"/>
6334 </section> 6412 </section>
6335 <param name="in" value="IDFilter_5_input.idXML"/> 6413 <param name="in" value="IDFilter_5_input.idXML"/>
6336 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6414 <output name="out" value="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6337 <param name="var_mods" value="false"/> 6415 <param name="var_mods" value="false"/>
6338 <param name="remove_shared_peptides" value="false"/> 6416 <param name="remove_shared_peptides" value="false"/>
6339 <param name="keep_unreferenced_protein_hits" value="false"/> 6417 <param name="keep_unreferenced_protein_hits" value="false"/>
6340 <param name="remove_decoys" value="false"/> 6418 <param name="remove_decoys" value="false"/>
6341 <param name="delete_unreferenced_peptide_hits" value="false"/> 6419 <param name="delete_unreferenced_peptide_hits" value="false"/>
6349 <param name="pep" value="32.0"/> 6427 <param name="pep" value="32.0"/>
6350 <param name="prot" value="25.0"/> 6428 <param name="prot" value="25.0"/>
6351 <param name="protgroup" value="0.0"/> 6429 <param name="protgroup" value="0.0"/>
6352 </section> 6430 </section>
6353 <section name="whitelist"> 6431 <section name="whitelist">
6354 <param name="protein_accessions" value=""/>
6355 <param name="ignore_modifications" value="false"/> 6432 <param name="ignore_modifications" value="false"/>
6356 <param name="modifications"/>
6357 </section> 6433 </section>
6358 <section name="blacklist"> 6434 <section name="blacklist">
6359 <param name="protein_accessions" value=""/>
6360 <param name="ignore_modifications" value="false"/> 6435 <param name="ignore_modifications" value="false"/>
6361 <param name="modifications"/>
6362 <param name="RegEx" value=""/> 6436 <param name="RegEx" value=""/>
6363 </section> 6437 </section>
6364 <section name="in_silico_digestion"> 6438 <section name="in_silico_digestion">
6365 <param name="enzyme" value="Trypsin"/> 6439 <param name="enzyme" value="Trypsin"/>
6366 <param name="specificity" value="full"/> 6440 <param name="specificity" value="full"/>
6380 <param name="unit" value="ppm"/> 6454 <param name="unit" value="ppm"/>
6381 </section> 6455 </section>
6382 <section name="best"> 6456 <section name="best">
6383 <param name="n_spectra" value="0"/> 6457 <param name="n_spectra" value="0"/>
6384 <param name="n_peptide_hits" value="0"/> 6458 <param name="n_peptide_hits" value="0"/>
6459 <param name="spectrum_per_peptide" value="false"/>
6385 <param name="n_protein_hits" value="0"/> 6460 <param name="n_protein_hits" value="0"/>
6386 <param name="strict" value="false"/> 6461 <param name="strict" value="false"/>
6387 <param name="n_to_m_peptide_hits" value=":"/> 6462 <param name="n_to_m_peptide_hits" value=":"/>
6388 </section> 6463 </section>
6389 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6464 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6390 <output name="ctd_out" ftype="xml"> 6465 <output name="ctd_out" ftype="xml">
6391 <assert_contents> 6466 <assert_contents>
6392 <is_valid_xml/> 6467 <is_valid_xml/>
6393 </assert_contents> 6468 </assert_contents>
6394 </output> 6469 </output>
6470 <assert_stdout>
6471 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6472 </assert_stdout>
6395 </test> 6473 </test>
6396 <!-- TOPP_IDFilter_5a --> 6474 <!-- TOPP_IDFilter_5a -->
6397 <test expect_num_outputs="2"> 6475 <test expect_num_outputs="2">
6398 <section name="adv_opts"> 6476 <section name="adv_opts">
6399 <param name="remove_duplicate_psm" value="false"/> 6477 <param name="remove_duplicate_psm" value="false"/>
6400 <param name="remove_peptide_hits_by_metavalue" value=""/>
6401 <param name="force" value="false"/> 6478 <param name="force" value="false"/>
6402 <param name="test" value="true"/> 6479 <param name="test" value="true"/>
6403 </section> 6480 </section>
6404 <param name="in" value="IDFilter_5_input.idXML"/> 6481 <param name="in" value="IDFilter_5_input.idXML"/>
6405 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6482 <output name="out" value="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6406 <param name="var_mods" value="false"/> 6483 <param name="var_mods" value="false"/>
6407 <param name="remove_shared_peptides" value="false"/> 6484 <param name="remove_shared_peptides" value="false"/>
6408 <param name="keep_unreferenced_protein_hits" value="false"/> 6485 <param name="keep_unreferenced_protein_hits" value="false"/>
6409 <param name="remove_decoys" value="false"/> 6486 <param name="remove_decoys" value="false"/>
6410 <param name="delete_unreferenced_peptide_hits" value="false"/> 6487 <param name="delete_unreferenced_peptide_hits" value="false"/>
6418 <param name="pep" value="32.0"/> 6495 <param name="pep" value="32.0"/>
6419 <param name="prot" value="0.0"/> 6496 <param name="prot" value="0.0"/>
6420 <param name="protgroup" value="0.0"/> 6497 <param name="protgroup" value="0.0"/>
6421 </section> 6498 </section>
6422 <section name="whitelist"> 6499 <section name="whitelist">
6423 <param name="protein_accessions" value=""/>
6424 <param name="ignore_modifications" value="false"/> 6500 <param name="ignore_modifications" value="false"/>
6425 <param name="modifications"/>
6426 </section> 6501 </section>
6427 <section name="blacklist"> 6502 <section name="blacklist">
6428 <param name="protein_accessions" value=""/>
6429 <param name="ignore_modifications" value="false"/> 6503 <param name="ignore_modifications" value="false"/>
6430 <param name="modifications"/>
6431 <param name="RegEx" value=""/> 6504 <param name="RegEx" value=""/>
6432 </section> 6505 </section>
6433 <section name="in_silico_digestion"> 6506 <section name="in_silico_digestion">
6434 <param name="enzyme" value="Trypsin"/> 6507 <param name="enzyme" value="Trypsin"/>
6435 <param name="specificity" value="full"/> 6508 <param name="specificity" value="full"/>
6449 <param name="unit" value="ppm"/> 6522 <param name="unit" value="ppm"/>
6450 </section> 6523 </section>
6451 <section name="best"> 6524 <section name="best">
6452 <param name="n_spectra" value="0"/> 6525 <param name="n_spectra" value="0"/>
6453 <param name="n_peptide_hits" value="0"/> 6526 <param name="n_peptide_hits" value="0"/>
6527 <param name="spectrum_per_peptide" value="false"/>
6454 <param name="n_protein_hits" value="0"/> 6528 <param name="n_protein_hits" value="0"/>
6455 <param name="strict" value="false"/> 6529 <param name="strict" value="false"/>
6456 <param name="n_to_m_peptide_hits" value=":"/> 6530 <param name="n_to_m_peptide_hits" value=":"/>
6457 </section> 6531 </section>
6458 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6532 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6459 <output name="ctd_out" ftype="xml"> 6533 <output name="ctd_out" ftype="xml">
6460 <assert_contents> 6534 <assert_contents>
6461 <is_valid_xml/> 6535 <is_valid_xml/>
6462 </assert_contents> 6536 </assert_contents>
6463 </output> 6537 </output>
6538 <assert_stdout>
6539 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6540 </assert_stdout>
6464 </test> 6541 </test>
6465 <!-- TOPP_IDFilter_5b --> 6542 <!-- TOPP_IDFilter_5b -->
6466 <test expect_num_outputs="2"> 6543 <test expect_num_outputs="2">
6467 <section name="adv_opts"> 6544 <section name="adv_opts">
6468 <param name="remove_duplicate_psm" value="false"/> 6545 <param name="remove_duplicate_psm" value="false"/>
6469 <param name="remove_peptide_hits_by_metavalue" value=""/>
6470 <param name="force" value="false"/> 6546 <param name="force" value="false"/>
6471 <param name="test" value="true"/> 6547 <param name="test" value="true"/>
6472 </section> 6548 </section>
6473 <param name="in" value="IDFilter_5_input.idXML"/> 6549 <param name="in" value="IDFilter_5_input.idXML"/>
6474 <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6550 <output name="out" value="IDFilter_5b_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6475 <param name="var_mods" value="false"/> 6551 <param name="var_mods" value="false"/>
6476 <param name="remove_shared_peptides" value="false"/> 6552 <param name="remove_shared_peptides" value="false"/>
6477 <param name="keep_unreferenced_protein_hits" value="false"/> 6553 <param name="keep_unreferenced_protein_hits" value="false"/>
6478 <param name="remove_decoys" value="false"/> 6554 <param name="remove_decoys" value="false"/>
6479 <param name="delete_unreferenced_peptide_hits" value="false"/> 6555 <param name="delete_unreferenced_peptide_hits" value="false"/>
6487 <param name="pep" value="0.0"/> 6563 <param name="pep" value="0.0"/>
6488 <param name="prot" value="25.0"/> 6564 <param name="prot" value="25.0"/>
6489 <param name="protgroup" value="0.0"/> 6565 <param name="protgroup" value="0.0"/>
6490 </section> 6566 </section>
6491 <section name="whitelist"> 6567 <section name="whitelist">
6492 <param name="protein_accessions" value=""/>
6493 <param name="ignore_modifications" value="false"/> 6568 <param name="ignore_modifications" value="false"/>
6494 <param name="modifications"/>
6495 </section> 6569 </section>
6496 <section name="blacklist"> 6570 <section name="blacklist">
6497 <param name="protein_accessions" value=""/>
6498 <param name="ignore_modifications" value="false"/> 6571 <param name="ignore_modifications" value="false"/>
6499 <param name="modifications"/>
6500 <param name="RegEx" value=""/> 6572 <param name="RegEx" value=""/>
6501 </section> 6573 </section>
6502 <section name="in_silico_digestion"> 6574 <section name="in_silico_digestion">
6503 <param name="enzyme" value="Trypsin"/> 6575 <param name="enzyme" value="Trypsin"/>
6504 <param name="specificity" value="full"/> 6576 <param name="specificity" value="full"/>
6518 <param name="unit" value="ppm"/> 6590 <param name="unit" value="ppm"/>
6519 </section> 6591 </section>
6520 <section name="best"> 6592 <section name="best">
6521 <param name="n_spectra" value="0"/> 6593 <param name="n_spectra" value="0"/>
6522 <param name="n_peptide_hits" value="0"/> 6594 <param name="n_peptide_hits" value="0"/>
6595 <param name="spectrum_per_peptide" value="false"/>
6523 <param name="n_protein_hits" value="0"/> 6596 <param name="n_protein_hits" value="0"/>
6524 <param name="strict" value="false"/> 6597 <param name="strict" value="false"/>
6525 <param name="n_to_m_peptide_hits" value=":"/> 6598 <param name="n_to_m_peptide_hits" value=":"/>
6526 </section> 6599 </section>
6527 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6600 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6528 <output name="ctd_out" ftype="xml"> 6601 <output name="ctd_out" ftype="xml">
6529 <assert_contents> 6602 <assert_contents>
6530 <is_valid_xml/> 6603 <is_valid_xml/>
6531 </assert_contents> 6604 </assert_contents>
6532 </output> 6605 </output>
6606 <assert_stdout>
6607 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6608 </assert_stdout>
6533 </test> 6609 </test>
6534 <!-- TOPP_IDFilter_5c --> 6610 <!-- TOPP_IDFilter_5c -->
6535 <test expect_num_outputs="2"> 6611 <test expect_num_outputs="2">
6536 <section name="adv_opts"> 6612 <section name="adv_opts">
6537 <param name="remove_duplicate_psm" value="false"/> 6613 <param name="remove_duplicate_psm" value="false"/>
6538 <param name="remove_peptide_hits_by_metavalue" value=""/>
6539 <param name="force" value="false"/> 6614 <param name="force" value="false"/>
6540 <param name="test" value="true"/> 6615 <param name="test" value="true"/>
6541 </section> 6616 </section>
6542 <param name="in" value="IDFilter_5_input.idXML"/> 6617 <param name="in" value="IDFilter_5_input.idXML"/>
6543 <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6618 <output name="out" value="IDFilter_5c_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6544 <param name="var_mods" value="false"/> 6619 <param name="var_mods" value="false"/>
6545 <param name="remove_shared_peptides" value="false"/> 6620 <param name="remove_shared_peptides" value="false"/>
6546 <param name="keep_unreferenced_protein_hits" value="false"/> 6621 <param name="keep_unreferenced_protein_hits" value="false"/>
6547 <param name="remove_decoys" value="false"/> 6622 <param name="remove_decoys" value="false"/>
6548 <param name="delete_unreferenced_peptide_hits" value="true"/> 6623 <param name="delete_unreferenced_peptide_hits" value="true"/>
6556 <param name="pep" value="0.0"/> 6631 <param name="pep" value="0.0"/>
6557 <param name="prot" value="25.0"/> 6632 <param name="prot" value="25.0"/>
6558 <param name="protgroup" value="0.0"/> 6633 <param name="protgroup" value="0.0"/>
6559 </section> 6634 </section>
6560 <section name="whitelist"> 6635 <section name="whitelist">
6561 <param name="protein_accessions" value=""/>
6562 <param name="ignore_modifications" value="false"/> 6636 <param name="ignore_modifications" value="false"/>
6563 <param name="modifications"/>
6564 </section> 6637 </section>
6565 <section name="blacklist"> 6638 <section name="blacklist">
6566 <param name="protein_accessions" value=""/>
6567 <param name="ignore_modifications" value="false"/> 6639 <param name="ignore_modifications" value="false"/>
6568 <param name="modifications"/>
6569 <param name="RegEx" value=""/> 6640 <param name="RegEx" value=""/>
6570 </section> 6641 </section>
6571 <section name="in_silico_digestion"> 6642 <section name="in_silico_digestion">
6572 <param name="enzyme" value="Trypsin"/> 6643 <param name="enzyme" value="Trypsin"/>
6573 <param name="specificity" value="full"/> 6644 <param name="specificity" value="full"/>
6587 <param name="unit" value="ppm"/> 6658 <param name="unit" value="ppm"/>
6588 </section> 6659 </section>
6589 <section name="best"> 6660 <section name="best">
6590 <param name="n_spectra" value="0"/> 6661 <param name="n_spectra" value="0"/>
6591 <param name="n_peptide_hits" value="0"/> 6662 <param name="n_peptide_hits" value="0"/>
6663 <param name="spectrum_per_peptide" value="false"/>
6592 <param name="n_protein_hits" value="0"/> 6664 <param name="n_protein_hits" value="0"/>
6593 <param name="strict" value="false"/> 6665 <param name="strict" value="false"/>
6594 <param name="n_to_m_peptide_hits" value=":"/> 6666 <param name="n_to_m_peptide_hits" value=":"/>
6595 </section> 6667 </section>
6596 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6668 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6597 <output name="ctd_out" ftype="xml"> 6669 <output name="ctd_out" ftype="xml">
6598 <assert_contents> 6670 <assert_contents>
6599 <is_valid_xml/> 6671 <is_valid_xml/>
6600 </assert_contents> 6672 </assert_contents>
6601 </output> 6673 </output>
6674 <assert_stdout>
6675 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6676 </assert_stdout>
6602 </test> 6677 </test>
6603 <!-- TOPP_IDFilter_6 --> 6678 <!-- TOPP_IDFilter_6 -->
6604 <test expect_num_outputs="2"> 6679 <test expect_num_outputs="2">
6605 <section name="adv_opts"> 6680 <section name="adv_opts">
6606 <param name="remove_duplicate_psm" value="false"/> 6681 <param name="remove_duplicate_psm" value="false"/>
6607 <param name="remove_peptide_hits_by_metavalue" value=""/>
6608 <param name="force" value="false"/> 6682 <param name="force" value="false"/>
6609 <param name="test" value="true"/> 6683 <param name="test" value="true"/>
6610 </section> 6684 </section>
6611 <param name="in" value="IDFilter_6_input.idXML"/> 6685 <param name="in" value="IDFilter_6_input.idXML"/>
6612 <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6686 <output name="out" value="IDFilter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6613 <param name="var_mods" value="false"/> 6687 <param name="var_mods" value="false"/>
6614 <param name="remove_shared_peptides" value="false"/> 6688 <param name="remove_shared_peptides" value="false"/>
6615 <param name="keep_unreferenced_protein_hits" value="false"/> 6689 <param name="keep_unreferenced_protein_hits" value="false"/>
6616 <param name="remove_decoys" value="false"/> 6690 <param name="remove_decoys" value="false"/>
6617 <param name="delete_unreferenced_peptide_hits" value="false"/> 6691 <param name="delete_unreferenced_peptide_hits" value="false"/>
6625 <param name="pep" value="0.0"/> 6699 <param name="pep" value="0.0"/>
6626 <param name="prot" value="0.0"/> 6700 <param name="prot" value="0.0"/>
6627 <param name="protgroup" value="0.0"/> 6701 <param name="protgroup" value="0.0"/>
6628 </section> 6702 </section>
6629 <section name="whitelist"> 6703 <section name="whitelist">
6630 <param name="protein_accessions" value=""/>
6631 <param name="ignore_modifications" value="false"/> 6704 <param name="ignore_modifications" value="false"/>
6632 <param name="modifications"/>
6633 </section> 6705 </section>
6634 <section name="blacklist"> 6706 <section name="blacklist">
6635 <param name="protein_accessions" value=""/>
6636 <param name="ignore_modifications" value="false"/> 6707 <param name="ignore_modifications" value="false"/>
6637 <param name="modifications"/>
6638 <param name="RegEx" value=""/> 6708 <param name="RegEx" value=""/>
6639 </section> 6709 </section>
6640 <section name="in_silico_digestion"> 6710 <section name="in_silico_digestion">
6641 <param name="enzyme" value="Trypsin"/> 6711 <param name="enzyme" value="Trypsin"/>
6642 <param name="specificity" value="full"/> 6712 <param name="specificity" value="full"/>
6656 <param name="unit" value="ppm"/> 6726 <param name="unit" value="ppm"/>
6657 </section> 6727 </section>
6658 <section name="best"> 6728 <section name="best">
6659 <param name="n_spectra" value="0"/> 6729 <param name="n_spectra" value="0"/>
6660 <param name="n_peptide_hits" value="2"/> 6730 <param name="n_peptide_hits" value="2"/>
6731 <param name="spectrum_per_peptide" value="false"/>
6661 <param name="n_protein_hits" value="10"/> 6732 <param name="n_protein_hits" value="10"/>
6662 <param name="strict" value="false"/> 6733 <param name="strict" value="false"/>
6663 <param name="n_to_m_peptide_hits" value=":"/> 6734 <param name="n_to_m_peptide_hits" value=":"/>
6664 </section> 6735 </section>
6665 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6736 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6666 <output name="ctd_out" ftype="xml"> 6737 <output name="ctd_out" ftype="xml">
6667 <assert_contents> 6738 <assert_contents>
6668 <is_valid_xml/> 6739 <is_valid_xml/>
6669 </assert_contents> 6740 </assert_contents>
6670 </output> 6741 </output>
6742 <assert_stdout>
6743 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6744 </assert_stdout>
6671 </test> 6745 </test>
6672 <!-- TOPP_IDFilter_7 --> 6746 <!-- TOPP_IDFilter_7 -->
6673 <test expect_num_outputs="2"> 6747 <test expect_num_outputs="2">
6674 <section name="adv_opts"> 6748 <section name="adv_opts">
6675 <param name="remove_duplicate_psm" value="true"/> 6749 <param name="remove_duplicate_psm" value="true"/>
6676 <param name="remove_peptide_hits_by_metavalue" value=""/>
6677 <param name="force" value="false"/> 6750 <param name="force" value="false"/>
6678 <param name="test" value="true"/> 6751 <param name="test" value="true"/>
6679 </section> 6752 </section>
6680 <param name="in" value="IDFilter_7_input.idXML"/> 6753 <param name="in" value="IDFilter_7_input.idXML"/>
6681 <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6754 <output name="out" value="IDFilter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6682 <param name="var_mods" value="false"/> 6755 <param name="var_mods" value="false"/>
6683 <param name="remove_shared_peptides" value="false"/> 6756 <param name="remove_shared_peptides" value="false"/>
6684 <param name="keep_unreferenced_protein_hits" value="false"/> 6757 <param name="keep_unreferenced_protein_hits" value="false"/>
6685 <param name="remove_decoys" value="false"/> 6758 <param name="remove_decoys" value="false"/>
6686 <param name="delete_unreferenced_peptide_hits" value="false"/> 6759 <param name="delete_unreferenced_peptide_hits" value="false"/>
6694 <param name="pep" value="0.0"/> 6767 <param name="pep" value="0.0"/>
6695 <param name="prot" value="0.0"/> 6768 <param name="prot" value="0.0"/>
6696 <param name="protgroup" value="0.0"/> 6769 <param name="protgroup" value="0.0"/>
6697 </section> 6770 </section>
6698 <section name="whitelist"> 6771 <section name="whitelist">
6699 <param name="protein_accessions" value=""/>
6700 <param name="ignore_modifications" value="false"/> 6772 <param name="ignore_modifications" value="false"/>
6701 <param name="modifications"/>
6702 </section> 6773 </section>
6703 <section name="blacklist"> 6774 <section name="blacklist">
6704 <param name="protein_accessions" value=""/>
6705 <param name="ignore_modifications" value="false"/> 6775 <param name="ignore_modifications" value="false"/>
6706 <param name="modifications"/>
6707 <param name="RegEx" value=""/> 6776 <param name="RegEx" value=""/>
6708 </section> 6777 </section>
6709 <section name="in_silico_digestion"> 6778 <section name="in_silico_digestion">
6710 <param name="enzyme" value="Trypsin"/> 6779 <param name="enzyme" value="Trypsin"/>
6711 <param name="specificity" value="full"/> 6780 <param name="specificity" value="full"/>
6725 <param name="unit" value="ppm"/> 6794 <param name="unit" value="ppm"/>
6726 </section> 6795 </section>
6727 <section name="best"> 6796 <section name="best">
6728 <param name="n_spectra" value="0"/> 6797 <param name="n_spectra" value="0"/>
6729 <param name="n_peptide_hits" value="0"/> 6798 <param name="n_peptide_hits" value="0"/>
6799 <param name="spectrum_per_peptide" value="false"/>
6730 <param name="n_protein_hits" value="0"/> 6800 <param name="n_protein_hits" value="0"/>
6731 <param name="strict" value="false"/> 6801 <param name="strict" value="false"/>
6732 <param name="n_to_m_peptide_hits" value=":"/> 6802 <param name="n_to_m_peptide_hits" value=":"/>
6733 </section> 6803 </section>
6734 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6804 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6735 <output name="ctd_out" ftype="xml"> 6805 <output name="ctd_out" ftype="xml">
6736 <assert_contents> 6806 <assert_contents>
6737 <is_valid_xml/> 6807 <is_valid_xml/>
6738 </assert_contents> 6808 </assert_contents>
6739 </output> 6809 </output>
6810 <assert_stdout>
6811 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6812 </assert_stdout>
6740 </test> 6813 </test>
6741 <!-- TOPP_IDFilter_8 --> 6814 <!-- TOPP_IDFilter_8 -->
6742 <test expect_num_outputs="2"> 6815 <test expect_num_outputs="2">
6743 <section name="adv_opts"> 6816 <section name="adv_opts">
6744 <param name="remove_duplicate_psm" value="false"/> 6817 <param name="remove_duplicate_psm" value="false"/>
6745 <param name="remove_peptide_hits_by_metavalue" value=""/>
6746 <param name="force" value="false"/> 6818 <param name="force" value="false"/>
6747 <param name="test" value="true"/> 6819 <param name="test" value="true"/>
6748 </section> 6820 </section>
6749 <param name="in" value="IDFilter_8_input.idXML"/> 6821 <param name="in" value="IDFilter_8_input.idXML"/>
6750 <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6822 <output name="out" value="IDFilter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6751 <param name="var_mods" value="false"/> 6823 <param name="var_mods" value="false"/>
6752 <param name="remove_shared_peptides" value="false"/> 6824 <param name="remove_shared_peptides" value="false"/>
6753 <param name="keep_unreferenced_protein_hits" value="false"/> 6825 <param name="keep_unreferenced_protein_hits" value="false"/>
6754 <param name="remove_decoys" value="false"/> 6826 <param name="remove_decoys" value="false"/>
6755 <param name="delete_unreferenced_peptide_hits" value="false"/> 6827 <param name="delete_unreferenced_peptide_hits" value="false"/>
6763 <param name="pep" value="0.0"/> 6835 <param name="pep" value="0.0"/>
6764 <param name="prot" value="0.0"/> 6836 <param name="prot" value="0.0"/>
6765 <param name="protgroup" value="0.0"/> 6837 <param name="protgroup" value="0.0"/>
6766 </section> 6838 </section>
6767 <section name="whitelist"> 6839 <section name="whitelist">
6768 <param name="protein_accessions" value=""/>
6769 <param name="ignore_modifications" value="false"/> 6840 <param name="ignore_modifications" value="false"/>
6770 <param name="modifications"/>
6771 </section> 6841 </section>
6772 <section name="blacklist"> 6842 <section name="blacklist">
6773 <param name="protein_accessions" value=""/>
6774 <param name="ignore_modifications" value="false"/> 6843 <param name="ignore_modifications" value="false"/>
6775 <param name="modifications"/>
6776 <param name="RegEx" value=""/> 6844 <param name="RegEx" value=""/>
6777 </section> 6845 </section>
6778 <section name="in_silico_digestion"> 6846 <section name="in_silico_digestion">
6779 <param name="enzyme" value="Trypsin"/> 6847 <param name="enzyme" value="Trypsin"/>
6780 <param name="specificity" value="full"/> 6848 <param name="specificity" value="full"/>
6794 <param name="unit" value="ppm"/> 6862 <param name="unit" value="ppm"/>
6795 </section> 6863 </section>
6796 <section name="best"> 6864 <section name="best">
6797 <param name="n_spectra" value="0"/> 6865 <param name="n_spectra" value="0"/>
6798 <param name="n_peptide_hits" value="0"/> 6866 <param name="n_peptide_hits" value="0"/>
6867 <param name="spectrum_per_peptide" value="false"/>
6799 <param name="n_protein_hits" value="0"/> 6868 <param name="n_protein_hits" value="0"/>
6800 <param name="strict" value="false"/> 6869 <param name="strict" value="false"/>
6801 <param name="n_to_m_peptide_hits" value=":"/> 6870 <param name="n_to_m_peptide_hits" value=":"/>
6802 </section> 6871 </section>
6803 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6872 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6804 <output name="ctd_out" ftype="xml"> 6873 <output name="ctd_out" ftype="xml">
6805 <assert_contents> 6874 <assert_contents>
6806 <is_valid_xml/> 6875 <is_valid_xml/>
6807 </assert_contents> 6876 </assert_contents>
6808 </output> 6877 </output>
6878 <assert_stdout>
6879 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6880 </assert_stdout>
6809 </test> 6881 </test>
6810 <!-- TOPP_IDFilter_9 --> 6882 <!-- TOPP_IDFilter_9 -->
6811 <test expect_num_outputs="2"> 6883 <test expect_num_outputs="2">
6812 <section name="adv_opts"> 6884 <section name="adv_opts">
6813 <param name="remove_duplicate_psm" value="false"/> 6885 <param name="remove_duplicate_psm" value="false"/>
6814 <param name="remove_peptide_hits_by_metavalue" value=""/>
6815 <param name="force" value="false"/> 6886 <param name="force" value="false"/>
6816 <param name="test" value="true"/> 6887 <param name="test" value="true"/>
6817 </section> 6888 </section>
6818 <param name="in" value="IDFilter_9_input.idXML"/> 6889 <param name="in" value="IDFilter_9_input.idXML"/>
6819 <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6890 <output name="out" value="IDFilter_9_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6820 <param name="var_mods" value="false"/> 6891 <param name="var_mods" value="false"/>
6821 <param name="remove_shared_peptides" value="false"/> 6892 <param name="remove_shared_peptides" value="false"/>
6822 <param name="keep_unreferenced_protein_hits" value="false"/> 6893 <param name="keep_unreferenced_protein_hits" value="false"/>
6823 <param name="remove_decoys" value="false"/> 6894 <param name="remove_decoys" value="false"/>
6824 <param name="delete_unreferenced_peptide_hits" value="false"/> 6895 <param name="delete_unreferenced_peptide_hits" value="false"/>
6832 <param name="pep" value="0.05"/> 6903 <param name="pep" value="0.05"/>
6833 <param name="prot" value="0.0"/> 6904 <param name="prot" value="0.0"/>
6834 <param name="protgroup" value="0.0"/> 6905 <param name="protgroup" value="0.0"/>
6835 </section> 6906 </section>
6836 <section name="whitelist"> 6907 <section name="whitelist">
6837 <param name="protein_accessions" value=""/>
6838 <param name="ignore_modifications" value="false"/> 6908 <param name="ignore_modifications" value="false"/>
6839 <param name="modifications"/>
6840 </section> 6909 </section>
6841 <section name="blacklist"> 6910 <section name="blacklist">
6842 <param name="protein_accessions" value=""/>
6843 <param name="ignore_modifications" value="false"/> 6911 <param name="ignore_modifications" value="false"/>
6844 <param name="modifications"/>
6845 <param name="RegEx" value=""/> 6912 <param name="RegEx" value=""/>
6846 </section> 6913 </section>
6847 <section name="in_silico_digestion"> 6914 <section name="in_silico_digestion">
6848 <param name="enzyme" value="Trypsin"/> 6915 <param name="enzyme" value="Trypsin"/>
6849 <param name="specificity" value="full"/> 6916 <param name="specificity" value="full"/>
6863 <param name="unit" value="ppm"/> 6930 <param name="unit" value="ppm"/>
6864 </section> 6931 </section>
6865 <section name="best"> 6932 <section name="best">
6866 <param name="n_spectra" value="0"/> 6933 <param name="n_spectra" value="0"/>
6867 <param name="n_peptide_hits" value="0"/> 6934 <param name="n_peptide_hits" value="0"/>
6935 <param name="spectrum_per_peptide" value="false"/>
6868 <param name="n_protein_hits" value="0"/> 6936 <param name="n_protein_hits" value="0"/>
6869 <param name="strict" value="false"/> 6937 <param name="strict" value="false"/>
6870 <param name="n_to_m_peptide_hits" value=":"/> 6938 <param name="n_to_m_peptide_hits" value=":"/>
6871 </section> 6939 </section>
6872 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 6940 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6873 <output name="ctd_out" ftype="xml"> 6941 <output name="ctd_out" ftype="xml">
6874 <assert_contents> 6942 <assert_contents>
6875 <is_valid_xml/> 6943 <is_valid_xml/>
6876 </assert_contents> 6944 </assert_contents>
6877 </output> 6945 </output>
6946 <assert_stdout>
6947 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6948 </assert_stdout>
6878 </test> 6949 </test>
6879 <!-- TOPP_IDFilter_10 --> 6950 <!-- TOPP_IDFilter_10 -->
6880 <test expect_num_outputs="2"> 6951 <test expect_num_outputs="2">
6881 <section name="adv_opts"> 6952 <section name="adv_opts">
6882 <param name="remove_duplicate_psm" value="false"/> 6953 <param name="remove_duplicate_psm" value="false"/>
6883 <param name="remove_peptide_hits_by_metavalue" value=""/>
6884 <param name="force" value="false"/> 6954 <param name="force" value="false"/>
6885 <param name="test" value="true"/> 6955 <param name="test" value="true"/>
6886 </section> 6956 </section>
6887 <param name="in" value="IDFilter_10_input.idXML"/> 6957 <param name="in" value="IDFilter_10_input.idXML"/>
6888 <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6958 <output name="out" value="IDFilter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6889 <param name="var_mods" value="false"/> 6959 <param name="var_mods" value="false"/>
6890 <param name="remove_shared_peptides" value="false"/> 6960 <param name="remove_shared_peptides" value="false"/>
6891 <param name="keep_unreferenced_protein_hits" value="false"/> 6961 <param name="keep_unreferenced_protein_hits" value="false"/>
6892 <param name="remove_decoys" value="false"/> 6962 <param name="remove_decoys" value="false"/>
6893 <param name="delete_unreferenced_peptide_hits" value="true"/> 6963 <param name="delete_unreferenced_peptide_hits" value="true"/>
6901 <param name="pep" value="0.0"/> 6971 <param name="pep" value="0.0"/>
6902 <param name="prot" value="0.3"/> 6972 <param name="prot" value="0.3"/>
6903 <param name="protgroup" value="0.0"/> 6973 <param name="protgroup" value="0.0"/>
6904 </section> 6974 </section>
6905 <section name="whitelist"> 6975 <section name="whitelist">
6906 <param name="protein_accessions" value=""/>
6907 <param name="ignore_modifications" value="false"/> 6976 <param name="ignore_modifications" value="false"/>
6908 <param name="modifications"/>
6909 </section> 6977 </section>
6910 <section name="blacklist"> 6978 <section name="blacklist">
6911 <param name="protein_accessions" value=""/>
6912 <param name="ignore_modifications" value="false"/> 6979 <param name="ignore_modifications" value="false"/>
6913 <param name="modifications"/>
6914 <param name="RegEx" value=""/> 6980 <param name="RegEx" value=""/>
6915 </section> 6981 </section>
6916 <section name="in_silico_digestion"> 6982 <section name="in_silico_digestion">
6917 <param name="enzyme" value="Trypsin"/> 6983 <param name="enzyme" value="Trypsin"/>
6918 <param name="specificity" value="full"/> 6984 <param name="specificity" value="full"/>
6932 <param name="unit" value="ppm"/> 6998 <param name="unit" value="ppm"/>
6933 </section> 6999 </section>
6934 <section name="best"> 7000 <section name="best">
6935 <param name="n_spectra" value="0"/> 7001 <param name="n_spectra" value="0"/>
6936 <param name="n_peptide_hits" value="0"/> 7002 <param name="n_peptide_hits" value="0"/>
7003 <param name="spectrum_per_peptide" value="false"/>
6937 <param name="n_protein_hits" value="0"/> 7004 <param name="n_protein_hits" value="0"/>
6938 <param name="strict" value="false"/> 7005 <param name="strict" value="false"/>
6939 <param name="n_to_m_peptide_hits" value=":"/> 7006 <param name="n_to_m_peptide_hits" value=":"/>
6940 </section> 7007 </section>
6941 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7008 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6942 <output name="ctd_out" ftype="xml"> 7009 <output name="ctd_out" ftype="xml">
6943 <assert_contents> 7010 <assert_contents>
6944 <is_valid_xml/> 7011 <is_valid_xml/>
6945 </assert_contents> 7012 </assert_contents>
6946 </output> 7013 </output>
7014 <assert_stdout>
7015 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7016 </assert_stdout>
6947 </test> 7017 </test>
6948 <!-- TOPP_IDFilter_11 --> 7018 <!-- TOPP_IDFilter_11 -->
6949 <test expect_num_outputs="2"> 7019 <test expect_num_outputs="2">
6950 <section name="adv_opts"> 7020 <section name="adv_opts">
6951 <param name="remove_duplicate_psm" value="false"/> 7021 <param name="remove_duplicate_psm" value="false"/>
6952 <param name="remove_peptide_hits_by_metavalue" value=""/>
6953 <param name="force" value="false"/> 7022 <param name="force" value="false"/>
6954 <param name="test" value="true"/> 7023 <param name="test" value="true"/>
6955 </section> 7024 </section>
6956 <param name="in" value="IDFilter_11_input.idXML"/> 7025 <param name="in" value="IDFilter_11_input.idXML"/>
6957 <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7026 <output name="out" value="IDFilter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6958 <param name="var_mods" value="false"/> 7027 <param name="var_mods" value="false"/>
6959 <param name="remove_shared_peptides" value="false"/> 7028 <param name="remove_shared_peptides" value="false"/>
6960 <param name="keep_unreferenced_protein_hits" value="false"/> 7029 <param name="keep_unreferenced_protein_hits" value="false"/>
6961 <param name="remove_decoys" value="true"/> 7030 <param name="remove_decoys" value="true"/>
6962 <param name="delete_unreferenced_peptide_hits" value="true"/> 7031 <param name="delete_unreferenced_peptide_hits" value="true"/>
6970 <param name="pep" value="0.0"/> 7039 <param name="pep" value="0.0"/>
6971 <param name="prot" value="0.0"/> 7040 <param name="prot" value="0.0"/>
6972 <param name="protgroup" value="0.0"/> 7041 <param name="protgroup" value="0.0"/>
6973 </section> 7042 </section>
6974 <section name="whitelist"> 7043 <section name="whitelist">
6975 <param name="protein_accessions" value=""/>
6976 <param name="ignore_modifications" value="false"/> 7044 <param name="ignore_modifications" value="false"/>
6977 <param name="modifications"/>
6978 </section> 7045 </section>
6979 <section name="blacklist"> 7046 <section name="blacklist">
6980 <param name="protein_accessions" value=""/>
6981 <param name="ignore_modifications" value="false"/> 7047 <param name="ignore_modifications" value="false"/>
6982 <param name="modifications"/>
6983 <param name="RegEx" value=""/> 7048 <param name="RegEx" value=""/>
6984 </section> 7049 </section>
6985 <section name="in_silico_digestion"> 7050 <section name="in_silico_digestion">
6986 <param name="enzyme" value="Trypsin"/> 7051 <param name="enzyme" value="Trypsin"/>
6987 <param name="specificity" value="full"/> 7052 <param name="specificity" value="full"/>
7001 <param name="unit" value="ppm"/> 7066 <param name="unit" value="ppm"/>
7002 </section> 7067 </section>
7003 <section name="best"> 7068 <section name="best">
7004 <param name="n_spectra" value="0"/> 7069 <param name="n_spectra" value="0"/>
7005 <param name="n_peptide_hits" value="0"/> 7070 <param name="n_peptide_hits" value="0"/>
7071 <param name="spectrum_per_peptide" value="false"/>
7006 <param name="n_protein_hits" value="0"/> 7072 <param name="n_protein_hits" value="0"/>
7007 <param name="strict" value="false"/> 7073 <param name="strict" value="false"/>
7008 <param name="n_to_m_peptide_hits" value=":"/> 7074 <param name="n_to_m_peptide_hits" value=":"/>
7009 </section> 7075 </section>
7010 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7076 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7011 <output name="ctd_out" ftype="xml"> 7077 <output name="ctd_out" ftype="xml">
7012 <assert_contents> 7078 <assert_contents>
7013 <is_valid_xml/> 7079 <is_valid_xml/>
7014 </assert_contents> 7080 </assert_contents>
7015 </output> 7081 </output>
7082 <assert_stdout>
7083 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7084 </assert_stdout>
7016 </test> 7085 </test>
7017 <!-- TOPP_IDFilter_12 --> 7086 <!-- TOPP_IDFilter_12 -->
7018 <test expect_num_outputs="2"> 7087 <test expect_num_outputs="2">
7019 <section name="adv_opts"> 7088 <section name="adv_opts">
7020 <param name="remove_duplicate_psm" value="false"/> 7089 <param name="remove_duplicate_psm" value="false"/>
7021 <param name="remove_peptide_hits_by_metavalue" value=""/>
7022 <param name="force" value="false"/> 7090 <param name="force" value="false"/>
7023 <param name="test" value="true"/> 7091 <param name="test" value="true"/>
7024 </section> 7092 </section>
7025 <param name="in" value="IDFilter_12_input.idXML"/> 7093 <param name="in" value="IDFilter_12_input.idXML"/>
7026 <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7094 <output name="out" value="IDFilter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7027 <param name="var_mods" value="false"/> 7095 <param name="var_mods" value="false"/>
7028 <param name="remove_shared_peptides" value="false"/> 7096 <param name="remove_shared_peptides" value="false"/>
7029 <param name="keep_unreferenced_protein_hits" value="false"/> 7097 <param name="keep_unreferenced_protein_hits" value="false"/>
7030 <param name="remove_decoys" value="false"/> 7098 <param name="remove_decoys" value="false"/>
7031 <param name="delete_unreferenced_peptide_hits" value="false"/> 7099 <param name="delete_unreferenced_peptide_hits" value="false"/>
7039 <param name="pep" value="0.0"/> 7107 <param name="pep" value="0.0"/>
7040 <param name="prot" value="0.0"/> 7108 <param name="prot" value="0.0"/>
7041 <param name="protgroup" value="0.0"/> 7109 <param name="protgroup" value="0.0"/>
7042 </section> 7110 </section>
7043 <section name="whitelist"> 7111 <section name="whitelist">
7044 <param name="protein_accessions" value=""/>
7045 <param name="ignore_modifications" value="false"/> 7112 <param name="ignore_modifications" value="false"/>
7046 <param name="modifications"/>
7047 </section> 7113 </section>
7048 <section name="blacklist"> 7114 <section name="blacklist">
7049 <param name="protein_accessions" value=""/>
7050 <param name="ignore_modifications" value="false"/> 7115 <param name="ignore_modifications" value="false"/>
7051 <param name="modifications"/>
7052 <param name="RegEx" value=""/> 7116 <param name="RegEx" value=""/>
7053 </section> 7117 </section>
7054 <section name="in_silico_digestion"> 7118 <section name="in_silico_digestion">
7055 <param name="fasta" value="IDFilter_12_input.fasta"/> 7119 <param name="fasta" value="IDFilter_12_input.fasta"/>
7056 <param name="enzyme" value="Trypsin"/> 7120 <param name="enzyme" value="Trypsin"/>
7071 <param name="unit" value="ppm"/> 7135 <param name="unit" value="ppm"/>
7072 </section> 7136 </section>
7073 <section name="best"> 7137 <section name="best">
7074 <param name="n_spectra" value="0"/> 7138 <param name="n_spectra" value="0"/>
7075 <param name="n_peptide_hits" value="0"/> 7139 <param name="n_peptide_hits" value="0"/>
7140 <param name="spectrum_per_peptide" value="false"/>
7076 <param name="n_protein_hits" value="0"/> 7141 <param name="n_protein_hits" value="0"/>
7077 <param name="strict" value="false"/> 7142 <param name="strict" value="false"/>
7078 <param name="n_to_m_peptide_hits" value=":"/> 7143 <param name="n_to_m_peptide_hits" value=":"/>
7079 </section> 7144 </section>
7080 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7081 <output name="ctd_out" ftype="xml"> 7146 <output name="ctd_out" ftype="xml">
7082 <assert_contents> 7147 <assert_contents>
7083 <is_valid_xml/> 7148 <is_valid_xml/>
7084 </assert_contents> 7149 </assert_contents>
7085 </output> 7150 </output>
7151 <assert_stdout>
7152 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7153 </assert_stdout>
7086 </test> 7154 </test>
7087 <!-- TOPP_IDFilter_13 --> 7155 <!-- TOPP_IDFilter_13 -->
7088 <test expect_num_outputs="2"> 7156 <test expect_num_outputs="2">
7089 <section name="adv_opts"> 7157 <section name="adv_opts">
7090 <param name="remove_duplicate_psm" value="false"/> 7158 <param name="remove_duplicate_psm" value="false"/>
7091 <param name="remove_peptide_hits_by_metavalue" value=""/>
7092 <param name="force" value="false"/> 7159 <param name="force" value="false"/>
7093 <param name="test" value="true"/> 7160 <param name="test" value="true"/>
7094 </section> 7161 </section>
7095 <param name="in" value="IDFilter_13_input.idXML"/> 7162 <param name="in" value="IDFilter_13_input.idXML"/>
7096 <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7163 <output name="out" value="IDFilter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7097 <param name="var_mods" value="false"/> 7164 <param name="var_mods" value="false"/>
7098 <param name="remove_shared_peptides" value="false"/> 7165 <param name="remove_shared_peptides" value="false"/>
7099 <param name="keep_unreferenced_protein_hits" value="false"/> 7166 <param name="keep_unreferenced_protein_hits" value="false"/>
7100 <param name="remove_decoys" value="false"/> 7167 <param name="remove_decoys" value="false"/>
7101 <param name="delete_unreferenced_peptide_hits" value="false"/> 7168 <param name="delete_unreferenced_peptide_hits" value="false"/>
7109 <param name="pep" value="0.0"/> 7176 <param name="pep" value="0.0"/>
7110 <param name="prot" value="0.0"/> 7177 <param name="prot" value="0.0"/>
7111 <param name="protgroup" value="0.0"/> 7178 <param name="protgroup" value="0.0"/>
7112 </section> 7179 </section>
7113 <section name="whitelist"> 7180 <section name="whitelist">
7114 <param name="protein_accessions" value=""/>
7115 <param name="ignore_modifications" value="false"/> 7181 <param name="ignore_modifications" value="false"/>
7116 <param name="modifications"/>
7117 </section> 7182 </section>
7118 <section name="blacklist"> 7183 <section name="blacklist">
7119 <param name="protein_accessions" value=""/>
7120 <param name="ignore_modifications" value="false"/> 7184 <param name="ignore_modifications" value="false"/>
7121 <param name="modifications"/>
7122 <param name="RegEx" value=""/> 7185 <param name="RegEx" value=""/>
7123 </section> 7186 </section>
7124 <section name="in_silico_digestion"> 7187 <section name="in_silico_digestion">
7125 <param name="fasta" value="IDFilter_13_input.fasta"/> 7188 <param name="fasta" value="IDFilter_13_input.fasta"/>
7126 <param name="enzyme" value="Trypsin"/> 7189 <param name="enzyme" value="Trypsin"/>
7141 <param name="unit" value="ppm"/> 7204 <param name="unit" value="ppm"/>
7142 </section> 7205 </section>
7143 <section name="best"> 7206 <section name="best">
7144 <param name="n_spectra" value="0"/> 7207 <param name="n_spectra" value="0"/>
7145 <param name="n_peptide_hits" value="0"/> 7208 <param name="n_peptide_hits" value="0"/>
7209 <param name="spectrum_per_peptide" value="false"/>
7146 <param name="n_protein_hits" value="0"/> 7210 <param name="n_protein_hits" value="0"/>
7147 <param name="strict" value="false"/> 7211 <param name="strict" value="false"/>
7148 <param name="n_to_m_peptide_hits" value=":"/> 7212 <param name="n_to_m_peptide_hits" value=":"/>
7149 </section> 7213 </section>
7150 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7151 <output name="ctd_out" ftype="xml"> 7215 <output name="ctd_out" ftype="xml">
7152 <assert_contents> 7216 <assert_contents>
7153 <is_valid_xml/> 7217 <is_valid_xml/>
7154 </assert_contents> 7218 </assert_contents>
7155 </output> 7219 </output>
7220 <assert_stdout>
7221 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7222 </assert_stdout>
7156 </test> 7223 </test>
7157 <!-- TOPP_IDFilter_14 --> 7224 <!-- TOPP_IDFilter_14 -->
7158 <test expect_num_outputs="2"> 7225 <test expect_num_outputs="2">
7159 <section name="adv_opts"> 7226 <section name="adv_opts">
7160 <param name="remove_duplicate_psm" value="false"/> 7227 <param name="remove_duplicate_psm" value="false"/>
7161 <param name="remove_peptide_hits_by_metavalue" value=""/>
7162 <param name="force" value="false"/> 7228 <param name="force" value="false"/>
7163 <param name="test" value="true"/> 7229 <param name="test" value="true"/>
7164 </section> 7230 </section>
7165 <param name="in" value="IDFilter_14_input.idXML"/> 7231 <param name="in" value="IDFilter_14_input.idXML"/>
7166 <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7232 <output name="out" value="IDFilter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7167 <param name="var_mods" value="false"/> 7233 <param name="var_mods" value="false"/>
7168 <param name="remove_shared_peptides" value="false"/> 7234 <param name="remove_shared_peptides" value="false"/>
7169 <param name="keep_unreferenced_protein_hits" value="false"/> 7235 <param name="keep_unreferenced_protein_hits" value="false"/>
7170 <param name="remove_decoys" value="false"/> 7236 <param name="remove_decoys" value="false"/>
7171 <param name="delete_unreferenced_peptide_hits" value="false"/> 7237 <param name="delete_unreferenced_peptide_hits" value="false"/>
7179 <param name="pep" value="0.0"/> 7245 <param name="pep" value="0.0"/>
7180 <param name="prot" value="0.0"/> 7246 <param name="prot" value="0.0"/>
7181 <param name="protgroup" value="0.0"/> 7247 <param name="protgroup" value="0.0"/>
7182 </section> 7248 </section>
7183 <section name="whitelist"> 7249 <section name="whitelist">
7184 <param name="protein_accessions" value=""/>
7185 <param name="ignore_modifications" value="false"/> 7250 <param name="ignore_modifications" value="false"/>
7186 <param name="modifications"/>
7187 </section> 7251 </section>
7188 <section name="blacklist"> 7252 <section name="blacklist">
7189 <param name="protein_accessions" value=""/>
7190 <param name="ignore_modifications" value="false"/> 7253 <param name="ignore_modifications" value="false"/>
7191 <param name="modifications"/>
7192 <param name="RegEx" value=""/> 7254 <param name="RegEx" value=""/>
7193 </section> 7255 </section>
7194 <section name="in_silico_digestion"> 7256 <section name="in_silico_digestion">
7195 <param name="fasta" value="IDFilter_14_input.fasta"/> 7257 <param name="fasta" value="IDFilter_14_input.fasta"/>
7196 <param name="enzyme" value="Trypsin/P"/> 7258 <param name="enzyme" value="Trypsin/P"/>
7211 <param name="unit" value="ppm"/> 7273 <param name="unit" value="ppm"/>
7212 </section> 7274 </section>
7213 <section name="best"> 7275 <section name="best">
7214 <param name="n_spectra" value="0"/> 7276 <param name="n_spectra" value="0"/>
7215 <param name="n_peptide_hits" value="0"/> 7277 <param name="n_peptide_hits" value="0"/>
7278 <param name="spectrum_per_peptide" value="false"/>
7216 <param name="n_protein_hits" value="0"/> 7279 <param name="n_protein_hits" value="0"/>
7217 <param name="strict" value="false"/> 7280 <param name="strict" value="false"/>
7218 <param name="n_to_m_peptide_hits" value=":"/> 7281 <param name="n_to_m_peptide_hits" value=":"/>
7219 </section> 7282 </section>
7220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7221 <output name="ctd_out" ftype="xml"> 7284 <output name="ctd_out" ftype="xml">
7222 <assert_contents> 7285 <assert_contents>
7223 <is_valid_xml/> 7286 <is_valid_xml/>
7224 </assert_contents> 7287 </assert_contents>
7225 </output> 7288 </output>
7289 <assert_stdout>
7290 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7291 </assert_stdout>
7226 </test> 7292 </test>
7227 <!-- TOPP_IDFilter_15 --> 7293 <!-- TOPP_IDFilter_15 -->
7228 <test expect_num_outputs="2"> 7294 <test expect_num_outputs="2">
7229 <section name="adv_opts"> 7295 <section name="adv_opts">
7230 <param name="remove_duplicate_psm" value="false"/> 7296 <param name="remove_duplicate_psm" value="false"/>
7231 <param name="remove_peptide_hits_by_metavalue" value=""/>
7232 <param name="force" value="false"/> 7297 <param name="force" value="false"/>
7233 <param name="test" value="true"/> 7298 <param name="test" value="true"/>
7234 </section> 7299 </section>
7235 <param name="in" value="IDFilter_15_input.idXML"/> 7300 <param name="in" value="IDFilter_15_input.idXML"/>
7236 <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7301 <output name="out" value="IDFilter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7237 <param name="var_mods" value="false"/> 7302 <param name="var_mods" value="false"/>
7238 <param name="remove_shared_peptides" value="false"/> 7303 <param name="remove_shared_peptides" value="false"/>
7239 <param name="keep_unreferenced_protein_hits" value="false"/> 7304 <param name="keep_unreferenced_protein_hits" value="false"/>
7240 <param name="remove_decoys" value="false"/> 7305 <param name="remove_decoys" value="false"/>
7241 <param name="delete_unreferenced_peptide_hits" value="false"/> 7306 <param name="delete_unreferenced_peptide_hits" value="false"/>
7249 <param name="pep" value="0.0"/> 7314 <param name="pep" value="0.0"/>
7250 <param name="prot" value="0.0"/> 7315 <param name="prot" value="0.0"/>
7251 <param name="protgroup" value="0.0"/> 7316 <param name="protgroup" value="0.0"/>
7252 </section> 7317 </section>
7253 <section name="whitelist"> 7318 <section name="whitelist">
7254 <param name="protein_accessions" value=""/>
7255 <param name="ignore_modifications" value="false"/> 7319 <param name="ignore_modifications" value="false"/>
7256 <param name="modifications"/>
7257 </section> 7320 </section>
7258 <section name="blacklist"> 7321 <section name="blacklist">
7259 <param name="protein_accessions" value=""/>
7260 <param name="ignore_modifications" value="false"/> 7322 <param name="ignore_modifications" value="false"/>
7261 <param name="modifications"/>
7262 <param name="RegEx" value=""/> 7323 <param name="RegEx" value=""/>
7263 </section> 7324 </section>
7264 <section name="in_silico_digestion"> 7325 <section name="in_silico_digestion">
7265 <param name="fasta" value="IDFilter_15_input.fasta"/> 7326 <param name="fasta" value="IDFilter_15_input.fasta"/>
7266 <param name="enzyme" value="Trypsin/P"/> 7327 <param name="enzyme" value="Trypsin/P"/>
7281 <param name="unit" value="ppm"/> 7342 <param name="unit" value="ppm"/>
7282 </section> 7343 </section>
7283 <section name="best"> 7344 <section name="best">
7284 <param name="n_spectra" value="0"/> 7345 <param name="n_spectra" value="0"/>
7285 <param name="n_peptide_hits" value="0"/> 7346 <param name="n_peptide_hits" value="0"/>
7347 <param name="spectrum_per_peptide" value="false"/>
7286 <param name="n_protein_hits" value="0"/> 7348 <param name="n_protein_hits" value="0"/>
7287 <param name="strict" value="false"/> 7349 <param name="strict" value="false"/>
7288 <param name="n_to_m_peptide_hits" value=":"/> 7350 <param name="n_to_m_peptide_hits" value=":"/>
7289 </section> 7351 </section>
7290 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7291 <output name="ctd_out" ftype="xml"> 7353 <output name="ctd_out" ftype="xml">
7292 <assert_contents> 7354 <assert_contents>
7293 <is_valid_xml/> 7355 <is_valid_xml/>
7294 </assert_contents> 7356 </assert_contents>
7295 </output> 7357 </output>
7358 <assert_stdout>
7359 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7360 </assert_stdout>
7296 </test> 7361 </test>
7297 <!-- TOPP_IDFilter_16 --> 7362 <!-- TOPP_IDFilter_16 -->
7298 <test expect_num_outputs="2"> 7363 <test expect_num_outputs="2">
7299 <section name="adv_opts"> 7364 <section name="adv_opts">
7300 <param name="remove_duplicate_psm" value="false"/> 7365 <param name="remove_duplicate_psm" value="false"/>
7301 <param name="remove_peptide_hits_by_metavalue" value=""/>
7302 <param name="force" value="false"/> 7366 <param name="force" value="false"/>
7303 <param name="test" value="true"/> 7367 <param name="test" value="true"/>
7304 </section> 7368 </section>
7305 <param name="in" value="IDFilter_16_input.idXML"/> 7369 <param name="in" value="IDFilter_16_input.idXML"/>
7306 <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7370 <output name="out" value="IDFilter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7307 <param name="var_mods" value="false"/> 7371 <param name="var_mods" value="false"/>
7308 <param name="remove_shared_peptides" value="false"/> 7372 <param name="remove_shared_peptides" value="false"/>
7309 <param name="keep_unreferenced_protein_hits" value="false"/> 7373 <param name="keep_unreferenced_protein_hits" value="false"/>
7310 <param name="remove_decoys" value="false"/> 7374 <param name="remove_decoys" value="false"/>
7311 <param name="delete_unreferenced_peptide_hits" value="false"/> 7375 <param name="delete_unreferenced_peptide_hits" value="false"/>
7319 <param name="pep" value="0.0"/> 7383 <param name="pep" value="0.0"/>
7320 <param name="prot" value="0.0"/> 7384 <param name="prot" value="0.0"/>
7321 <param name="protgroup" value="0.0"/> 7385 <param name="protgroup" value="0.0"/>
7322 </section> 7386 </section>
7323 <section name="whitelist"> 7387 <section name="whitelist">
7324 <param name="protein_accessions" value=""/>
7325 <param name="ignore_modifications" value="false"/> 7388 <param name="ignore_modifications" value="false"/>
7326 <param name="modifications"/>
7327 </section> 7389 </section>
7328 <section name="blacklist"> 7390 <section name="blacklist">
7329 <param name="protein_accessions" value=""/>
7330 <param name="ignore_modifications" value="false"/> 7391 <param name="ignore_modifications" value="false"/>
7331 <param name="modifications"/>
7332 <param name="RegEx" value=""/> 7392 <param name="RegEx" value=""/>
7333 </section> 7393 </section>
7334 <section name="in_silico_digestion"> 7394 <section name="in_silico_digestion">
7335 <param name="fasta" value="IDFilter_16_input.fasta"/> 7395 <param name="fasta" value="IDFilter_16_input.fasta"/>
7336 <param name="enzyme" value="Trypsin/P"/> 7396 <param name="enzyme" value="Trypsin/P"/>
7351 <param name="unit" value="ppm"/> 7411 <param name="unit" value="ppm"/>
7352 </section> 7412 </section>
7353 <section name="best"> 7413 <section name="best">
7354 <param name="n_spectra" value="0"/> 7414 <param name="n_spectra" value="0"/>
7355 <param name="n_peptide_hits" value="0"/> 7415 <param name="n_peptide_hits" value="0"/>
7416 <param name="spectrum_per_peptide" value="false"/>
7356 <param name="n_protein_hits" value="0"/> 7417 <param name="n_protein_hits" value="0"/>
7357 <param name="strict" value="false"/> 7418 <param name="strict" value="false"/>
7358 <param name="n_to_m_peptide_hits" value=":"/> 7419 <param name="n_to_m_peptide_hits" value=":"/>
7359 </section> 7420 </section>
7360 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7421 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7361 <output name="ctd_out" ftype="xml"> 7422 <output name="ctd_out" ftype="xml">
7362 <assert_contents> 7423 <assert_contents>
7363 <is_valid_xml/> 7424 <is_valid_xml/>
7364 </assert_contents> 7425 </assert_contents>
7365 </output> 7426 </output>
7427 <assert_stdout>
7428 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7429 </assert_stdout>
7366 </test> 7430 </test>
7367 <!-- TOPP_IDFilter_17 --> 7431 <!-- TOPP_IDFilter_17 -->
7368 <test expect_num_outputs="2"> 7432 <test expect_num_outputs="2">
7369 <section name="adv_opts"> 7433 <section name="adv_opts">
7370 <param name="remove_duplicate_psm" value="false"/> 7434 <param name="remove_duplicate_psm" value="false"/>
7371 <param name="remove_peptide_hits_by_metavalue" value=""/>
7372 <param name="force" value="false"/> 7435 <param name="force" value="false"/>
7373 <param name="test" value="true"/> 7436 <param name="test" value="true"/>
7374 </section> 7437 </section>
7375 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> 7438 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
7376 <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7439 <output name="out" value="IDFilter_17_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7377 <param name="var_mods" value="false"/> 7440 <param name="var_mods" value="false"/>
7378 <param name="remove_shared_peptides" value="false"/> 7441 <param name="remove_shared_peptides" value="false"/>
7379 <param name="keep_unreferenced_protein_hits" value="false"/> 7442 <param name="keep_unreferenced_protein_hits" value="false"/>
7380 <param name="remove_decoys" value="false"/> 7443 <param name="remove_decoys" value="false"/>
7381 <param name="delete_unreferenced_peptide_hits" value="false"/> 7444 <param name="delete_unreferenced_peptide_hits" value="false"/>
7389 <param name="pep" value="0.0"/> 7452 <param name="pep" value="0.0"/>
7390 <param name="prot" value="0.0"/> 7453 <param name="prot" value="0.0"/>
7391 <param name="protgroup" value="0.0"/> 7454 <param name="protgroup" value="0.0"/>
7392 </section> 7455 </section>
7393 <section name="whitelist"> 7456 <section name="whitelist">
7394 <param name="protein_accessions" value=""/>
7395 <param name="ignore_modifications" value="false"/> 7457 <param name="ignore_modifications" value="false"/>
7396 <param name="modifications"/>
7397 </section> 7458 </section>
7398 <section name="blacklist"> 7459 <section name="blacklist">
7399 <param name="protein_accessions" value=""/>
7400 <param name="ignore_modifications" value="false"/> 7460 <param name="ignore_modifications" value="false"/>
7401 <param name="modifications"/>
7402 <param name="RegEx" value=""/> 7461 <param name="RegEx" value=""/>
7403 </section> 7462 </section>
7404 <section name="in_silico_digestion"> 7463 <section name="in_silico_digestion">
7405 <param name="enzyme" value="Trypsin"/> 7464 <param name="enzyme" value="Trypsin"/>
7406 <param name="specificity" value="full"/> 7465 <param name="specificity" value="full"/>
7420 <param name="unit" value="ppm"/> 7479 <param name="unit" value="ppm"/>
7421 </section> 7480 </section>
7422 <section name="best"> 7481 <section name="best">
7423 <param name="n_spectra" value="0"/> 7482 <param name="n_spectra" value="0"/>
7424 <param name="n_peptide_hits" value="0"/> 7483 <param name="n_peptide_hits" value="0"/>
7484 <param name="spectrum_per_peptide" value="false"/>
7425 <param name="n_protein_hits" value="0"/> 7485 <param name="n_protein_hits" value="0"/>
7426 <param name="strict" value="false"/> 7486 <param name="strict" value="false"/>
7427 <param name="n_to_m_peptide_hits" value=":"/> 7487 <param name="n_to_m_peptide_hits" value=":"/>
7428 </section> 7488 </section>
7429 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7430 <output name="ctd_out" ftype="xml"> 7490 <output name="ctd_out" ftype="xml">
7431 <assert_contents> 7491 <assert_contents>
7432 <is_valid_xml/> 7492 <is_valid_xml/>
7433 </assert_contents> 7493 </assert_contents>
7434 </output> 7494 </output>
7495 <assert_stdout>
7496 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7497 </assert_stdout>
7435 </test> 7498 </test>
7436 <!-- TOPP_IDFilter_18 --> 7499 <!-- TOPP_IDFilter_18 -->
7437 <test expect_num_outputs="2"> 7500 <test expect_num_outputs="2">
7438 <section name="adv_opts"> 7501 <section name="adv_opts">
7439 <param name="remove_duplicate_psm" value="false"/> 7502 <param name="remove_duplicate_psm" value="false"/>
7440 <param name="remove_peptide_hits_by_metavalue" value=""/>
7441 <param name="force" value="false"/> 7503 <param name="force" value="false"/>
7442 <param name="test" value="true"/> 7504 <param name="test" value="true"/>
7443 </section> 7505 </section>
7444 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> 7506 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
7445 <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7507 <output name="out" value="IDFilter_18_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7446 <param name="var_mods" value="false"/> 7508 <param name="var_mods" value="false"/>
7447 <param name="remove_shared_peptides" value="false"/> 7509 <param name="remove_shared_peptides" value="false"/>
7448 <param name="keep_unreferenced_protein_hits" value="false"/> 7510 <param name="keep_unreferenced_protein_hits" value="false"/>
7449 <param name="remove_decoys" value="false"/> 7511 <param name="remove_decoys" value="false"/>
7450 <param name="delete_unreferenced_peptide_hits" value="false"/> 7512 <param name="delete_unreferenced_peptide_hits" value="false"/>
7458 <param name="pep" value="0.0"/> 7520 <param name="pep" value="0.0"/>
7459 <param name="prot" value="0.0"/> 7521 <param name="prot" value="0.0"/>
7460 <param name="protgroup" value="0.0"/> 7522 <param name="protgroup" value="0.0"/>
7461 </section> 7523 </section>
7462 <section name="whitelist"> 7524 <section name="whitelist">
7463 <param name="protein_accessions" value=""/>
7464 <param name="ignore_modifications" value="false"/> 7525 <param name="ignore_modifications" value="false"/>
7465 <param name="modifications"/>
7466 </section> 7526 </section>
7467 <section name="blacklist"> 7527 <section name="blacklist">
7468 <param name="protein_accessions" value=""/>
7469 <param name="ignore_modifications" value="false"/> 7528 <param name="ignore_modifications" value="false"/>
7470 <param name="modifications"/>
7471 <param name="RegEx" value=""/> 7529 <param name="RegEx" value=""/>
7472 </section> 7530 </section>
7473 <section name="in_silico_digestion"> 7531 <section name="in_silico_digestion">
7474 <param name="enzyme" value="Trypsin"/> 7532 <param name="enzyme" value="Trypsin"/>
7475 <param name="specificity" value="full"/> 7533 <param name="specificity" value="full"/>
7489 <param name="unit" value="ppm"/> 7547 <param name="unit" value="ppm"/>
7490 </section> 7548 </section>
7491 <section name="best"> 7549 <section name="best">
7492 <param name="n_spectra" value="0"/> 7550 <param name="n_spectra" value="0"/>
7493 <param name="n_peptide_hits" value="0"/> 7551 <param name="n_peptide_hits" value="0"/>
7552 <param name="spectrum_per_peptide" value="false"/>
7494 <param name="n_protein_hits" value="0"/> 7553 <param name="n_protein_hits" value="0"/>
7495 <param name="strict" value="false"/> 7554 <param name="strict" value="false"/>
7496 <param name="n_to_m_peptide_hits" value=":"/> 7555 <param name="n_to_m_peptide_hits" value=":"/>
7497 </section> 7556 </section>
7498 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7557 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7499 <output name="ctd_out" ftype="xml"> 7558 <output name="ctd_out" ftype="xml">
7500 <assert_contents> 7559 <assert_contents>
7501 <is_valid_xml/> 7560 <is_valid_xml/>
7502 </assert_contents> 7561 </assert_contents>
7503 </output> 7562 </output>
7563 <assert_stdout>
7564 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7565 </assert_stdout>
7504 </test> 7566 </test>
7505 <!-- TOPP_IDFilter_19 --> 7567 <!-- TOPP_IDFilter_19 -->
7506 <test expect_num_outputs="2"> 7568 <test expect_num_outputs="2">
7507 <section name="adv_opts"> 7569 <section name="adv_opts">
7508 <param name="remove_duplicate_psm" value="false"/> 7570 <param name="remove_duplicate_psm" value="false"/>
7509 <param name="remove_peptide_hits_by_metavalue" value=""/>
7510 <param name="force" value="false"/> 7571 <param name="force" value="false"/>
7511 <param name="test" value="true"/> 7572 <param name="test" value="true"/>
7512 </section> 7573 </section>
7513 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> 7574 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
7514 <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7575 <output name="out" value="IDFilter_19_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7515 <param name="var_mods" value="false"/> 7576 <param name="var_mods" value="false"/>
7516 <param name="remove_shared_peptides" value="false"/> 7577 <param name="remove_shared_peptides" value="false"/>
7517 <param name="keep_unreferenced_protein_hits" value="false"/> 7578 <param name="keep_unreferenced_protein_hits" value="false"/>
7518 <param name="remove_decoys" value="false"/> 7579 <param name="remove_decoys" value="false"/>
7519 <param name="delete_unreferenced_peptide_hits" value="false"/> 7580 <param name="delete_unreferenced_peptide_hits" value="false"/>
7527 <param name="pep" value="0.0"/> 7588 <param name="pep" value="0.0"/>
7528 <param name="prot" value="0.0"/> 7589 <param name="prot" value="0.0"/>
7529 <param name="protgroup" value="0.0"/> 7590 <param name="protgroup" value="0.0"/>
7530 </section> 7591 </section>
7531 <section name="whitelist"> 7592 <section name="whitelist">
7532 <param name="protein_accessions" value=""/>
7533 <param name="ignore_modifications" value="false"/> 7593 <param name="ignore_modifications" value="false"/>
7534 <param name="modifications"/>
7535 </section> 7594 </section>
7536 <section name="blacklist"> 7595 <section name="blacklist">
7537 <param name="protein_accessions" value=""/>
7538 <param name="ignore_modifications" value="false"/> 7596 <param name="ignore_modifications" value="false"/>
7539 <param name="modifications"/>
7540 <param name="RegEx" value=""/> 7597 <param name="RegEx" value=""/>
7541 </section> 7598 </section>
7542 <section name="in_silico_digestion"> 7599 <section name="in_silico_digestion">
7543 <param name="enzyme" value="Trypsin"/> 7600 <param name="enzyme" value="Trypsin"/>
7544 <param name="specificity" value="full"/> 7601 <param name="specificity" value="full"/>
7558 <param name="unit" value="ppm"/> 7615 <param name="unit" value="ppm"/>
7559 </section> 7616 </section>
7560 <section name="best"> 7617 <section name="best">
7561 <param name="n_spectra" value="0"/> 7618 <param name="n_spectra" value="0"/>
7562 <param name="n_peptide_hits" value="0"/> 7619 <param name="n_peptide_hits" value="0"/>
7620 <param name="spectrum_per_peptide" value="false"/>
7563 <param name="n_protein_hits" value="0"/> 7621 <param name="n_protein_hits" value="0"/>
7564 <param name="strict" value="false"/> 7622 <param name="strict" value="false"/>
7565 <param name="n_to_m_peptide_hits" value=":"/> 7623 <param name="n_to_m_peptide_hits" value=":"/>
7566 </section> 7624 </section>
7567 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7625 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7568 <output name="ctd_out" ftype="xml"> 7626 <output name="ctd_out" ftype="xml">
7569 <assert_contents> 7627 <assert_contents>
7570 <is_valid_xml/> 7628 <is_valid_xml/>
7571 </assert_contents> 7629 </assert_contents>
7572 </output> 7630 </output>
7631 <assert_stdout>
7632 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7633 </assert_stdout>
7573 </test> 7634 </test>
7574 <!-- TOPP_IDFilter_20 --> 7635 <!-- TOPP_IDFilter_20 -->
7575 <test expect_num_outputs="2"> 7636 <test expect_num_outputs="2">
7576 <section name="adv_opts"> 7637 <section name="adv_opts">
7577 <param name="remove_duplicate_psm" value="false"/> 7638 <param name="remove_duplicate_psm" value="false"/>
7578 <param name="remove_peptide_hits_by_metavalue" value=""/>
7579 <param name="force" value="false"/> 7639 <param name="force" value="false"/>
7580 <param name="test" value="true"/> 7640 <param name="test" value="true"/>
7581 </section> 7641 </section>
7582 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> 7642 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
7583 <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7643 <output name="out" value="IDFilter_20_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7584 <param name="var_mods" value="false"/> 7644 <param name="var_mods" value="false"/>
7585 <param name="remove_shared_peptides" value="false"/> 7645 <param name="remove_shared_peptides" value="false"/>
7586 <param name="keep_unreferenced_protein_hits" value="false"/> 7646 <param name="keep_unreferenced_protein_hits" value="false"/>
7587 <param name="remove_decoys" value="false"/> 7647 <param name="remove_decoys" value="false"/>
7588 <param name="delete_unreferenced_peptide_hits" value="false"/> 7648 <param name="delete_unreferenced_peptide_hits" value="false"/>
7596 <param name="pep" value="0.0"/> 7656 <param name="pep" value="0.0"/>
7597 <param name="prot" value="0.0"/> 7657 <param name="prot" value="0.0"/>
7598 <param name="protgroup" value="0.0"/> 7658 <param name="protgroup" value="0.0"/>
7599 </section> 7659 </section>
7600 <section name="whitelist"> 7660 <section name="whitelist">
7601 <param name="protein_accessions" value=""/>
7602 <param name="ignore_modifications" value="false"/> 7661 <param name="ignore_modifications" value="false"/>
7603 <param name="modifications"/>
7604 </section> 7662 </section>
7605 <section name="blacklist"> 7663 <section name="blacklist">
7606 <param name="protein_accessions" value=""/>
7607 <param name="ignore_modifications" value="false"/> 7664 <param name="ignore_modifications" value="false"/>
7608 <param name="modifications"/>
7609 <param name="RegEx" value=""/> 7665 <param name="RegEx" value=""/>
7610 </section> 7666 </section>
7611 <section name="in_silico_digestion"> 7667 <section name="in_silico_digestion">
7612 <param name="enzyme" value="Trypsin"/> 7668 <param name="enzyme" value="Trypsin"/>
7613 <param name="specificity" value="full"/> 7669 <param name="specificity" value="full"/>
7627 <param name="unit" value="ppm"/> 7683 <param name="unit" value="ppm"/>
7628 </section> 7684 </section>
7629 <section name="best"> 7685 <section name="best">
7630 <param name="n_spectra" value="0"/> 7686 <param name="n_spectra" value="0"/>
7631 <param name="n_peptide_hits" value="0"/> 7687 <param name="n_peptide_hits" value="0"/>
7688 <param name="spectrum_per_peptide" value="false"/>
7632 <param name="n_protein_hits" value="0"/> 7689 <param name="n_protein_hits" value="0"/>
7633 <param name="strict" value="false"/> 7690 <param name="strict" value="false"/>
7634 <param name="n_to_m_peptide_hits" value=":"/> 7691 <param name="n_to_m_peptide_hits" value=":"/>
7635 </section> 7692 </section>
7636 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7693 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7637 <output name="ctd_out" ftype="xml"> 7694 <output name="ctd_out" ftype="xml">
7638 <assert_contents> 7695 <assert_contents>
7639 <is_valid_xml/> 7696 <is_valid_xml/>
7640 </assert_contents> 7697 </assert_contents>
7641 </output> 7698 </output>
7699 <assert_stdout>
7700 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7701 </assert_stdout>
7642 </test> 7702 </test>
7643 <!-- TOPP_IDFilter_21 --> 7703 <!-- TOPP_IDFilter_21 -->
7644 <test expect_num_outputs="2"> 7704 <test expect_num_outputs="2">
7645 <section name="adv_opts"> 7705 <section name="adv_opts">
7646 <param name="remove_duplicate_psm" value="false"/> 7706 <param name="remove_duplicate_psm" value="false"/>
7647 <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/> 7707 <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/>
7648 <param name="force" value="false"/> 7708 <param name="force" value="false"/>
7649 <param name="test" value="true"/> 7709 <param name="test" value="true"/>
7650 </section> 7710 </section>
7651 <param name="in" value="IDFilter_16_input.idXML"/> 7711 <param name="in" value="IDFilter_16_input.idXML"/>
7652 <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7712 <output name="out" value="IDFilter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7653 <param name="var_mods" value="false"/> 7713 <param name="var_mods" value="false"/>
7654 <param name="remove_shared_peptides" value="false"/> 7714 <param name="remove_shared_peptides" value="false"/>
7655 <param name="keep_unreferenced_protein_hits" value="false"/> 7715 <param name="keep_unreferenced_protein_hits" value="false"/>
7656 <param name="remove_decoys" value="false"/> 7716 <param name="remove_decoys" value="false"/>
7657 <param name="delete_unreferenced_peptide_hits" value="false"/> 7717 <param name="delete_unreferenced_peptide_hits" value="false"/>
7665 <param name="pep" value="0.0"/> 7725 <param name="pep" value="0.0"/>
7666 <param name="prot" value="0.0"/> 7726 <param name="prot" value="0.0"/>
7667 <param name="protgroup" value="0.0"/> 7727 <param name="protgroup" value="0.0"/>
7668 </section> 7728 </section>
7669 <section name="whitelist"> 7729 <section name="whitelist">
7670 <param name="protein_accessions" value=""/>
7671 <param name="ignore_modifications" value="false"/> 7730 <param name="ignore_modifications" value="false"/>
7672 <param name="modifications"/>
7673 </section> 7731 </section>
7674 <section name="blacklist"> 7732 <section name="blacklist">
7675 <param name="protein_accessions" value=""/>
7676 <param name="ignore_modifications" value="false"/> 7733 <param name="ignore_modifications" value="false"/>
7677 <param name="modifications"/>
7678 <param name="RegEx" value=""/> 7734 <param name="RegEx" value=""/>
7679 </section> 7735 </section>
7680 <section name="in_silico_digestion"> 7736 <section name="in_silico_digestion">
7681 <param name="enzyme" value="Trypsin"/> 7737 <param name="enzyme" value="Trypsin"/>
7682 <param name="specificity" value="full"/> 7738 <param name="specificity" value="full"/>
7696 <param name="unit" value="ppm"/> 7752 <param name="unit" value="ppm"/>
7697 </section> 7753 </section>
7698 <section name="best"> 7754 <section name="best">
7699 <param name="n_spectra" value="0"/> 7755 <param name="n_spectra" value="0"/>
7700 <param name="n_peptide_hits" value="0"/> 7756 <param name="n_peptide_hits" value="0"/>
7757 <param name="spectrum_per_peptide" value="false"/>
7701 <param name="n_protein_hits" value="0"/> 7758 <param name="n_protein_hits" value="0"/>
7702 <param name="strict" value="false"/> 7759 <param name="strict" value="false"/>
7703 <param name="n_to_m_peptide_hits" value=":"/> 7760 <param name="n_to_m_peptide_hits" value=":"/>
7704 </section> 7761 </section>
7705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7762 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7706 <output name="ctd_out" ftype="xml"> 7763 <output name="ctd_out" ftype="xml">
7707 <assert_contents> 7764 <assert_contents>
7708 <is_valid_xml/> 7765 <is_valid_xml/>
7709 </assert_contents> 7766 </assert_contents>
7710 </output> 7767 </output>
7768 <assert_stdout>
7769 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7770 </assert_stdout>
7711 </test> 7771 </test>
7712 <!-- TOPP_IDFilter_22 --> 7772 <!-- TOPP_IDFilter_22 -->
7713 <test expect_num_outputs="2"> 7773 <test expect_num_outputs="2">
7714 <section name="adv_opts"> 7774 <section name="adv_opts">
7715 <param name="remove_duplicate_psm" value="false"/> 7775 <param name="remove_duplicate_psm" value="false"/>
7716 <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/> 7776 <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/>
7717 <param name="force" value="false"/> 7777 <param name="force" value="false"/>
7718 <param name="test" value="true"/> 7778 <param name="test" value="true"/>
7719 </section> 7779 </section>
7720 <param name="in" value="IDFilter_16_input.idXML"/> 7780 <param name="in" value="IDFilter_16_input.idXML"/>
7721 <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 7781 <output name="out" value="IDFilter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7722 <param name="var_mods" value="false"/> 7782 <param name="var_mods" value="false"/>
7723 <param name="remove_shared_peptides" value="false"/> 7783 <param name="remove_shared_peptides" value="false"/>
7724 <param name="keep_unreferenced_protein_hits" value="false"/> 7784 <param name="keep_unreferenced_protein_hits" value="false"/>
7725 <param name="remove_decoys" value="false"/> 7785 <param name="remove_decoys" value="false"/>
7726 <param name="delete_unreferenced_peptide_hits" value="false"/> 7786 <param name="delete_unreferenced_peptide_hits" value="false"/>
7734 <param name="pep" value="0.0"/> 7794 <param name="pep" value="0.0"/>
7735 <param name="prot" value="0.0"/> 7795 <param name="prot" value="0.0"/>
7736 <param name="protgroup" value="0.0"/> 7796 <param name="protgroup" value="0.0"/>
7737 </section> 7797 </section>
7738 <section name="whitelist"> 7798 <section name="whitelist">
7739 <param name="protein_accessions" value=""/>
7740 <param name="ignore_modifications" value="false"/> 7799 <param name="ignore_modifications" value="false"/>
7741 <param name="modifications"/>
7742 </section> 7800 </section>
7743 <section name="blacklist"> 7801 <section name="blacklist">
7744 <param name="protein_accessions" value=""/>
7745 <param name="ignore_modifications" value="false"/> 7802 <param name="ignore_modifications" value="false"/>
7746 <param name="modifications"/>
7747 <param name="RegEx" value=""/> 7803 <param name="RegEx" value=""/>
7748 </section> 7804 </section>
7749 <section name="in_silico_digestion"> 7805 <section name="in_silico_digestion">
7750 <param name="enzyme" value="Trypsin"/> 7806 <param name="enzyme" value="Trypsin"/>
7751 <param name="specificity" value="full"/> 7807 <param name="specificity" value="full"/>
7765 <param name="unit" value="ppm"/> 7821 <param name="unit" value="ppm"/>
7766 </section> 7822 </section>
7767 <section name="best"> 7823 <section name="best">
7768 <param name="n_spectra" value="0"/> 7824 <param name="n_spectra" value="0"/>
7769 <param name="n_peptide_hits" value="0"/> 7825 <param name="n_peptide_hits" value="0"/>
7826 <param name="spectrum_per_peptide" value="false"/>
7770 <param name="n_protein_hits" value="0"/> 7827 <param name="n_protein_hits" value="0"/>
7771 <param name="strict" value="false"/> 7828 <param name="strict" value="false"/>
7772 <param name="n_to_m_peptide_hits" value=":"/> 7829 <param name="n_to_m_peptide_hits" value=":"/>
7773 </section> 7830 </section>
7774 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7775 <output name="ctd_out" ftype="xml"> 7832 <output name="ctd_out" ftype="xml">
7776 <assert_contents> 7833 <assert_contents>
7777 <is_valid_xml/> 7834 <is_valid_xml/>
7778 </assert_contents> 7835 </assert_contents>
7779 </output> 7836 </output>
7837 <assert_stdout>
7838 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7839 </assert_stdout>
7780 </test> 7840 </test>
7781 <!-- TOPP_IDFilter_23 --> 7841 <!-- TOPP_IDFilter_23 -->
7782 <test expect_num_outputs="2"> 7842 <test expect_num_outputs="2">
7783 <section name="adv_opts"> 7843 <section name="adv_opts">
7784 <param name="remove_duplicate_psm" value="false"/> 7844 <param name="remove_duplicate_psm" value="false"/>
7785 <param name="remove_peptide_hits_by_metavalue" value=""/>
7786 <param name="force" value="false"/> 7845 <param name="force" value="false"/>
7787 <param name="test" value="true"/> 7846 <param name="test" value="true"/>
7788 </section> 7847 </section>
7789 <param name="in" value="IDMapper_2_output.consensusXML"/> 7848 <param name="in" value="IDMapper_2_output.consensusXML"/>
7790 <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 7849 <output name="out" value="IDFilter_23_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
7791 <param name="var_mods" value="false"/> 7850 <param name="var_mods" value="false"/>
7792 <param name="remove_shared_peptides" value="false"/> 7851 <param name="remove_shared_peptides" value="false"/>
7793 <param name="keep_unreferenced_protein_hits" value="false"/> 7852 <param name="keep_unreferenced_protein_hits" value="false"/>
7794 <param name="remove_decoys" value="false"/> 7853 <param name="remove_decoys" value="false"/>
7795 <param name="delete_unreferenced_peptide_hits" value="false"/> 7854 <param name="delete_unreferenced_peptide_hits" value="false"/>
7805 <param name="protgroup" value="0.0"/> 7864 <param name="protgroup" value="0.0"/>
7806 </section> 7865 </section>
7807 <section name="whitelist"> 7866 <section name="whitelist">
7808 <param name="protein_accessions" value="&quot;Q9HP81&quot;"/> 7867 <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
7809 <param name="ignore_modifications" value="false"/> 7868 <param name="ignore_modifications" value="false"/>
7810 <param name="modifications"/>
7811 </section> 7869 </section>
7812 <section name="blacklist"> 7870 <section name="blacklist">
7813 <param name="protein_accessions" value=""/>
7814 <param name="ignore_modifications" value="false"/> 7871 <param name="ignore_modifications" value="false"/>
7815 <param name="modifications"/>
7816 <param name="RegEx" value=""/> 7872 <param name="RegEx" value=""/>
7817 </section> 7873 </section>
7818 <section name="in_silico_digestion"> 7874 <section name="in_silico_digestion">
7819 <param name="enzyme" value="Trypsin"/> 7875 <param name="enzyme" value="Trypsin"/>
7820 <param name="specificity" value="full"/> 7876 <param name="specificity" value="full"/>
7834 <param name="unit" value="ppm"/> 7890 <param name="unit" value="ppm"/>
7835 </section> 7891 </section>
7836 <section name="best"> 7892 <section name="best">
7837 <param name="n_spectra" value="0"/> 7893 <param name="n_spectra" value="0"/>
7838 <param name="n_peptide_hits" value="0"/> 7894 <param name="n_peptide_hits" value="0"/>
7895 <param name="spectrum_per_peptide" value="false"/>
7839 <param name="n_protein_hits" value="0"/> 7896 <param name="n_protein_hits" value="0"/>
7840 <param name="strict" value="false"/> 7897 <param name="strict" value="false"/>
7841 <param name="n_to_m_peptide_hits" value=":"/> 7898 <param name="n_to_m_peptide_hits" value=":"/>
7842 </section> 7899 </section>
7843 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7900 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7844 <output name="ctd_out" ftype="xml"> 7901 <output name="ctd_out" ftype="xml">
7845 <assert_contents> 7902 <assert_contents>
7846 <is_valid_xml/> 7903 <is_valid_xml/>
7847 </assert_contents> 7904 </assert_contents>
7848 </output> 7905 </output>
7906 <assert_stdout>
7907 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7908 </assert_stdout>
7849 </test> 7909 </test>
7850 <!-- TOPP_IDFilter_24 --> 7910 <!-- TOPP_IDFilter_24 -->
7851 <test expect_num_outputs="2"> 7911 <test expect_num_outputs="2">
7852 <section name="adv_opts"> 7912 <section name="adv_opts">
7853 <param name="remove_duplicate_psm" value="false"/> 7913 <param name="remove_duplicate_psm" value="false"/>
7854 <param name="remove_peptide_hits_by_metavalue" value=""/>
7855 <param name="force" value="false"/> 7914 <param name="force" value="false"/>
7856 <param name="test" value="true"/> 7915 <param name="test" value="true"/>
7857 </section> 7916 </section>
7858 <param name="in" value="Epifany_3_out.consensusXML"/> 7917 <param name="in" value="Epifany_3_out.consensusXML"/>
7859 <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 7918 <output name="out" value="IDFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
7860 <param name="var_mods" value="false"/> 7919 <param name="var_mods" value="false"/>
7861 <param name="remove_shared_peptides" value="false"/> 7920 <param name="remove_shared_peptides" value="false"/>
7862 <param name="keep_unreferenced_protein_hits" value="false"/> 7921 <param name="keep_unreferenced_protein_hits" value="false"/>
7863 <param name="remove_decoys" value="false"/> 7922 <param name="remove_decoys" value="false"/>
7864 <param name="delete_unreferenced_peptide_hits" value="false"/> 7923 <param name="delete_unreferenced_peptide_hits" value="false"/>
7872 <param name="pep" value="0.0"/> 7931 <param name="pep" value="0.0"/>
7873 <param name="prot" value="0.0"/> 7932 <param name="prot" value="0.0"/>
7874 <param name="protgroup" value="0.99"/> 7933 <param name="protgroup" value="0.99"/>
7875 </section> 7934 </section>
7876 <section name="whitelist"> 7935 <section name="whitelist">
7877 <param name="protein_accessions" value=""/>
7878 <param name="ignore_modifications" value="false"/> 7936 <param name="ignore_modifications" value="false"/>
7879 <param name="modifications"/>
7880 </section> 7937 </section>
7881 <section name="blacklist"> 7938 <section name="blacklist">
7882 <param name="protein_accessions" value=""/>
7883 <param name="ignore_modifications" value="false"/> 7939 <param name="ignore_modifications" value="false"/>
7884 <param name="modifications"/>
7885 <param name="RegEx" value=""/> 7940 <param name="RegEx" value=""/>
7886 </section> 7941 </section>
7887 <section name="in_silico_digestion"> 7942 <section name="in_silico_digestion">
7888 <param name="enzyme" value="Trypsin"/> 7943 <param name="enzyme" value="Trypsin"/>
7889 <param name="specificity" value="full"/> 7944 <param name="specificity" value="full"/>
7903 <param name="unit" value="ppm"/> 7958 <param name="unit" value="ppm"/>
7904 </section> 7959 </section>
7905 <section name="best"> 7960 <section name="best">
7906 <param name="n_spectra" value="0"/> 7961 <param name="n_spectra" value="0"/>
7907 <param name="n_peptide_hits" value="0"/> 7962 <param name="n_peptide_hits" value="0"/>
7963 <param name="spectrum_per_peptide" value="false"/>
7908 <param name="n_protein_hits" value="0"/> 7964 <param name="n_protein_hits" value="0"/>
7909 <param name="strict" value="false"/> 7965 <param name="strict" value="false"/>
7910 <param name="n_to_m_peptide_hits" value=":"/> 7966 <param name="n_to_m_peptide_hits" value=":"/>
7911 </section> 7967 </section>
7912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 7968 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7913 <output name="ctd_out" ftype="xml"> 7969 <output name="ctd_out" ftype="xml">
7914 <assert_contents> 7970 <assert_contents>
7915 <is_valid_xml/> 7971 <is_valid_xml/>
7916 </assert_contents> 7972 </assert_contents>
7917 </output> 7973 </output>
7974 <assert_stdout>
7975 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
7976 </assert_stdout>
7918 </test> 7977 </test>
7919 </tests> 7978 </tests>
7920 <help><![CDATA[Filters results from protein or peptide identification engines based on different criteria. 7979 <help><![CDATA[Filters results from protein or peptide identification engines based on different criteria.
7921 7980
7922 7981
7923 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFilter.html]]></help> 7982 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFilter.html]]></help>
7924 <expand macro="references"/> 7983 <expand macro="references"/>
7925 </tool> 7984 </tool>