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comparison CometAdapter.xml @ 9:df0c77da6c87 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 21:35:36 +0000
parents e75929491905
children
comparison
equal deleted inserted replaced
8:e75929491905 9:df0c77da6c87
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: [Identification]--> 2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
4 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using Comet.</description> 4 <description>Annotates MS/MS spectra using Comet</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">CometAdapter</token> 6 <token name="@EXECUTABLE@">CometAdapter</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($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 mkdir database && 19 mkdir database &&
21 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 20 cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
22 #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir pin_out && 22 mkdir pin_out &&
24 #end if 23 #end if
25 #if $default_params_file: 24 #if $default_params_file:
26 mkdir default_params_file && 25 mkdir default_params_file &&
27 ln -s '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' && 26 cp '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' &&
28 #end if 27 #end if
29 28
30 ## Main program call 29 ## Main program call
31 30
32 set -o pipefail && 31 set -o pipefail &&
62 <configfiles> 61 <configfiles>
63 <inputs name="args_json" data_style="paths"/> 62 <inputs name="args_json" data_style="paths"/>
64 <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 63 <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
65 </configfiles> 64 </configfiles>
66 <inputs> 65 <inputs>
67 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 66 <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
68 <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/> 67 <param argument="-database" type="data" format="fasta" label="FASTA file" help=" select fasta data sets(s)"/>
69 <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/> 68 <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
70 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/> 69 <param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
71 <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help=""> 70 <param argument="-precursor_error_units" type="select" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
72 <option value="amu">amu</option> 71 <option value="amu">amu</option>
73 <option value="ppm" selected="true">ppm</option> 72 <option value="ppm" selected="true">ppm</option>
74 <option value="Da">Da</option> 73 <option value="Da">Da</option>
75 <expand macro="list_string_san" name="precursor_error_units"/> 74 <expand macro="list_string_san" name="precursor_error_units"/>
76 </param> 75 </param>
77 <param argument="-isotope_error" type="select" optional="true" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC"> 76 <param argument="-isotope_error" type="select" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
78 <option value="off" selected="true">off</option> 77 <option value="off" selected="true">off</option>
79 <option value="0/1">0/1</option> 78 <option value="0/1">0/1</option>
80 <option value="0/1/2">0/1/2</option> 79 <option value="0/1/2">0/1/2</option>
81 <option value="0/1/2/3">0/1/2/3</option> 80 <option value="0/1/2/3">0/1/2/3</option>
82 <option value="-8/-4/0/4/8">-8/-4/0/4/8</option> 81 <option value="-8/-4/0/4/8">-8/-4/0/4/8</option>
83 <option value="-1/0/1/2/3">-1/0/1/2/3</option> 82 <option value="-1/0/1/2/3">-1/0/1/2/3</option>
84 <expand macro="list_string_san" name="isotope_error"/> 83 <expand macro="list_string_san" name="isotope_error"/>
85 </param> 84 </param>
86 <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/> 85 <param argument="-fragment_mass_tolerance" type="float" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
87 <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help=""> 86 <param argument="-fragment_error_units" type="select" label="Fragment monoisotopic mass error units" help="">
88 <option value="Da" selected="true">Da</option> 87 <option value="Da" selected="true">Da</option>
89 <expand macro="list_string_san" name="fragment_error_units"/> 88 <expand macro="list_string_san" name="fragment_error_units"/>
90 </param> 89 </param>
91 <param argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/> 90 <param argument="-fragment_bin_offset" type="float" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
92 <param argument="-instrument" type="select" optional="true" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help=""> 91 <param argument="-instrument" type="select" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
93 <option value="low_res">low_res</option> 92 <option value="low_res">low_res</option>
94 <option value="high_res" selected="true">high_res</option> 93 <option value="high_res" selected="true">high_res</option>
95 <expand macro="list_string_san" name="instrument"/> 94 <expand macro="list_string_san" name="instrument"/>
96 </param> 95 </param>
97 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> 96 <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
97 <option value="Asp-N">Asp-N</option>
98 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
99 <option value="Trypsin" selected="true">Trypsin</option>
100 <option value="Arg-C">Arg-C</option>
101 <option value="no cleavage">no cleavage</option>
102 <option value="unspecific cleavage">unspecific cleavage</option>
103 <option value="Chymotrypsin">Chymotrypsin</option>
98 <option value="CNBr">CNBr</option> 104 <option value="CNBr">CNBr</option>
99 <option value="Lys-C">Lys-C</option> 105 <option value="Lys-C">Lys-C</option>
100 <option value="Trypsin" selected="true">Trypsin</option>
101 <option value="Arg-C">Arg-C</option>
102 <option value="Chymotrypsin">Chymotrypsin</option>
103 <option value="Asp-N">Asp-N</option>
104 <option value="unspecific cleavage">unspecific cleavage</option>
105 <option value="Lys-N">Lys-N</option> 106 <option value="Lys-N">Lys-N</option>
106 <option value="PepsinA">PepsinA</option> 107 <option value="PepsinA">PepsinA</option>
107 <option value="Trypsin/P">Trypsin/P</option> 108 <option value="Trypsin/P">Trypsin/P</option>
108 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
109 <expand macro="list_string_san" name="enzyme"/> 109 <expand macro="list_string_san" name="enzyme"/>
110 </param> 110 </param>
111 <param argument="-num_enzyme_termini" type="select" optional="true" label="Specify the termini where the cleavage rule has to match" help=""> 111 <param argument="-num_enzyme_termini" type="select" label="Specify the termini where the cleavage rule has to match" help="">
112 <option value="semi">semi</option> 112 <option value="semi">semi</option>
113 <option value="fully" selected="true">fully</option> 113 <option value="fully" selected="true">fully</option>
114 <option value="C-term unspecific">C-term unspecific</option> 114 <option value="C-term unspecific">C-term unspecific</option>
115 <option value="N-term unspecific">N-term unspecific</option> 115 <option value="N-term unspecific">N-term unspecific</option>
116 <expand macro="list_string_san" name="num_enzyme_termini"/> 116 <expand macro="list_string_san" name="num_enzyme_termini"/>
117 </param> 117 </param>
118 <param argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/> 118 <param argument="-missed_cleavages" type="integer" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
119 <param argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/> 119 <param argument="-min_peptide_length" type="integer" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
120 <param argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/> 120 <param argument="-max_peptide_length" type="integer" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
121 <param argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/> 121 <param argument="-num_hits" type="integer" value="1" label="Number of peptide hits (PSMs) per spectrum in output file" help=""/>
122 <param argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help=""> 122 <param argument="-precursor_charge" type="text" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
123 <expand macro="list_string_san" name="precursor_charge"/> 123 <expand macro="list_string_san" name="precursor_charge"/>
124 </param> 124 </param>
125 <param argument="-override_charge" type="select" optional="true" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range"> 125 <param argument="-override_charge" type="select" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
126 <option value="keep any known">keep any known</option> 126 <option value="keep any known">keep any known</option>
127 <option value="ignore known">ignore known</option> 127 <option value="ignore known">ignore known</option>
128 <option value="ignore outside range">ignore outside range</option> 128 <option value="ignore outside range">ignore outside range</option>
129 <option value="keep known search unknown" selected="true">keep known search unknown</option> 129 <option value="keep known search unknown" selected="true">keep known search unknown</option>
130 <expand macro="list_string_san" name="override_charge"/> 130 <expand macro="list_string_san" name="override_charge"/>
131 </param> 131 </param>
132 <param argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/> 132 <param argument="-ms_level" type="integer" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
133 <param argument="-activation_method" type="select" optional="true" label="If not ALL, only searches spectra of the given method" help=""> 133 <param argument="-activation_method" type="select" label="If not ALL, only searches spectra of the given method" help="">
134 <option value="ALL" selected="true">ALL</option> 134 <option value="ALL" selected="true">ALL</option>
135 <option value="CID">CID</option> 135 <option value="CID">CID</option>
136 <option value="ECD">ECD</option> 136 <option value="ECD">ECD</option>
137 <option value="ETD">ETD</option> 137 <option value="ETD">ETD</option>
138 <option value="PQD">PQD</option> 138 <option value="PQD">PQD</option>
139 <option value="HCD">HCD</option> 139 <option value="HCD">HCD</option>
140 <option value="IRMPD">IRMPD</option> 140 <option value="IRMPD">IRMPD</option>
141 <expand macro="list_string_san" name="activation_method"/> 141 <expand macro="list_string_san" name="activation_method"/>
142 </param> 142 </param>
143 <param argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/> 143 <param argument="-max_fragment_charge" type="integer" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
144 <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/> 144 <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/>
145 <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 145 <param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
146 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 146 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
147 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 147 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
148 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 148 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
149 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 149 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
150 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 150 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
151 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 151 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
152 <option value="2-succinyl (C)">2-succinyl (C)</option> 152 <option value="2-succinyl (C)">2-succinyl (C)</option>
153 <option value="2HPG (R)">2HPG (R)</option> 153 <option value="2HPG (R)">2HPG (R)</option>
154 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 154 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
155 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
156 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
157 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
158 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
155 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 159 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
156 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 160 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
157 <option value="4-ONE (C)">4-ONE (C)</option> 161 <option value="4-ONE (C)">4-ONE (C)</option>
158 <option value="4-ONE (H)">4-ONE (H)</option> 162 <option value="4-ONE (H)">4-ONE (H)</option>
159 <option value="4-ONE (K)">4-ONE (K)</option> 163 <option value="4-ONE (K)">4-ONE (K)</option>
239 <option value="Ammonium (D)">Ammonium (D)</option> 243 <option value="Ammonium (D)">Ammonium (D)</option>
240 <option value="Ammonium (E)">Ammonium (E)</option> 244 <option value="Ammonium (E)">Ammonium (E)</option>
241 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 245 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
242 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 246 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
243 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 247 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
248 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
244 <option value="Archaeol (C)">Archaeol (C)</option> 249 <option value="Archaeol (C)">Archaeol (C)</option>
245 <option value="Arg (N-term)">Arg (N-term)</option> 250 <option value="Arg (N-term)">Arg (N-term)</option>
246 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 251 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
247 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 252 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
248 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 253 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
342 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 347 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
343 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 348 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
344 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 349 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
345 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 350 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
346 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 351 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
352 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
347 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 353 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
348 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 354 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
349 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 355 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
350 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 356 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
351 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 357 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
374 <option value="BITC (C)">BITC (C)</option> 380 <option value="BITC (C)">BITC (C)</option>
375 <option value="BITC (K)">BITC (K)</option> 381 <option value="BITC (K)">BITC (K)</option>
376 <option value="BITC (N-term)">BITC (N-term)</option> 382 <option value="BITC (N-term)">BITC (N-term)</option>
377 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 383 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
378 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 384 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
379 <option value="Bodipy (C)">Bodipy (C)</option>
380 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 385 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
381 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 386 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
382 <option value="Bromo (F)">Bromo (F)</option> 387 <option value="Bromo (F)">Bromo (F)</option>
383 <option value="Bromo (H)">Bromo (H)</option> 388 <option value="Bromo (H)">Bromo (H)</option>
384 <option value="Bromo (W)">Bromo (W)</option> 389 <option value="Bromo (W)">Bromo (W)</option>
806 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 811 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
807 <option value="Dehydrated (S)">Dehydrated (S)</option> 812 <option value="Dehydrated (S)">Dehydrated (S)</option>
808 <option value="Dehydrated (T)">Dehydrated (T)</option> 813 <option value="Dehydrated (T)">Dehydrated (T)</option>
809 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 814 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
810 <option value="Dehydro (C)">Dehydro (C)</option> 815 <option value="Dehydro (C)">Dehydro (C)</option>
816 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
811 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 817 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
812 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 818 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
813 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
814 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 819 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
815 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 820 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
816 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 821 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
817 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 822 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
818 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 823 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
819 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 824 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
820 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 825 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
821 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 826 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
822 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 827 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
823 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
824 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 828 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
825 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 829 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
826 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 830 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
827 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 831 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
828 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 832 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
830 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 834 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
831 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 835 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
832 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 836 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
833 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 837 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
834 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 838 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
839 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
835 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 840 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
836 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 841 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
837 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 842 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
838 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 843 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
839 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 844 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
1402 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 1407 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
1403 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 1408 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
1404 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 1409 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
1405 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 1410 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
1406 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 1411 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
1407 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
1408 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 1412 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
1409 <option value="Ethyl (D)">Ethyl (D)</option> 1413 <option value="Ethyl (D)">Ethyl (D)</option>
1410 <option value="Ethyl (E)">Ethyl (E)</option> 1414 <option value="Ethyl (E)">Ethyl (E)</option>
1411 <option value="Ethyl (K)">Ethyl (K)</option> 1415 <option value="Ethyl (K)">Ethyl (K)</option>
1412 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 1416 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
1496 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 1500 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
1497 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 1501 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
1498 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 1502 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
1499 <option value="Glu (E)">Glu (E)</option> 1503 <option value="Glu (E)">Glu (E)</option>
1500 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 1504 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
1505 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
1501 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 1506 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
1502 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 1507 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
1503 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 1508 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
1504 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 1509 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
1505 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 1510 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
1510 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1515 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1511 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1516 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1512 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1517 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1513 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1518 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1514 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1519 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1515 <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>
1516 <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> 1520 <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>
1517 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1521 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1518 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1522 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
1519 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 1523 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
1520 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 1524 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
1534 <option value="Gluratylation (K)">Gluratylation (K)</option> 1538 <option value="Gluratylation (K)">Gluratylation (K)</option>
1535 <option value="Glutathione (C)">Glutathione (C)</option> 1539 <option value="Glutathione (C)">Glutathione (C)</option>
1536 <option value="Gly (K)">Gly (K)</option> 1540 <option value="Gly (K)">Gly (K)</option>
1537 <option value="Gly (S)">Gly (S)</option> 1541 <option value="Gly (S)">Gly (S)</option>
1538 <option value="Gly (T)">Gly (T)</option> 1542 <option value="Gly (T)">Gly (T)</option>
1543 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
1539 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 1544 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
1540 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 1545 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
1541 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 1546 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
1542 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 1547 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
1543 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 1548 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
1924 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 1929 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
1925 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 1930 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
1926 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 1931 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
1927 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 1932 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
1928 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 1933 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
1934 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
1929 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 1935 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
1930 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 1936 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
1931 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 1937 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
1932 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 1938 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
1933 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 1939 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
1935 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 1941 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
1936 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 1942 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
1937 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 1943 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
1938 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 1944 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
1939 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 1945 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
1946 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
1947 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
1948 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
1940 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 1949 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
1941 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 1950 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
1942 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 1951 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
1943 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 1952 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
1944 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 1953 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
1990 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 1999 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
1991 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 2000 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
1992 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 2001 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
1993 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 2002 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
1994 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 2003 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
2004 <option value="His+O(2) (H)">His+O(2) (H)</option>
1995 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 2005 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
1996 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 2006 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
1997 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 2007 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
1998 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 2008 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
1999 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 2009 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
2127 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 2137 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
2128 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 2138 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
2129 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 2139 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
2130 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 2140 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
2131 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 2141 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
2142 <option value="Kdo (S)">Kdo (S)</option>
2143 <option value="Kdo (T)">Kdo (T)</option>
2132 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 2144 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
2133 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 2145 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
2134 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 2146 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
2135 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 2147 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
2136 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 2148 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
2149 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
2137 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 2150 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
2138 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 2151 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
2139 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 2152 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
2140 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 2153 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
2141 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 2154 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
2216 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 2229 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
2217 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 2230 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
2218 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 2231 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
2219 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 2232 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
2220 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 2233 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
2234 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
2221 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 2235 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
2222 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 2236 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
2223 <option value="Lipoyl (K)">Lipoyl (K)</option> 2237 <option value="Lipoyl (K)">Lipoyl (K)</option>
2224 <option value="LRGG (K)">LRGG (K)</option> 2238 <option value="LRGG (K)">LRGG (K)</option>
2225 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 2239 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
2226 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 2240 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
2241 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
2227 <option value="Lys (N-term)">Lys (N-term)</option> 2242 <option value="Lys (N-term)">Lys (N-term)</option>
2243 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
2228 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 2244 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
2229 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 2245 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
2230 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 2246 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
2231 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 2247 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
2232 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 2248 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
2257 <option value="maleimide5 (C)">maleimide5 (C)</option> 2273 <option value="maleimide5 (C)">maleimide5 (C)</option>
2258 <option value="maleimide5 (K)">maleimide5 (K)</option> 2274 <option value="maleimide5 (K)">maleimide5 (K)</option>
2259 <option value="Malonyl (C)">Malonyl (C)</option> 2275 <option value="Malonyl (C)">Malonyl (C)</option>
2260 <option value="Malonyl (K)">Malonyl (K)</option> 2276 <option value="Malonyl (K)">Malonyl (K)</option>
2261 <option value="Malonyl (S)">Malonyl (S)</option> 2277 <option value="Malonyl (S)">Malonyl (S)</option>
2278 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
2262 <option value="MDCC (C)">MDCC (C)</option> 2279 <option value="MDCC (C)">MDCC (C)</option>
2263 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 2280 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
2264 <option value="Menadione (C)">Menadione (C)</option> 2281 <option value="Menadione (C)">Menadione (C)</option>
2265 <option value="Menadione (K)">Menadione (K)</option> 2282 <option value="Menadione (K)">Menadione (K)</option>
2266 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 2283 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
2268 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 2285 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
2269 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 2286 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
2270 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 2287 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
2271 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 2288 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
2272 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 2289 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
2290 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
2273 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 2291 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
2274 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 2292 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
2275 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 2293 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
2276 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 2294 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
2277 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 2295 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
2451 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 2469 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
2452 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 2470 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
2453 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 2471 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
2454 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 2472 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
2455 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 2473 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
2456 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
2457 <option value="NP40 (N-term)">NP40 (N-term)</option> 2474 <option value="NP40 (N-term)">NP40 (N-term)</option>
2458 <option value="NQIGG (K)">NQIGG (K)</option> 2475 <option value="NQIGG (K)">NQIGG (K)</option>
2459 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 2476 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
2460 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 2477 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
2461 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 2478 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
2539 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 2556 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
2540 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 2557 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
2541 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 2558 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
2542 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 2559 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
2543 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 2560 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
2561 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
2562 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
2563 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
2564 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
2544 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 2565 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
2545 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 2566 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
2546 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 2567 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
2547 <option value="Phospho (C)">Phospho (C)</option> 2568 <option value="Phospho (C)">Phospho (C)</option>
2548 <option value="Phospho (D)">Phospho (D)</option> 2569 <option value="Phospho (D)">Phospho (D)</option>
2553 <option value="Phospho (S)">Phospho (S)</option> 2574 <option value="Phospho (S)">Phospho (S)</option>
2554 <option value="Phospho (T)">Phospho (T)</option> 2575 <option value="Phospho (T)">Phospho (T)</option>
2555 <option value="Phospho (Y)">Phospho (Y)</option> 2576 <option value="Phospho (Y)">Phospho (Y)</option>
2556 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 2577 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
2557 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 2578 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
2579 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
2558 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 2580 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
2559 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 2581 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
2560 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 2582 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
2561 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 2583 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
2562 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 2584 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
2584 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 2606 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
2585 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 2607 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
2586 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 2608 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
2587 <option value="Piperidine (K)">Piperidine (K)</option> 2609 <option value="Piperidine (K)">Piperidine (K)</option>
2588 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 2610 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
2611 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
2589 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 2612 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
2590 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 2613 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
2591 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 2614 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
2592 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 2615 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
2593 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 2616 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
2661 <option value="QEQTGG (K)">QEQTGG (K)</option> 2684 <option value="QEQTGG (K)">QEQTGG (K)</option>
2662 <option value="QQQTGG (K)">QQQTGG (K)</option> 2685 <option value="QQQTGG (K)">QQQTGG (K)</option>
2663 <option value="QTGG (K)">QTGG (K)</option> 2686 <option value="QTGG (K)">QTGG (K)</option>
2664 <option value="Quinone (W)">Quinone (W)</option> 2687 <option value="Quinone (W)">Quinone (W)</option>
2665 <option value="Quinone (Y)">Quinone (Y)</option> 2688 <option value="Quinone (Y)">Quinone (Y)</option>
2689 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
2690 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
2691 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
2692 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
2693 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
2694 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
2695 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
2696 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
2697 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
2698 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
2699 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
2700 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
2701 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
2702 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
2703 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
2704 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
2705 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
2706 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
2707 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
2708 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
2666 <option value="Retinylidene (K)">Retinylidene (K)</option> 2709 <option value="Retinylidene (K)">Retinylidene (K)</option>
2667 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 2710 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
2668 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 2711 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
2669 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 2712 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
2670 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
2671 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
2672 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
2673 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
2674 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
2675 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
2676 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
2677 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
2678 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 2713 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
2679 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 2714 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
2680 <option value="Saligenin (H)">Saligenin (H)</option> 2715 <option value="Saligenin (H)">Saligenin (H)</option>
2681 <option value="Saligenin (K)">Saligenin (K)</option> 2716 <option value="Saligenin (K)">Saligenin (K)</option>
2682 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 2717 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
2700 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 2735 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
2701 <option value="serotonylation (Q)">serotonylation (Q)</option> 2736 <option value="serotonylation (Q)">serotonylation (Q)</option>
2702 <option value="shTMT (K)">shTMT (K)</option> 2737 <option value="shTMT (K)">shTMT (K)</option>
2703 <option value="shTMT (N-term)">shTMT (N-term)</option> 2738 <option value="shTMT (N-term)">shTMT (N-term)</option>
2704 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 2739 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
2740 <option value="shTMTpro (K)">shTMTpro (K)</option>
2741 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
2742 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
2705 <option value="SMA (K)">SMA (K)</option> 2743 <option value="SMA (K)">SMA (K)</option>
2706 <option value="SMA (N-term)">SMA (N-term)</option> 2744 <option value="SMA (N-term)">SMA (N-term)</option>
2707 <option value="spermidine (Q)">spermidine (Q)</option> 2745 <option value="spermidine (Q)">spermidine (Q)</option>
2708 <option value="spermine (Q)">spermine (Q)</option> 2746 <option value="spermine (Q)">spermine (Q)</option>
2709 <option value="SPITC (K)">SPITC (K)</option> 2747 <option value="SPITC (K)">SPITC (K)</option>
2875 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 2913 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
2876 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 2914 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
2877 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 2915 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
2878 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 2916 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
2879 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 2917 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
2880 <option value="Ub-amide (C)">Ub-amide (C)</option>
2881 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 2918 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
2882 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 2919 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
2883 <option value="Ub-VME (C)">Ub-VME (C)</option> 2920 <option value="Ub-VME (C)">Ub-VME (C)</option>
2884 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 2921 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
2885 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 2922 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
3070 <option value="ZGB (K)">ZGB (K)</option> 3107 <option value="ZGB (K)">ZGB (K)</option>
3071 <option value="ZGB (N-term)">ZGB (N-term)</option> 3108 <option value="ZGB (N-term)">ZGB (N-term)</option>
3072 <option value="ZQG (K)">ZQG (K)</option> 3109 <option value="ZQG (K)">ZQG (K)</option>
3073 <expand macro="list_string_san" name="fixed_modifications"/> 3110 <expand macro="list_string_san" name="fixed_modifications"/>
3074 </param> 3111 </param>
3075 <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 3112 <param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
3076 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3113 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3077 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3114 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3078 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3115 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3079 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3116 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3080 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3117 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
3081 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 3118 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
3082 <option value="2-succinyl (C)">2-succinyl (C)</option> 3119 <option value="2-succinyl (C)">2-succinyl (C)</option>
3083 <option value="2HPG (R)">2HPG (R)</option> 3120 <option value="2HPG (R)">2HPG (R)</option>
3084 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 3121 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
3122 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
3123 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
3124 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
3125 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
3085 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 3126 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
3086 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 3127 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
3087 <option value="4-ONE (C)">4-ONE (C)</option> 3128 <option value="4-ONE (C)">4-ONE (C)</option>
3088 <option value="4-ONE (H)">4-ONE (H)</option> 3129 <option value="4-ONE (H)">4-ONE (H)</option>
3089 <option value="4-ONE (K)">4-ONE (K)</option> 3130 <option value="4-ONE (K)">4-ONE (K)</option>
3169 <option value="Ammonium (D)">Ammonium (D)</option> 3210 <option value="Ammonium (D)">Ammonium (D)</option>
3170 <option value="Ammonium (E)">Ammonium (E)</option> 3211 <option value="Ammonium (E)">Ammonium (E)</option>
3171 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 3212 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
3172 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 3213 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
3173 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 3214 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
3215 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
3174 <option value="Archaeol (C)">Archaeol (C)</option> 3216 <option value="Archaeol (C)">Archaeol (C)</option>
3175 <option value="Arg (N-term)">Arg (N-term)</option> 3217 <option value="Arg (N-term)">Arg (N-term)</option>
3176 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 3218 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
3177 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 3219 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
3178 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 3220 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
3272 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 3314 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
3273 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 3315 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
3274 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 3316 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
3275 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 3317 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
3276 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 3318 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
3319 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
3277 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 3320 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
3278 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 3321 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
3279 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 3322 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
3280 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 3323 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
3281 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 3324 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
3304 <option value="BITC (C)">BITC (C)</option> 3347 <option value="BITC (C)">BITC (C)</option>
3305 <option value="BITC (K)">BITC (K)</option> 3348 <option value="BITC (K)">BITC (K)</option>
3306 <option value="BITC (N-term)">BITC (N-term)</option> 3349 <option value="BITC (N-term)">BITC (N-term)</option>
3307 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 3350 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
3308 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 3351 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
3309 <option value="Bodipy (C)">Bodipy (C)</option>
3310 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 3352 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
3311 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 3353 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
3312 <option value="Bromo (F)">Bromo (F)</option> 3354 <option value="Bromo (F)">Bromo (F)</option>
3313 <option value="Bromo (H)">Bromo (H)</option> 3355 <option value="Bromo (H)">Bromo (H)</option>
3314 <option value="Bromo (W)">Bromo (W)</option> 3356 <option value="Bromo (W)">Bromo (W)</option>
3736 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 3778 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
3737 <option value="Dehydrated (S)">Dehydrated (S)</option> 3779 <option value="Dehydrated (S)">Dehydrated (S)</option>
3738 <option value="Dehydrated (T)">Dehydrated (T)</option> 3780 <option value="Dehydrated (T)">Dehydrated (T)</option>
3739 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 3781 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
3740 <option value="Dehydro (C)">Dehydro (C)</option> 3782 <option value="Dehydro (C)">Dehydro (C)</option>
3783 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
3741 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 3784 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
3742 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 3785 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
3743 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
3744 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 3786 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
3745 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 3787 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
3746 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 3788 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
3747 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 3789 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
3748 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 3790 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
3749 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 3791 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
3750 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 3792 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
3751 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 3793 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
3752 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 3794 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
3753 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
3754 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 3795 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
3755 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 3796 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
3756 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 3797 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
3757 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 3798 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
3758 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 3799 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
3760 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 3801 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
3761 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 3802 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
3762 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 3803 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
3763 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 3804 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
3764 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 3805 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
3806 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
3765 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 3807 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
3766 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 3808 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
3767 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 3809 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
3768 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 3810 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
3769 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 3811 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
4332 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 4374 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
4333 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 4375 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
4334 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 4376 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
4335 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 4377 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
4336 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 4378 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
4337 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
4338 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 4379 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
4339 <option value="Ethyl (D)">Ethyl (D)</option> 4380 <option value="Ethyl (D)">Ethyl (D)</option>
4340 <option value="Ethyl (E)">Ethyl (E)</option> 4381 <option value="Ethyl (E)">Ethyl (E)</option>
4341 <option value="Ethyl (K)">Ethyl (K)</option> 4382 <option value="Ethyl (K)">Ethyl (K)</option>
4342 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 4383 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
4426 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 4467 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
4427 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 4468 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
4428 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 4469 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
4429 <option value="Glu (E)">Glu (E)</option> 4470 <option value="Glu (E)">Glu (E)</option>
4430 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 4471 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
4472 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
4431 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 4473 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
4432 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 4474 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
4433 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 4475 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
4434 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 4476 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
4435 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 4477 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
4440 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4482 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4441 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4483 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4442 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4484 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4443 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4485 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4444 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4486 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4445 <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>
4446 <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> 4487 <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>
4447 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4488 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4448 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4489 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
4449 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 4490 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
4450 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 4491 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
4464 <option value="Gluratylation (K)">Gluratylation (K)</option> 4505 <option value="Gluratylation (K)">Gluratylation (K)</option>
4465 <option value="Glutathione (C)">Glutathione (C)</option> 4506 <option value="Glutathione (C)">Glutathione (C)</option>
4466 <option value="Gly (K)">Gly (K)</option> 4507 <option value="Gly (K)">Gly (K)</option>
4467 <option value="Gly (S)">Gly (S)</option> 4508 <option value="Gly (S)">Gly (S)</option>
4468 <option value="Gly (T)">Gly (T)</option> 4509 <option value="Gly (T)">Gly (T)</option>
4510 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
4469 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 4511 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
4470 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 4512 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
4471 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 4513 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
4472 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 4514 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
4473 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 4515 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
4854 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 4896 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
4855 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 4897 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
4856 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 4898 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
4857 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 4899 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
4858 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 4900 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
4901 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
4859 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 4902 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
4860 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 4903 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
4861 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 4904 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
4862 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 4905 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
4863 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 4906 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
4865 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 4908 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
4866 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 4909 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
4867 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 4910 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
4868 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 4911 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
4869 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 4912 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
4913 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
4914 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
4915 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
4870 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 4916 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
4871 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 4917 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
4872 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 4918 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
4873 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 4919 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
4874 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 4920 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
4920 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 4966 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
4921 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 4967 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
4922 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 4968 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
4923 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 4969 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
4924 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 4970 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
4971 <option value="His+O(2) (H)">His+O(2) (H)</option>
4925 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 4972 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
4926 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 4973 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
4927 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 4974 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
4928 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 4975 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
4929 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 4976 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
5057 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 5104 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
5058 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 5105 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
5059 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 5106 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
5060 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 5107 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
5061 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 5108 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
5109 <option value="Kdo (S)">Kdo (S)</option>
5110 <option value="Kdo (T)">Kdo (T)</option>
5062 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 5111 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
5063 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 5112 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
5064 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 5113 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
5065 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 5114 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
5066 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 5115 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
5116 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
5067 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 5117 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
5068 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 5118 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
5069 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 5119 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
5070 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 5120 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
5071 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 5121 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
5146 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 5196 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
5147 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 5197 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
5148 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 5198 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
5149 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 5199 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
5150 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 5200 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
5201 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
5151 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 5202 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
5152 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 5203 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
5153 <option value="Lipoyl (K)">Lipoyl (K)</option> 5204 <option value="Lipoyl (K)">Lipoyl (K)</option>
5154 <option value="LRGG (K)">LRGG (K)</option> 5205 <option value="LRGG (K)">LRGG (K)</option>
5155 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 5206 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
5156 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 5207 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
5208 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
5157 <option value="Lys (N-term)">Lys (N-term)</option> 5209 <option value="Lys (N-term)">Lys (N-term)</option>
5210 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
5158 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 5211 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
5159 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 5212 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
5160 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 5213 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
5161 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 5214 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
5162 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 5215 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
5187 <option value="maleimide5 (C)">maleimide5 (C)</option> 5240 <option value="maleimide5 (C)">maleimide5 (C)</option>
5188 <option value="maleimide5 (K)">maleimide5 (K)</option> 5241 <option value="maleimide5 (K)">maleimide5 (K)</option>
5189 <option value="Malonyl (C)">Malonyl (C)</option> 5242 <option value="Malonyl (C)">Malonyl (C)</option>
5190 <option value="Malonyl (K)">Malonyl (K)</option> 5243 <option value="Malonyl (K)">Malonyl (K)</option>
5191 <option value="Malonyl (S)">Malonyl (S)</option> 5244 <option value="Malonyl (S)">Malonyl (S)</option>
5245 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
5192 <option value="MDCC (C)">MDCC (C)</option> 5246 <option value="MDCC (C)">MDCC (C)</option>
5193 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 5247 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
5194 <option value="Menadione (C)">Menadione (C)</option> 5248 <option value="Menadione (C)">Menadione (C)</option>
5195 <option value="Menadione (K)">Menadione (K)</option> 5249 <option value="Menadione (K)">Menadione (K)</option>
5196 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 5250 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
5198 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 5252 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
5199 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 5253 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
5200 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 5254 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
5201 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 5255 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
5202 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 5256 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
5257 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
5203 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 5258 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
5204 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 5259 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
5205 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 5260 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
5206 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 5261 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
5207 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 5262 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
5381 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 5436 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
5382 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 5437 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
5383 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 5438 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
5384 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 5439 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
5385 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 5440 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
5386 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
5387 <option value="NP40 (N-term)">NP40 (N-term)</option> 5441 <option value="NP40 (N-term)">NP40 (N-term)</option>
5388 <option value="NQIGG (K)">NQIGG (K)</option> 5442 <option value="NQIGG (K)">NQIGG (K)</option>
5389 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 5443 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
5390 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 5444 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
5391 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 5445 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
5469 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 5523 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
5470 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 5524 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
5471 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 5525 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
5472 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 5526 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
5473 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 5527 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
5528 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
5529 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
5530 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
5531 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
5474 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 5532 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
5475 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 5533 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
5476 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 5534 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
5477 <option value="Phospho (C)">Phospho (C)</option> 5535 <option value="Phospho (C)">Phospho (C)</option>
5478 <option value="Phospho (D)">Phospho (D)</option> 5536 <option value="Phospho (D)">Phospho (D)</option>
5483 <option value="Phospho (S)">Phospho (S)</option> 5541 <option value="Phospho (S)">Phospho (S)</option>
5484 <option value="Phospho (T)">Phospho (T)</option> 5542 <option value="Phospho (T)">Phospho (T)</option>
5485 <option value="Phospho (Y)">Phospho (Y)</option> 5543 <option value="Phospho (Y)">Phospho (Y)</option>
5486 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 5544 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
5487 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 5545 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
5546 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
5488 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 5547 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
5489 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 5548 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
5490 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 5549 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
5491 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 5550 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
5492 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 5551 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
5514 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 5573 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
5515 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 5574 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
5516 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 5575 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
5517 <option value="Piperidine (K)">Piperidine (K)</option> 5576 <option value="Piperidine (K)">Piperidine (K)</option>
5518 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 5577 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
5578 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
5519 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 5579 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
5520 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 5580 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
5521 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 5581 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
5522 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 5582 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
5523 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 5583 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
5591 <option value="QEQTGG (K)">QEQTGG (K)</option> 5651 <option value="QEQTGG (K)">QEQTGG (K)</option>
5592 <option value="QQQTGG (K)">QQQTGG (K)</option> 5652 <option value="QQQTGG (K)">QQQTGG (K)</option>
5593 <option value="QTGG (K)">QTGG (K)</option> 5653 <option value="QTGG (K)">QTGG (K)</option>
5594 <option value="Quinone (W)">Quinone (W)</option> 5654 <option value="Quinone (W)">Quinone (W)</option>
5595 <option value="Quinone (Y)">Quinone (Y)</option> 5655 <option value="Quinone (Y)">Quinone (Y)</option>
5656 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
5657 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
5658 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
5659 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
5660 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
5661 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
5662 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
5663 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
5664 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
5665 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
5666 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
5667 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
5668 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
5669 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
5670 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
5671 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
5672 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
5673 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
5674 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
5675 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
5596 <option value="Retinylidene (K)">Retinylidene (K)</option> 5676 <option value="Retinylidene (K)">Retinylidene (K)</option>
5597 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 5677 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
5598 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 5678 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
5599 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 5679 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
5600 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
5601 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
5602 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
5603 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
5604 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
5605 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
5606 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
5607 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
5608 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 5680 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
5609 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 5681 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
5610 <option value="Saligenin (H)">Saligenin (H)</option> 5682 <option value="Saligenin (H)">Saligenin (H)</option>
5611 <option value="Saligenin (K)">Saligenin (K)</option> 5683 <option value="Saligenin (K)">Saligenin (K)</option>
5612 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 5684 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
5630 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 5702 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
5631 <option value="serotonylation (Q)">serotonylation (Q)</option> 5703 <option value="serotonylation (Q)">serotonylation (Q)</option>
5632 <option value="shTMT (K)">shTMT (K)</option> 5704 <option value="shTMT (K)">shTMT (K)</option>
5633 <option value="shTMT (N-term)">shTMT (N-term)</option> 5705 <option value="shTMT (N-term)">shTMT (N-term)</option>
5634 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 5706 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
5707 <option value="shTMTpro (K)">shTMTpro (K)</option>
5708 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
5709 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
5635 <option value="SMA (K)">SMA (K)</option> 5710 <option value="SMA (K)">SMA (K)</option>
5636 <option value="SMA (N-term)">SMA (N-term)</option> 5711 <option value="SMA (N-term)">SMA (N-term)</option>
5637 <option value="spermidine (Q)">spermidine (Q)</option> 5712 <option value="spermidine (Q)">spermidine (Q)</option>
5638 <option value="spermine (Q)">spermine (Q)</option> 5713 <option value="spermine (Q)">spermine (Q)</option>
5639 <option value="SPITC (K)">SPITC (K)</option> 5714 <option value="SPITC (K)">SPITC (K)</option>
5805 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 5880 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
5806 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 5881 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
5807 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 5882 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
5808 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 5883 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
5809 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 5884 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
5810 <option value="Ub-amide (C)">Ub-amide (C)</option>
5811 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 5885 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
5812 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 5886 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
5813 <option value="Ub-VME (C)">Ub-VME (C)</option> 5887 <option value="Ub-VME (C)">Ub-VME (C)</option>
5814 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 5888 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
5815 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 5889 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
6008 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/> 6082 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
6009 <section name="PeptideIndexing" title="" help="" expanded="false"> 6083 <section name="PeptideIndexing" title="" help="" expanded="false">
6010 <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> 6084 <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
6011 <expand macro="list_string_san" name="decoy_string"/> 6085 <expand macro="list_string_san" name="decoy_string"/>
6012 </param> 6086 </param>
6013 <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> 6087 <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
6014 <option value="prefix" selected="true">prefix</option> 6088 <option value="prefix" selected="true">prefix</option>
6015 <option value="suffix">suffix</option> 6089 <option value="suffix">suffix</option>
6016 <expand macro="list_string_san" name="decoy_string_position"/> 6090 <expand macro="list_string_san" name="decoy_string_position"/>
6017 </param> 6091 </param>
6018 <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> 6092 <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
6019 <option value="error">error</option> 6093 <option value="error">error</option>
6020 <option value="warn" selected="true">warn</option> 6094 <option value="warn" selected="true">warn</option>
6021 <option value="silent">silent</option> 6095 <option value="silent">silent</option>
6022 <expand macro="list_string_san" name="missing_decoy_action"/> 6096 <expand macro="list_string_san" name="missing_decoy_action"/>
6023 </param> 6097 </param>
6024 <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> 6098 <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
6025 <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> 6099 <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
6026 <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> 6100 <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
6027 <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> 6101 <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
6028 <option value="error" selected="true">error</option> 6102 <option value="error" selected="true">error</option>
6029 <option value="warn">warn</option> 6103 <option value="warn">warn</option>
6030 <option value="remove">remove</option> 6104 <option value="remove">remove</option>
6031 <expand macro="list_string_san" name="unmatched_action"/> 6105 <expand macro="list_string_san" name="unmatched_action"/>
6032 </param> 6106 </param>
6033 <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> 6107 <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
6034 <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> 6108 <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
6035 <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> 6109 <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
6110 <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
6036 <section name="enzyme" title="" help="" expanded="false"> 6111 <section name="enzyme" title="" help="" expanded="false">
6037 <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> 6112 <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
6038 <option value="auto" selected="true">auto</option> 6113 <option value="auto" selected="true">auto</option>
6114 <option value="Arg-C">Arg-C</option>
6115 <option value="Arg-C/P">Arg-C/P</option>
6116 <option value="Asp-N">Asp-N</option>
6117 <option value="Asp-N/B">Asp-N/B</option>
6118 <option value="Asp-N_ambic">Asp-N_ambic</option>
6039 <option value="Trypsin">Trypsin</option> 6119 <option value="Trypsin">Trypsin</option>
6120 <option value="Chymotrypsin">Chymotrypsin</option>
6121 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6122 <option value="CNBr">CNBr</option>
6123 <option value="Formic_acid">Formic_acid</option>
6040 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 6124 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6041 <option value="Glu-C+P">Glu-C+P</option> 6125 <option value="Glu-C+P">Glu-C+P</option>
6042 <option value="PepsinA + P">PepsinA + P</option> 6126 <option value="PepsinA + P">PepsinA + P</option>
6043 <option value="cyanogen-bromide">cyanogen-bromide</option> 6127 <option value="cyanogen-bromide">cyanogen-bromide</option>
6044 <option value="Clostripain/P">Clostripain/P</option> 6128 <option value="Clostripain/P">Clostripain/P</option>
6045 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 6129 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6046 <option value="no cleavage">no cleavage</option> 6130 <option value="no cleavage">no cleavage</option>
6131 <option value="unspecific cleavage">unspecific cleavage</option>
6132 <option value="TrypChymo">TrypChymo</option>
6133 <option value="Trypsin/P">Trypsin/P</option>
6134 <option value="V8-DE">V8-DE</option>
6135 <option value="V8-E">V8-E</option>
6136 <option value="leukocyte elastase">leukocyte elastase</option>
6047 <option value="proline endopeptidase">proline endopeptidase</option> 6137 <option value="proline endopeptidase">proline endopeptidase</option>
6048 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 6138 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6049 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 6139 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6050 <option value="2-iodobenzoate">2-iodobenzoate</option> 6140 <option value="2-iodobenzoate">2-iodobenzoate</option>
6051 <option value="iodosobenzoate">iodosobenzoate</option> 6141 <option value="iodosobenzoate">iodosobenzoate</option>
6052 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 6142 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6053 <option value="Trypsin/P">Trypsin/P</option> 6143 <option value="Lys-C">Lys-C</option>
6054 <option value="V8-DE">V8-DE</option>
6055 <option value="V8-E">V8-E</option>
6056 <option value="leukocyte elastase">leukocyte elastase</option>
6057 <option value="PepsinA">PepsinA</option>
6058 <option value="TrypChymo">TrypChymo</option>
6059 <option value="Asp-N">Asp-N</option>
6060 <option value="unspecific cleavage">unspecific cleavage</option>
6061 <option value="Asp-N/B">Asp-N/B</option>
6062 <option value="Asp-N_ambic">Asp-N_ambic</option>
6063 <option value="Chymotrypsin">Chymotrypsin</option>
6064 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6065 <option value="CNBr">CNBr</option>
6066 <option value="Arg-C/P">Arg-C/P</option>
6067 <option value="Lys-N">Lys-N</option> 6144 <option value="Lys-N">Lys-N</option>
6068 <option value="Lys-C/P">Lys-C/P</option> 6145 <option value="Lys-C/P">Lys-C/P</option>
6069 <option value="Formic_acid">Formic_acid</option> 6146 <option value="PepsinA">PepsinA</option>
6070 <option value="Lys-C">Lys-C</option>
6071 <option value="Arg-C">Arg-C</option>
6072 <expand macro="list_string_san" name="name"/> 6147 <expand macro="list_string_san" name="name"/>
6073 </param> 6148 </param>
6074 <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> 6149 <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
6075 <option value="auto" selected="true">auto</option> 6150 <option value="auto" selected="true">auto</option>
6076 <option value="full">full</option> 6151 <option value="full">full</option>
6077 <option value="semi">semi</option> 6152 <option value="semi">semi</option>
6078 <option value="none">none</option> 6153 <option value="none">none</option>
6079 <expand macro="list_string_san" name="specificity"/> 6154 <expand macro="list_string_san" name="specificity"/>
6087 <param argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/> 6162 <param argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/>
6088 <param argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/> 6163 <param argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/>
6089 <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/> 6164 <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/>
6090 <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/> 6165 <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/>
6091 <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help=""> 6166 <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help="">
6167 <option value="Asp-N">Asp-N</option>
6168 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6169 <option value="Trypsin">Trypsin</option>
6170 <option value="Arg-C">Arg-C</option>
6171 <option value="no cleavage">no cleavage</option>
6172 <option value="unspecific cleavage">unspecific cleavage</option>
6173 <option value="Chymotrypsin">Chymotrypsin</option>
6092 <option value="CNBr">CNBr</option> 6174 <option value="CNBr">CNBr</option>
6093 <option value="Lys-C">Lys-C</option> 6175 <option value="Lys-C">Lys-C</option>
6094 <option value="Trypsin">Trypsin</option>
6095 <option value="Arg-C">Arg-C</option>
6096 <option value="Chymotrypsin">Chymotrypsin</option>
6097 <option value="Asp-N">Asp-N</option>
6098 <option value="unspecific cleavage">unspecific cleavage</option>
6099 <option value="Lys-N">Lys-N</option> 6176 <option value="Lys-N">Lys-N</option>
6100 <option value="PepsinA">PepsinA</option> 6177 <option value="PepsinA">PepsinA</option>
6101 <option value="Trypsin/P">Trypsin/P</option> 6178 <option value="Trypsin/P">Trypsin/P</option>
6102 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6103 <expand macro="list_string_san" name="second_enzyme"/> 6179 <expand macro="list_string_san" name="second_enzyme"/>
6104 </param> 6180 </param>
6105 <param argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help=""> 6181 <param argument="-digest_mass_range" type="text" value="600:5000" label="MH+ peptide mass range to analyze" help="">
6106 <expand macro="list_string_san" name="digest_mass_range"/> 6182 <expand macro="list_string_san" name="digest_mass_range"/>
6107 </param> 6183 </param>
6108 <param argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/> 6184 <param argument="-max_precursor_charge" type="integer" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
6109 <param argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/> 6185 <param argument="-spectrum_batch_size" type="integer" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
6110 <param argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6186 <param argument="-mass_offsets" type="text" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6111 <expand macro="list_float_valsan" name="mass_offsets"/> 6187 <expand macro="list_float_valsan" name="mass_offsets"/>
6112 </param> 6188 </param>
6113 <param argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/> 6189 <param argument="-minimum_peaks" type="integer" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
6114 <param argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/> 6190 <param argument="-minimum_intensity" type="float" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
6115 <param argument="-remove_precursor_peak" type="select" optional="true" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance"> 6191 <param argument="-remove_precursor_peak" type="select" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
6116 <option value="no" selected="true">no</option> 6192 <option value="no" selected="true">no</option>
6117 <option value="yes">yes</option> 6193 <option value="yes">yes</option>
6118 <option value="charge_reduced">charge_reduced</option> 6194 <option value="charge_reduced">charge_reduced</option>
6119 <option value="phosphate_loss">phosphate_loss</option> 6195 <option value="phosphate_loss">phosphate_loss</option>
6120 <expand macro="list_string_san" name="remove_precursor_peak"/> 6196 <expand macro="list_string_san" name="remove_precursor_peak"/>
6121 </param> 6197 </param>
6122 <param argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/> 6198 <param argument="-remove_precursor_tolerance" type="float" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
6123 <param argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help=""> 6199 <param argument="-clear_mz_range" type="text" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
6124 <expand macro="list_string_san" name="clear_mz_range"/> 6200 <expand macro="list_string_san" name="clear_mz_range"/>
6125 </param> 6201 </param>
6126 <param argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/> 6202 <param argument="-max_variable_mods_in_peptide" type="integer" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
6127 <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/> 6203 <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/>
6128 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6204 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6129 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6205 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
6130 <expand macro="list_string_san" name="test"/> 6206 <expand macro="list_string_san" name="test"/>
6131 </param> 6207 </param>
6132 </expand> 6208 </expand>
6133 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6209 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6134 <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option> 6210 <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option>
6142 </data> 6218 </data>
6143 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6219 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6144 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6220 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6145 </data> 6221 </data>
6146 </outputs> 6222 </outputs>
6147 <tests><!-- TOPP_CometAdapter_1 --> 6223 <tests>
6224 <!-- TOPP_CometAdapter_1 -->
6148 <test expect_num_outputs="3"> 6225 <test expect_num_outputs="3">
6149 <section name="adv_opts"> 6226 <section name="adv_opts">
6150 <param name="use_A_ions" value="false"/> 6227 <param name="use_A_ions" value="false"/>
6151 <param name="use_B_ions" value="true"/> 6228 <param name="use_B_ions" value="true"/>
6152 <param name="use_C_ions" value="false"/> 6229 <param name="use_C_ions" value="false"/>
6153 <param name="use_X_ions" value="false"/> 6230 <param name="use_X_ions" value="false"/>
6154 <param name="use_Y_ions" value="true"/> 6231 <param name="use_Y_ions" value="true"/>
6155 <param name="use_Z_ions" value="false"/> 6232 <param name="use_Z_ions" value="false"/>
6156 <param name="use_NL_ions" value="false"/> 6233 <param name="use_NL_ions" value="false"/>
6157 <param name="second_enzyme"/>
6158 <param name="digest_mass_range" value="600:5000"/> 6234 <param name="digest_mass_range" value="600:5000"/>
6159 <param name="max_precursor_charge" value="5"/> 6235 <param name="max_precursor_charge" value="5"/>
6160 <param name="spectrum_batch_size" value="1000"/> 6236 <param name="spectrum_batch_size" value="1000"/>
6161 <param name="mass_offsets" value="0.0"/> 6237 <param name="mass_offsets" value="0.0"/>
6162 <param name="minimum_peaks" value="10"/> 6238 <param name="minimum_peaks" value="10"/>
6168 <param name="require_variable_mod" value="false"/> 6244 <param name="require_variable_mod" value="false"/>
6169 <param name="force" value="true"/> 6245 <param name="force" value="true"/>
6170 <param name="test" value="true"/> 6246 <param name="test" value="true"/>
6171 </section> 6247 </section>
6172 <param name="in" value="spectra_comet.mzML"/> 6248 <param name="in" value="spectra_comet.mzML"/>
6173 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6249 <output name="out" value="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6174 <param name="database" value="proteins.fasta"/> 6250 <param name="database" value="proteins.fasta"/>
6175 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 6251 <output name="pin_out" value="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6176 <param name="precursor_mass_tolerance" value="3.0"/> 6252 <param name="precursor_mass_tolerance" value="3.0"/>
6177 <param name="precursor_error_units" value="ppm"/> 6253 <param name="precursor_error_units" value="ppm"/>
6178 <param name="isotope_error" value="off"/> 6254 <param name="isotope_error" value="off"/>
6179 <param name="fragment_mass_tolerance" value="0.50025"/> 6255 <param name="fragment_mass_tolerance" value="0.50025"/>
6180 <param name="fragment_error_units" value="Da"/> 6256 <param name="fragment_error_units" value="Da"/>
6190 <param name="override_charge" value="keep any known"/> 6266 <param name="override_charge" value="keep any known"/>
6191 <param name="ms_level" value="2"/> 6267 <param name="ms_level" value="2"/>
6192 <param name="activation_method" value="ALL"/> 6268 <param name="activation_method" value="ALL"/>
6193 <param name="max_fragment_charge" value="3"/> 6269 <param name="max_fragment_charge" value="3"/>
6194 <param name="clip_nterm_methionine" value="false"/> 6270 <param name="clip_nterm_methionine" value="false"/>
6195 <param name="fixed_modifications"/>
6196 <param name="variable_modifications"/>
6197 <param name="binary_modifications" value=""/>
6198 <param name="reindex" value="true"/> 6271 <param name="reindex" value="true"/>
6199 <section name="PeptideIndexing"> 6272 <section name="PeptideIndexing">
6200 <param name="decoy_string" value=""/> 6273 <param name="decoy_string" value=""/>
6201 <param name="decoy_string_position" value="prefix"/> 6274 <param name="decoy_string_position" value="prefix"/>
6202 <param name="missing_decoy_action" value="warn"/> 6275 <param name="missing_decoy_action" value="warn"/>
6205 <param name="keep_unreferenced_proteins" value="false"/> 6278 <param name="keep_unreferenced_proteins" value="false"/>
6206 <param name="unmatched_action" value="error"/> 6279 <param name="unmatched_action" value="error"/>
6207 <param name="aaa_max" value="3"/> 6280 <param name="aaa_max" value="3"/>
6208 <param name="mismatches_max" value="0"/> 6281 <param name="mismatches_max" value="0"/>
6209 <param name="IL_equivalent" value="false"/> 6282 <param name="IL_equivalent" value="false"/>
6283 <param name="allow_nterm_protein_cleavage" value="true"/>
6210 <section name="enzyme"> 6284 <section name="enzyme">
6211 <param name="name" value="auto"/> 6285 <param name="name" value="auto"/>
6212 <param name="specificity" value="auto"/> 6286 <param name="specificity" value="auto"/>
6213 </section> 6287 </section>
6214 </section> 6288 </section>
6216 <output name="ctd_out" ftype="xml"> 6290 <output name="ctd_out" ftype="xml">
6217 <assert_contents> 6291 <assert_contents>
6218 <is_valid_xml/> 6292 <is_valid_xml/>
6219 </assert_contents> 6293 </assert_contents>
6220 </output> 6294 </output>
6295 <assert_stdout>
6296 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6297 </assert_stdout>
6221 </test> 6298 </test>
6222 <!-- TOPP_CometAdapter_2 --> 6299 <!-- TOPP_CometAdapter_2 -->
6223 <test expect_num_outputs="3"> 6300 <test expect_num_outputs="3">
6224 <section name="adv_opts"> 6301 <section name="adv_opts">
6225 <param name="use_A_ions" value="false"/> 6302 <param name="use_A_ions" value="false"/>
6227 <param name="use_C_ions" value="false"/> 6304 <param name="use_C_ions" value="false"/>
6228 <param name="use_X_ions" value="false"/> 6305 <param name="use_X_ions" value="false"/>
6229 <param name="use_Y_ions" value="true"/> 6306 <param name="use_Y_ions" value="true"/>
6230 <param name="use_Z_ions" value="false"/> 6307 <param name="use_Z_ions" value="false"/>
6231 <param name="use_NL_ions" value="false"/> 6308 <param name="use_NL_ions" value="false"/>
6232 <param name="second_enzyme"/>
6233 <param name="digest_mass_range" value="600:5000"/> 6309 <param name="digest_mass_range" value="600:5000"/>
6234 <param name="max_precursor_charge" value="5"/> 6310 <param name="max_precursor_charge" value="5"/>
6235 <param name="spectrum_batch_size" value="1000"/> 6311 <param name="spectrum_batch_size" value="1000"/>
6236 <param name="mass_offsets" value="0.0"/> 6312 <param name="mass_offsets" value="0.0"/>
6237 <param name="minimum_peaks" value="10"/> 6313 <param name="minimum_peaks" value="10"/>
6243 <param name="require_variable_mod" value="false"/> 6319 <param name="require_variable_mod" value="false"/>
6244 <param name="force" value="true"/> 6320 <param name="force" value="true"/>
6245 <param name="test" value="true"/> 6321 <param name="test" value="true"/>
6246 </section> 6322 </section>
6247 <param name="in" value="CometAdapter_2_prepared.mzML"/> 6323 <param name="in" value="CometAdapter_2_prepared.mzML"/>
6248 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6324 <output name="out" value="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6249 <param name="database" value="CometAdapter_2_in.fasta"/> 6325 <param name="database" value="CometAdapter_2_in.fasta"/>
6250 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 6326 <output name="pin_out" value="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6251 <param name="precursor_mass_tolerance" value="3.0"/> 6327 <param name="precursor_mass_tolerance" value="3.0"/>
6252 <param name="precursor_error_units" value="Da"/> 6328 <param name="precursor_error_units" value="Da"/>
6253 <param name="isotope_error" value="off"/> 6329 <param name="isotope_error" value="off"/>
6254 <param name="fragment_mass_tolerance" value="0.50025"/> 6330 <param name="fragment_mass_tolerance" value="0.50025"/>
6255 <param name="fragment_error_units" value="Da"/> 6331 <param name="fragment_error_units" value="Da"/>
6265 <param name="override_charge" value="keep any known"/> 6341 <param name="override_charge" value="keep any known"/>
6266 <param name="ms_level" value="2"/> 6342 <param name="ms_level" value="2"/>
6267 <param name="activation_method" value="ALL"/> 6343 <param name="activation_method" value="ALL"/>
6268 <param name="max_fragment_charge" value="3"/> 6344 <param name="max_fragment_charge" value="3"/>
6269 <param name="clip_nterm_methionine" value="false"/> 6345 <param name="clip_nterm_methionine" value="false"/>
6270 <param name="fixed_modifications"/>
6271 <param name="variable_modifications"/>
6272 <param name="binary_modifications" value=""/>
6273 <param name="reindex" value="true"/> 6346 <param name="reindex" value="true"/>
6274 <section name="PeptideIndexing"> 6347 <section name="PeptideIndexing">
6275 <param name="decoy_string" value=""/> 6348 <param name="decoy_string" value=""/>
6276 <param name="decoy_string_position" value="prefix"/> 6349 <param name="decoy_string_position" value="prefix"/>
6277 <param name="missing_decoy_action" value="warn"/> 6350 <param name="missing_decoy_action" value="warn"/>
6280 <param name="keep_unreferenced_proteins" value="false"/> 6353 <param name="keep_unreferenced_proteins" value="false"/>
6281 <param name="unmatched_action" value="error"/> 6354 <param name="unmatched_action" value="error"/>
6282 <param name="aaa_max" value="3"/> 6355 <param name="aaa_max" value="3"/>
6283 <param name="mismatches_max" value="0"/> 6356 <param name="mismatches_max" value="0"/>
6284 <param name="IL_equivalent" value="false"/> 6357 <param name="IL_equivalent" value="false"/>
6358 <param name="allow_nterm_protein_cleavage" value="true"/>
6285 <section name="enzyme"> 6359 <section name="enzyme">
6286 <param name="name" value="auto"/> 6360 <param name="name" value="auto"/>
6287 <param name="specificity" value="auto"/> 6361 <param name="specificity" value="auto"/>
6288 </section> 6362 </section>
6289 </section> 6363 </section>
6291 <output name="ctd_out" ftype="xml"> 6365 <output name="ctd_out" ftype="xml">
6292 <assert_contents> 6366 <assert_contents>
6293 <is_valid_xml/> 6367 <is_valid_xml/>
6294 </assert_contents> 6368 </assert_contents>
6295 </output> 6369 </output>
6370 <assert_stdout>
6371 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6372 </assert_stdout>
6296 </test> 6373 </test>
6297 <!-- TOPP_CometAdapter_3 --> 6374 <!-- TOPP_CometAdapter_3 -->
6298 <test expect_num_outputs="3"> 6375 <test expect_num_outputs="3">
6299 <section name="adv_opts"> 6376 <section name="adv_opts">
6300 <param name="use_A_ions" value="false"/> 6377 <param name="use_A_ions" value="false"/>
6302 <param name="use_C_ions" value="false"/> 6379 <param name="use_C_ions" value="false"/>
6303 <param name="use_X_ions" value="false"/> 6380 <param name="use_X_ions" value="false"/>
6304 <param name="use_Y_ions" value="true"/> 6381 <param name="use_Y_ions" value="true"/>
6305 <param name="use_Z_ions" value="false"/> 6382 <param name="use_Z_ions" value="false"/>
6306 <param name="use_NL_ions" value="false"/> 6383 <param name="use_NL_ions" value="false"/>
6307 <param name="second_enzyme"/>
6308 <param name="digest_mass_range" value="600:5000"/> 6384 <param name="digest_mass_range" value="600:5000"/>
6309 <param name="max_precursor_charge" value="5"/> 6385 <param name="max_precursor_charge" value="5"/>
6310 <param name="spectrum_batch_size" value="20000"/> 6386 <param name="spectrum_batch_size" value="20000"/>
6311 <param name="mass_offsets" value="0.0"/> 6387 <param name="mass_offsets" value="0.0"/>
6312 <param name="minimum_peaks" value="10"/> 6388 <param name="minimum_peaks" value="10"/>
6318 <param name="require_variable_mod" value="false"/> 6394 <param name="require_variable_mod" value="false"/>
6319 <param name="force" value="false"/> 6395 <param name="force" value="false"/>
6320 <param name="test" value="true"/> 6396 <param name="test" value="true"/>
6321 </section> 6397 </section>
6322 <param name="in" value="CometAdapter_3.mzML"/> 6398 <param name="in" value="CometAdapter_3.mzML"/>
6323 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6399 <output name="out" value="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6324 <param name="database" value="CometAdapter_3.fasta"/> 6400 <param name="database" value="CometAdapter_3.fasta"/>
6325 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 6401 <output name="pin_out" value="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6326 <param name="precursor_mass_tolerance" value="5.0"/> 6402 <param name="precursor_mass_tolerance" value="5.0"/>
6327 <param name="precursor_error_units" value="ppm"/> 6403 <param name="precursor_error_units" value="ppm"/>
6328 <param name="isotope_error" value="off"/> 6404 <param name="isotope_error" value="off"/>
6329 <param name="fragment_mass_tolerance" value="0.01"/> 6405 <param name="fragment_mass_tolerance" value="0.01"/>
6330 <param name="fragment_error_units" value="Da"/> 6406 <param name="fragment_error_units" value="Da"/>
6342 <param name="activation_method" value="ALL"/> 6418 <param name="activation_method" value="ALL"/>
6343 <param name="max_fragment_charge" value="3"/> 6419 <param name="max_fragment_charge" value="3"/>
6344 <param name="clip_nterm_methionine" value="false"/> 6420 <param name="clip_nterm_methionine" value="false"/>
6345 <param name="fixed_modifications" value="Carbamidomethyl (C)"/> 6421 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
6346 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/> 6422 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/>
6347 <param name="binary_modifications" value=""/>
6348 <param name="reindex" value="true"/> 6423 <param name="reindex" value="true"/>
6349 <section name="PeptideIndexing"> 6424 <section name="PeptideIndexing">
6350 <param name="decoy_string" value=""/> 6425 <param name="decoy_string" value=""/>
6351 <param name="decoy_string_position" value="prefix"/> 6426 <param name="decoy_string_position" value="prefix"/>
6352 <param name="missing_decoy_action" value="warn"/> 6427 <param name="missing_decoy_action" value="warn"/>
6355 <param name="keep_unreferenced_proteins" value="false"/> 6430 <param name="keep_unreferenced_proteins" value="false"/>
6356 <param name="unmatched_action" value="error"/> 6431 <param name="unmatched_action" value="error"/>
6357 <param name="aaa_max" value="3"/> 6432 <param name="aaa_max" value="3"/>
6358 <param name="mismatches_max" value="0"/> 6433 <param name="mismatches_max" value="0"/>
6359 <param name="IL_equivalent" value="false"/> 6434 <param name="IL_equivalent" value="false"/>
6435 <param name="allow_nterm_protein_cleavage" value="true"/>
6360 <section name="enzyme"> 6436 <section name="enzyme">
6361 <param name="name" value="auto"/> 6437 <param name="name" value="auto"/>
6362 <param name="specificity" value="auto"/> 6438 <param name="specificity" value="auto"/>
6363 </section> 6439 </section>
6364 </section> 6440 </section>
6366 <output name="ctd_out" ftype="xml"> 6442 <output name="ctd_out" ftype="xml">
6367 <assert_contents> 6443 <assert_contents>
6368 <is_valid_xml/> 6444 <is_valid_xml/>
6369 </assert_contents> 6445 </assert_contents>
6370 </output> 6446 </output>
6447 <assert_stdout>
6448 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6449 </assert_stdout>
6371 </test> 6450 </test>
6372 <!-- TOPP_CometAdapter_4 --> 6451 <!-- TOPP_CometAdapter_4 -->
6373 <test expect_num_outputs="2"> 6452 <test expect_num_outputs="2">
6374 <section name="adv_opts"> 6453 <section name="adv_opts">
6375 <param name="use_A_ions" value="false"/> 6454 <param name="use_A_ions" value="false"/>
6377 <param name="use_C_ions" value="false"/> 6456 <param name="use_C_ions" value="false"/>
6378 <param name="use_X_ions" value="false"/> 6457 <param name="use_X_ions" value="false"/>
6379 <param name="use_Y_ions" value="true"/> 6458 <param name="use_Y_ions" value="true"/>
6380 <param name="use_Z_ions" value="false"/> 6459 <param name="use_Z_ions" value="false"/>
6381 <param name="use_NL_ions" value="false"/> 6460 <param name="use_NL_ions" value="false"/>
6382 <param name="second_enzyme"/>
6383 <param name="digest_mass_range" value="600:1200"/> 6461 <param name="digest_mass_range" value="600:1200"/>
6384 <param name="max_precursor_charge" value="5"/> 6462 <param name="max_precursor_charge" value="5"/>
6385 <param name="spectrum_batch_size" value="20000"/> 6463 <param name="spectrum_batch_size" value="20000"/>
6386 <param name="mass_offsets" value="0.0"/> 6464 <param name="mass_offsets" value="0.0"/>
6387 <param name="minimum_peaks" value="10"/> 6465 <param name="minimum_peaks" value="10"/>
6393 <param name="require_variable_mod" value="false"/> 6471 <param name="require_variable_mod" value="false"/>
6394 <param name="force" value="false"/> 6472 <param name="force" value="false"/>
6395 <param name="test" value="true"/> 6473 <param name="test" value="true"/>
6396 </section> 6474 </section>
6397 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> 6475 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
6398 <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6476 <output name="out" value="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6399 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> 6477 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
6400 <param name="precursor_mass_tolerance" value="5.0"/> 6478 <param name="precursor_mass_tolerance" value="5.0"/>
6401 <param name="precursor_error_units" value="ppm"/> 6479 <param name="precursor_error_units" value="ppm"/>
6402 <param name="isotope_error" value="off"/> 6480 <param name="isotope_error" value="off"/>
6403 <param name="fragment_mass_tolerance" value="0.01"/> 6481 <param name="fragment_mass_tolerance" value="0.01"/>
6416 <param name="activation_method" value="ALL"/> 6494 <param name="activation_method" value="ALL"/>
6417 <param name="max_fragment_charge" value="3"/> 6495 <param name="max_fragment_charge" value="3"/>
6418 <param name="clip_nterm_methionine" value="false"/> 6496 <param name="clip_nterm_methionine" value="false"/>
6419 <param name="fixed_modifications" value="Carbamidomethyl (C)"/> 6497 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
6420 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> 6498 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
6421 <param name="binary_modifications" value=""/>
6422 <param name="reindex" value="true"/> 6499 <param name="reindex" value="true"/>
6423 <section name="PeptideIndexing"> 6500 <section name="PeptideIndexing">
6424 <param name="decoy_string" value=""/> 6501 <param name="decoy_string" value=""/>
6425 <param name="decoy_string_position" value="prefix"/> 6502 <param name="decoy_string_position" value="prefix"/>
6426 <param name="missing_decoy_action" value="warn"/> 6503 <param name="missing_decoy_action" value="warn"/>
6429 <param name="keep_unreferenced_proteins" value="false"/> 6506 <param name="keep_unreferenced_proteins" value="false"/>
6430 <param name="unmatched_action" value="error"/> 6507 <param name="unmatched_action" value="error"/>
6431 <param name="aaa_max" value="3"/> 6508 <param name="aaa_max" value="3"/>
6432 <param name="mismatches_max" value="0"/> 6509 <param name="mismatches_max" value="0"/>
6433 <param name="IL_equivalent" value="false"/> 6510 <param name="IL_equivalent" value="false"/>
6511 <param name="allow_nterm_protein_cleavage" value="true"/>
6434 <section name="enzyme"> 6512 <section name="enzyme">
6435 <param name="name" value="auto"/> 6513 <param name="name" value="auto"/>
6436 <param name="specificity" value="auto"/> 6514 <param name="specificity" value="auto"/>
6437 </section> 6515 </section>
6438 </section> 6516 </section>
6440 <output name="ctd_out" ftype="xml"> 6518 <output name="ctd_out" ftype="xml">
6441 <assert_contents> 6519 <assert_contents>
6442 <is_valid_xml/> 6520 <is_valid_xml/>
6443 </assert_contents> 6521 </assert_contents>
6444 </output> 6522 </output>
6523 <assert_stdout>
6524 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6525 </assert_stdout>
6445 </test> 6526 </test>
6446 </tests> 6527 </tests>
6447 <help><![CDATA[Annotates MS/MS spectra using Comet. 6528 <help><![CDATA[Annotates MS/MS spectra using Comet.
6448 6529
6449 6530
6450 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CometAdapter.html]]></help> 6531 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CometAdapter.html]]></help>
6451 <expand macro="references"/> 6532 <expand macro="references"/>
6452 </tool> 6533 </tool>