Mercurial > repos > galaxyp > openms_xtandemadapter

comparison XTandemAdapter.xml @ 15:567de7cb1766 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:35:51 +0000
parents 5c2a97a234d6
children
comparison
equal deleted inserted replaced
14:5c2a97a234d6 15:567de7cb1766
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="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using X! Tandem.</description> 4 <description>Annotates MS/MS spectra using X! Tandem</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">XTandemAdapter</token> 6 <token name="@EXECUTABLE@">XTandemAdapter</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($in.ext)' &&
19 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 18 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
20 mkdir out && 19 mkdir out &&
21 #end if 20 #end if
22 #if "xml_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "xml_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir xml_out && 22 mkdir xml_out &&
24 #end if 23 #end if
25 mkdir database && 24 mkdir database &&
26 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 25 cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
27 #if $default_config_file: 26 #if $default_config_file:
28 mkdir default_config_file && 27 mkdir default_config_file &&
29 ln -s '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' && 28 cp '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' &&
30 #end if 29 #end if
31 30
32 ## Main program call 31 ## Main program call
33 32
34 set -o pipefail && 33 set -o pipefail &&
68 <configfiles> 67 <configfiles>
69 <inputs name="args_json" data_style="paths"/> 68 <inputs name="args_json" data_style="paths"/>
70 <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 69 <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
71 </configfiles> 70 </configfiles>
72 <inputs> 71 <inputs>
73 <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/> 72 <param argument="-in" type="data" format="mzml" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/>
74 <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> 73 <param argument="-database" type="data" format="fasta" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
75 <param argument="-default_config_file" type="data" format="xml" optional="true" label="Default X" help="Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_config.xml' select xml data sets(s)"/> 74 <param argument="-default_config_file" type="data" format="xml" optional="true" label="Default X" help="Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_config.xml' select xml data sets(s)"/>
76 <param argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/> 75 <param argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/>
77 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/> 76 <param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance" help=""/>
78 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/> 77 <param argument="-fragment_mass_tolerance" type="float" value="0.3" label="Fragment mass erro" help=""/>
79 <param argument="-precursor_error_units" type="select" optional="true" label="Parent monoisotopic mass error units" help=""> 78 <param argument="-precursor_error_units" type="select" label="Parent monoisotopic mass error units" help="">
80 <option value="ppm" selected="true">ppm</option> 79 <option value="ppm" selected="true">ppm</option>
81 <option value="Da">Da</option> 80 <option value="Da">Da</option>
82 <expand macro="list_string_san" name="precursor_error_units"/> 81 <expand macro="list_string_san" name="precursor_error_units"/>
83 </param> 82 </param>
84 <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help=""> 83 <param argument="-fragment_error_units" type="select" label="Fragment monoisotopic mass error units" help="">
85 <option value="ppm">ppm</option> 84 <option value="ppm">ppm</option>
86 <option value="Da" selected="true">Da</option> 85 <option value="Da" selected="true">Da</option>
87 <expand macro="list_string_san" name="fragment_error_units"/> 86 <expand macro="list_string_san" name="fragment_error_units"/>
88 </param> 87 </param>
89 <param argument="-max_precursor_charge" type="integer" optional="true" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/> 88 <param argument="-max_precursor_charge" type="integer" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/>
90 <param argument="-no_isotope_error" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="Set this flag to disable"/> 89 <param argument="-no_isotope_error" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="Set this flag to disable"/>
91 <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)'"> 90 <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)'">
92 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 91 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
93 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 92 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
94 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 93 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
95 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 94 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
96 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 95 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
97 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 96 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
98 <option value="2-succinyl (C)">2-succinyl (C)</option> 97 <option value="2-succinyl (C)">2-succinyl (C)</option>
99 <option value="2HPG (R)">2HPG (R)</option> 98 <option value="2HPG (R)">2HPG (R)</option>
100 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 99 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
100 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
101 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
102 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
103 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
101 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 104 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
102 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 105 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
103 <option value="4-ONE (C)">4-ONE (C)</option> 106 <option value="4-ONE (C)">4-ONE (C)</option>
104 <option value="4-ONE (H)">4-ONE (H)</option> 107 <option value="4-ONE (H)">4-ONE (H)</option>
105 <option value="4-ONE (K)">4-ONE (K)</option> 108 <option value="4-ONE (K)">4-ONE (K)</option>
185 <option value="Ammonium (D)">Ammonium (D)</option> 188 <option value="Ammonium (D)">Ammonium (D)</option>
186 <option value="Ammonium (E)">Ammonium (E)</option> 189 <option value="Ammonium (E)">Ammonium (E)</option>
187 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 190 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
188 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 191 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
189 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 192 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
193 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
190 <option value="Archaeol (C)">Archaeol (C)</option> 194 <option value="Archaeol (C)">Archaeol (C)</option>
191 <option value="Arg (N-term)">Arg (N-term)</option> 195 <option value="Arg (N-term)">Arg (N-term)</option>
192 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 196 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
193 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 197 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
194 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 198 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
288 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 292 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
289 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 293 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
290 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 294 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
291 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 295 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
292 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 296 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
297 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
293 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 298 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
294 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 299 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
295 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 300 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
296 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 301 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
297 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 302 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
320 <option value="BITC (C)">BITC (C)</option> 325 <option value="BITC (C)">BITC (C)</option>
321 <option value="BITC (K)">BITC (K)</option> 326 <option value="BITC (K)">BITC (K)</option>
322 <option value="BITC (N-term)">BITC (N-term)</option> 327 <option value="BITC (N-term)">BITC (N-term)</option>
323 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 328 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
324 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 329 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
325 <option value="Bodipy (C)">Bodipy (C)</option>
326 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 330 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
327 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 331 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
328 <option value="Bromo (F)">Bromo (F)</option> 332 <option value="Bromo (F)">Bromo (F)</option>
329 <option value="Bromo (H)">Bromo (H)</option> 333 <option value="Bromo (H)">Bromo (H)</option>
330 <option value="Bromo (W)">Bromo (W)</option> 334 <option value="Bromo (W)">Bromo (W)</option>
752 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 756 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
753 <option value="Dehydrated (S)">Dehydrated (S)</option> 757 <option value="Dehydrated (S)">Dehydrated (S)</option>
754 <option value="Dehydrated (T)">Dehydrated (T)</option> 758 <option value="Dehydrated (T)">Dehydrated (T)</option>
755 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 759 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
756 <option value="Dehydro (C)">Dehydro (C)</option> 760 <option value="Dehydro (C)">Dehydro (C)</option>
761 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
757 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 762 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
758 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 763 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
759 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
760 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 764 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
761 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 765 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
762 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 766 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
763 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 767 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
764 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 768 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
765 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 769 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
766 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 770 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
767 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 771 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
768 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 772 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
769 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
770 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 773 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
771 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 774 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
772 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 775 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
773 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 776 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
774 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 777 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
776 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 779 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
777 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 780 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
778 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 781 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
779 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 782 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
780 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 783 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
784 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
781 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 785 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
782 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 786 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
783 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 787 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
784 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 788 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
785 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 789 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
1348 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 1352 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
1349 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 1353 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
1350 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 1354 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
1351 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 1355 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
1352 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 1356 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
1353 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
1354 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 1357 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
1355 <option value="Ethyl (D)">Ethyl (D)</option> 1358 <option value="Ethyl (D)">Ethyl (D)</option>
1356 <option value="Ethyl (E)">Ethyl (E)</option> 1359 <option value="Ethyl (E)">Ethyl (E)</option>
1357 <option value="Ethyl (K)">Ethyl (K)</option> 1360 <option value="Ethyl (K)">Ethyl (K)</option>
1358 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 1361 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
1442 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 1445 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
1443 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 1446 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
1444 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 1447 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
1445 <option value="Glu (E)">Glu (E)</option> 1448 <option value="Glu (E)">Glu (E)</option>
1446 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 1449 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
1450 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
1447 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 1451 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
1448 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 1452 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
1449 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 1453 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
1450 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 1454 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
1451 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 1455 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
1456 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1460 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1457 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1461 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1458 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1462 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1459 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1463 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1460 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1464 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1461 <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>
1462 <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> 1465 <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>
1463 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1466 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1464 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1467 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
1465 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 1468 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
1466 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 1469 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
1480 <option value="Gluratylation (K)">Gluratylation (K)</option> 1483 <option value="Gluratylation (K)">Gluratylation (K)</option>
1481 <option value="Glutathione (C)">Glutathione (C)</option> 1484 <option value="Glutathione (C)">Glutathione (C)</option>
1482 <option value="Gly (K)">Gly (K)</option> 1485 <option value="Gly (K)">Gly (K)</option>
1483 <option value="Gly (S)">Gly (S)</option> 1486 <option value="Gly (S)">Gly (S)</option>
1484 <option value="Gly (T)">Gly (T)</option> 1487 <option value="Gly (T)">Gly (T)</option>
1488 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
1485 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 1489 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
1486 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 1490 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
1487 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 1491 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
1488 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 1492 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
1489 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 1493 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
1870 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 1874 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
1871 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 1875 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
1872 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 1876 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
1873 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 1877 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
1874 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 1878 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
1879 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
1875 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 1880 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
1876 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 1881 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
1877 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 1882 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
1878 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 1883 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
1879 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 1884 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
1881 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 1886 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
1882 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 1887 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
1883 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 1888 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
1884 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 1889 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
1885 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 1890 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
1891 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
1892 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
1893 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
1886 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 1894 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
1887 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 1895 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
1888 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 1896 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
1889 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 1897 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
1890 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 1898 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
1936 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 1944 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
1937 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 1945 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
1938 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 1946 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
1939 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 1947 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
1940 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 1948 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
1949 <option value="His+O(2) (H)">His+O(2) (H)</option>
1941 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 1950 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
1942 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 1951 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
1943 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 1952 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
1944 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 1953 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
1945 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 1954 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
2073 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 2082 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
2074 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 2083 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
2075 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 2084 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
2076 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 2085 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
2077 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 2086 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
2087 <option value="Kdo (S)">Kdo (S)</option>
2088 <option value="Kdo (T)">Kdo (T)</option>
2078 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 2089 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
2079 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 2090 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
2080 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 2091 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
2081 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 2092 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
2082 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 2093 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
2094 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
2083 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 2095 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
2084 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 2096 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
2085 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 2097 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
2086 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 2098 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
2087 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 2099 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
2162 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 2174 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
2163 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 2175 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
2164 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 2176 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
2165 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 2177 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
2166 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 2178 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
2179 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
2167 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 2180 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
2168 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 2181 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
2169 <option value="Lipoyl (K)">Lipoyl (K)</option> 2182 <option value="Lipoyl (K)">Lipoyl (K)</option>
2170 <option value="LRGG (K)">LRGG (K)</option> 2183 <option value="LRGG (K)">LRGG (K)</option>
2171 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 2184 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
2172 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 2185 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
2186 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
2173 <option value="Lys (N-term)">Lys (N-term)</option> 2187 <option value="Lys (N-term)">Lys (N-term)</option>
2188 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
2174 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 2189 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
2175 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 2190 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
2176 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 2191 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
2177 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 2192 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
2178 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 2193 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
2203 <option value="maleimide5 (C)">maleimide5 (C)</option> 2218 <option value="maleimide5 (C)">maleimide5 (C)</option>
2204 <option value="maleimide5 (K)">maleimide5 (K)</option> 2219 <option value="maleimide5 (K)">maleimide5 (K)</option>
2205 <option value="Malonyl (C)">Malonyl (C)</option> 2220 <option value="Malonyl (C)">Malonyl (C)</option>
2206 <option value="Malonyl (K)">Malonyl (K)</option> 2221 <option value="Malonyl (K)">Malonyl (K)</option>
2207 <option value="Malonyl (S)">Malonyl (S)</option> 2222 <option value="Malonyl (S)">Malonyl (S)</option>
2223 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
2208 <option value="MDCC (C)">MDCC (C)</option> 2224 <option value="MDCC (C)">MDCC (C)</option>
2209 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 2225 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
2210 <option value="Menadione (C)">Menadione (C)</option> 2226 <option value="Menadione (C)">Menadione (C)</option>
2211 <option value="Menadione (K)">Menadione (K)</option> 2227 <option value="Menadione (K)">Menadione (K)</option>
2212 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 2228 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
2214 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 2230 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
2215 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 2231 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
2216 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 2232 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
2217 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 2233 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
2218 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 2234 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
2235 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
2219 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 2236 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
2220 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 2237 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
2221 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 2238 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
2222 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 2239 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
2223 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 2240 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
2397 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 2414 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
2398 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 2415 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
2399 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 2416 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
2400 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 2417 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
2401 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 2418 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
2402 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
2403 <option value="NP40 (N-term)">NP40 (N-term)</option> 2419 <option value="NP40 (N-term)">NP40 (N-term)</option>
2404 <option value="NQIGG (K)">NQIGG (K)</option> 2420 <option value="NQIGG (K)">NQIGG (K)</option>
2405 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 2421 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
2406 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 2422 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
2407 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 2423 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
2485 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 2501 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
2486 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 2502 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
2487 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 2503 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
2488 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 2504 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
2489 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 2505 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
2506 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
2507 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
2508 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
2509 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
2490 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 2510 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
2491 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 2511 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
2492 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 2512 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
2493 <option value="Phospho (C)">Phospho (C)</option> 2513 <option value="Phospho (C)">Phospho (C)</option>
2494 <option value="Phospho (D)">Phospho (D)</option> 2514 <option value="Phospho (D)">Phospho (D)</option>
2499 <option value="Phospho (S)">Phospho (S)</option> 2519 <option value="Phospho (S)">Phospho (S)</option>
2500 <option value="Phospho (T)">Phospho (T)</option> 2520 <option value="Phospho (T)">Phospho (T)</option>
2501 <option value="Phospho (Y)">Phospho (Y)</option> 2521 <option value="Phospho (Y)">Phospho (Y)</option>
2502 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 2522 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
2503 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 2523 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
2524 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
2504 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 2525 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
2505 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 2526 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
2506 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 2527 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
2507 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 2528 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
2508 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 2529 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
2530 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 2551 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
2531 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 2552 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
2532 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 2553 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
2533 <option value="Piperidine (K)">Piperidine (K)</option> 2554 <option value="Piperidine (K)">Piperidine (K)</option>
2534 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 2555 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
2556 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
2535 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 2557 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
2536 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 2558 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
2537 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 2559 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
2538 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 2560 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
2539 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 2561 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
2607 <option value="QEQTGG (K)">QEQTGG (K)</option> 2629 <option value="QEQTGG (K)">QEQTGG (K)</option>
2608 <option value="QQQTGG (K)">QQQTGG (K)</option> 2630 <option value="QQQTGG (K)">QQQTGG (K)</option>
2609 <option value="QTGG (K)">QTGG (K)</option> 2631 <option value="QTGG (K)">QTGG (K)</option>
2610 <option value="Quinone (W)">Quinone (W)</option> 2632 <option value="Quinone (W)">Quinone (W)</option>
2611 <option value="Quinone (Y)">Quinone (Y)</option> 2633 <option value="Quinone (Y)">Quinone (Y)</option>
2634 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
2635 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
2636 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
2637 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
2638 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
2639 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
2640 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
2641 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
2642 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
2643 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
2644 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
2645 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
2646 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
2647 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
2648 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
2649 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
2650 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
2651 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
2652 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
2653 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
2612 <option value="Retinylidene (K)">Retinylidene (K)</option> 2654 <option value="Retinylidene (K)">Retinylidene (K)</option>
2613 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 2655 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
2614 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 2656 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
2615 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 2657 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
2616 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
2617 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
2618 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
2619 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
2620 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
2621 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
2622 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
2623 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
2624 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 2658 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
2625 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 2659 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
2626 <option value="Saligenin (H)">Saligenin (H)</option> 2660 <option value="Saligenin (H)">Saligenin (H)</option>
2627 <option value="Saligenin (K)">Saligenin (K)</option> 2661 <option value="Saligenin (K)">Saligenin (K)</option>
2628 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 2662 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
2646 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 2680 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
2647 <option value="serotonylation (Q)">serotonylation (Q)</option> 2681 <option value="serotonylation (Q)">serotonylation (Q)</option>
2648 <option value="shTMT (K)">shTMT (K)</option> 2682 <option value="shTMT (K)">shTMT (K)</option>
2649 <option value="shTMT (N-term)">shTMT (N-term)</option> 2683 <option value="shTMT (N-term)">shTMT (N-term)</option>
2650 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 2684 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
2685 <option value="shTMTpro (K)">shTMTpro (K)</option>
2686 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
2687 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
2651 <option value="SMA (K)">SMA (K)</option> 2688 <option value="SMA (K)">SMA (K)</option>
2652 <option value="SMA (N-term)">SMA (N-term)</option> 2689 <option value="SMA (N-term)">SMA (N-term)</option>
2653 <option value="spermidine (Q)">spermidine (Q)</option> 2690 <option value="spermidine (Q)">spermidine (Q)</option>
2654 <option value="spermine (Q)">spermine (Q)</option> 2691 <option value="spermine (Q)">spermine (Q)</option>
2655 <option value="SPITC (K)">SPITC (K)</option> 2692 <option value="SPITC (K)">SPITC (K)</option>
2821 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 2858 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
2822 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 2859 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
2823 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 2860 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
2824 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 2861 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
2825 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 2862 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
2826 <option value="Ub-amide (C)">Ub-amide (C)</option>
2827 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 2863 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
2828 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 2864 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
2829 <option value="Ub-VME (C)">Ub-VME (C)</option> 2865 <option value="Ub-VME (C)">Ub-VME (C)</option>
2830 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 2866 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
2831 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 2867 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
3016 <option value="ZGB (K)">ZGB (K)</option> 3052 <option value="ZGB (K)">ZGB (K)</option>
3017 <option value="ZGB (N-term)">ZGB (N-term)</option> 3053 <option value="ZGB (N-term)">ZGB (N-term)</option>
3018 <option value="ZQG (K)">ZQG (K)</option> 3054 <option value="ZQG (K)">ZQG (K)</option>
3019 <expand macro="list_string_san" name="fixed_modifications"/> 3055 <expand macro="list_string_san" name="fixed_modifications"/>
3020 </param> 3056 </param>
3021 <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)'"> 3057 <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)'">
3022 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3058 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3023 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3059 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3024 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3060 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3025 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3061 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3026 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3062 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
3027 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 3063 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
3028 <option value="2-succinyl (C)">2-succinyl (C)</option> 3064 <option value="2-succinyl (C)">2-succinyl (C)</option>
3029 <option value="2HPG (R)">2HPG (R)</option> 3065 <option value="2HPG (R)">2HPG (R)</option>
3030 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 3066 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
3067 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
3068 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
3069 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
3070 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
3031 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 3071 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
3032 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 3072 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
3033 <option value="4-ONE (C)">4-ONE (C)</option> 3073 <option value="4-ONE (C)">4-ONE (C)</option>
3034 <option value="4-ONE (H)">4-ONE (H)</option> 3074 <option value="4-ONE (H)">4-ONE (H)</option>
3035 <option value="4-ONE (K)">4-ONE (K)</option> 3075 <option value="4-ONE (K)">4-ONE (K)</option>
3115 <option value="Ammonium (D)">Ammonium (D)</option> 3155 <option value="Ammonium (D)">Ammonium (D)</option>
3116 <option value="Ammonium (E)">Ammonium (E)</option> 3156 <option value="Ammonium (E)">Ammonium (E)</option>
3117 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 3157 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
3118 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 3158 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
3119 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 3159 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
3160 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
3120 <option value="Archaeol (C)">Archaeol (C)</option> 3161 <option value="Archaeol (C)">Archaeol (C)</option>
3121 <option value="Arg (N-term)">Arg (N-term)</option> 3162 <option value="Arg (N-term)">Arg (N-term)</option>
3122 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 3163 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
3123 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 3164 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
3124 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 3165 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
3218 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 3259 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
3219 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 3260 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
3220 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 3261 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
3221 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 3262 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
3222 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 3263 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
3264 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
3223 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 3265 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
3224 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 3266 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
3225 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 3267 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
3226 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 3268 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
3227 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 3269 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
3250 <option value="BITC (C)">BITC (C)</option> 3292 <option value="BITC (C)">BITC (C)</option>
3251 <option value="BITC (K)">BITC (K)</option> 3293 <option value="BITC (K)">BITC (K)</option>
3252 <option value="BITC (N-term)">BITC (N-term)</option> 3294 <option value="BITC (N-term)">BITC (N-term)</option>
3253 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 3295 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
3254 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 3296 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
3255 <option value="Bodipy (C)">Bodipy (C)</option>
3256 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 3297 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
3257 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 3298 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
3258 <option value="Bromo (F)">Bromo (F)</option> 3299 <option value="Bromo (F)">Bromo (F)</option>
3259 <option value="Bromo (H)">Bromo (H)</option> 3300 <option value="Bromo (H)">Bromo (H)</option>
3260 <option value="Bromo (W)">Bromo (W)</option> 3301 <option value="Bromo (W)">Bromo (W)</option>
3682 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 3723 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
3683 <option value="Dehydrated (S)">Dehydrated (S)</option> 3724 <option value="Dehydrated (S)">Dehydrated (S)</option>
3684 <option value="Dehydrated (T)">Dehydrated (T)</option> 3725 <option value="Dehydrated (T)">Dehydrated (T)</option>
3685 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 3726 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
3686 <option value="Dehydro (C)">Dehydro (C)</option> 3727 <option value="Dehydro (C)">Dehydro (C)</option>
3728 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
3687 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 3729 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
3688 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 3730 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
3689 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
3690 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 3731 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
3691 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 3732 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
3692 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 3733 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
3693 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 3734 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
3694 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 3735 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
3695 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 3736 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
3696 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 3737 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
3697 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 3738 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
3698 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 3739 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
3699 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
3700 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 3740 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
3701 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 3741 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
3702 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 3742 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
3703 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 3743 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
3704 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 3744 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
3706 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 3746 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
3707 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 3747 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
3708 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 3748 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
3709 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 3749 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
3710 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 3750 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
3751 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
3711 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 3752 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
3712 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 3753 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
3713 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 3754 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
3714 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 3755 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
3715 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 3756 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
4278 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 4319 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
4279 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 4320 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
4280 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 4321 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
4281 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 4322 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
4282 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 4323 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
4283 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
4284 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 4324 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
4285 <option value="Ethyl (D)">Ethyl (D)</option> 4325 <option value="Ethyl (D)">Ethyl (D)</option>
4286 <option value="Ethyl (E)">Ethyl (E)</option> 4326 <option value="Ethyl (E)">Ethyl (E)</option>
4287 <option value="Ethyl (K)">Ethyl (K)</option> 4327 <option value="Ethyl (K)">Ethyl (K)</option>
4288 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 4328 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
4372 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 4412 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
4373 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 4413 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
4374 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 4414 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
4375 <option value="Glu (E)">Glu (E)</option> 4415 <option value="Glu (E)">Glu (E)</option>
4376 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 4416 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
4417 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
4377 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 4418 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
4378 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 4419 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
4379 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 4420 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
4380 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 4421 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
4381 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 4422 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
4386 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4427 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4387 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4428 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4388 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4429 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4389 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4430 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4390 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4431 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4391 <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>
4392 <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> 4432 <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>
4393 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4433 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4394 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4434 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
4395 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 4435 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
4396 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 4436 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
4410 <option value="Gluratylation (K)">Gluratylation (K)</option> 4450 <option value="Gluratylation (K)">Gluratylation (K)</option>
4411 <option value="Glutathione (C)">Glutathione (C)</option> 4451 <option value="Glutathione (C)">Glutathione (C)</option>
4412 <option value="Gly (K)">Gly (K)</option> 4452 <option value="Gly (K)">Gly (K)</option>
4413 <option value="Gly (S)">Gly (S)</option> 4453 <option value="Gly (S)">Gly (S)</option>
4414 <option value="Gly (T)">Gly (T)</option> 4454 <option value="Gly (T)">Gly (T)</option>
4455 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
4415 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 4456 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
4416 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 4457 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
4417 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 4458 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
4418 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 4459 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
4419 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 4460 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
4800 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 4841 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
4801 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 4842 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
4802 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 4843 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
4803 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 4844 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
4804 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 4845 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
4846 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
4805 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 4847 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
4806 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 4848 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
4807 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 4849 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
4808 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 4850 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
4809 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 4851 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
4811 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 4853 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
4812 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 4854 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
4813 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 4855 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
4814 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 4856 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
4815 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 4857 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
4858 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
4859 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
4860 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
4816 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 4861 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
4817 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 4862 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
4818 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 4863 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
4819 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 4864 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
4820 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 4865 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
4866 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 4911 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
4867 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 4912 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
4868 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 4913 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
4869 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 4914 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
4870 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 4915 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
4916 <option value="His+O(2) (H)">His+O(2) (H)</option>
4871 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 4917 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
4872 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 4918 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
4873 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 4919 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
4874 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 4920 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
4875 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 4921 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
5003 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 5049 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
5004 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 5050 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
5005 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 5051 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
5006 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 5052 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
5007 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 5053 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
5054 <option value="Kdo (S)">Kdo (S)</option>
5055 <option value="Kdo (T)">Kdo (T)</option>
5008 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 5056 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
5009 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 5057 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
5010 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 5058 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
5011 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 5059 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
5012 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 5060 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
5061 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
5013 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 5062 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
5014 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 5063 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
5015 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 5064 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
5016 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 5065 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
5017 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 5066 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
5092 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 5141 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
5093 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 5142 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
5094 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 5143 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
5095 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 5144 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
5096 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 5145 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
5146 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
5097 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 5147 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
5098 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 5148 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
5099 <option value="Lipoyl (K)">Lipoyl (K)</option> 5149 <option value="Lipoyl (K)">Lipoyl (K)</option>
5100 <option value="LRGG (K)">LRGG (K)</option> 5150 <option value="LRGG (K)">LRGG (K)</option>
5101 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 5151 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
5102 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 5152 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
5153 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
5103 <option value="Lys (N-term)">Lys (N-term)</option> 5154 <option value="Lys (N-term)">Lys (N-term)</option>
5155 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
5104 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 5156 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
5105 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 5157 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
5106 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 5158 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
5107 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 5159 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
5108 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 5160 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
5133 <option value="maleimide5 (C)">maleimide5 (C)</option> 5185 <option value="maleimide5 (C)">maleimide5 (C)</option>
5134 <option value="maleimide5 (K)">maleimide5 (K)</option> 5186 <option value="maleimide5 (K)">maleimide5 (K)</option>
5135 <option value="Malonyl (C)">Malonyl (C)</option> 5187 <option value="Malonyl (C)">Malonyl (C)</option>
5136 <option value="Malonyl (K)">Malonyl (K)</option> 5188 <option value="Malonyl (K)">Malonyl (K)</option>
5137 <option value="Malonyl (S)">Malonyl (S)</option> 5189 <option value="Malonyl (S)">Malonyl (S)</option>
5190 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
5138 <option value="MDCC (C)">MDCC (C)</option> 5191 <option value="MDCC (C)">MDCC (C)</option>
5139 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 5192 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
5140 <option value="Menadione (C)">Menadione (C)</option> 5193 <option value="Menadione (C)">Menadione (C)</option>
5141 <option value="Menadione (K)">Menadione (K)</option> 5194 <option value="Menadione (K)">Menadione (K)</option>
5142 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 5195 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
5144 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 5197 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
5145 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 5198 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
5146 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 5199 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
5147 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 5200 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
5148 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 5201 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
5202 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
5149 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 5203 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
5150 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 5204 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
5151 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 5205 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
5152 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 5206 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
5153 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 5207 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
5327 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 5381 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
5328 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 5382 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
5329 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 5383 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
5330 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 5384 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
5331 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 5385 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
5332 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
5333 <option value="NP40 (N-term)">NP40 (N-term)</option> 5386 <option value="NP40 (N-term)">NP40 (N-term)</option>
5334 <option value="NQIGG (K)">NQIGG (K)</option> 5387 <option value="NQIGG (K)">NQIGG (K)</option>
5335 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 5388 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
5336 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 5389 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
5337 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 5390 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
5415 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 5468 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
5416 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 5469 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
5417 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 5470 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
5418 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 5471 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
5419 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 5472 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
5473 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
5474 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
5475 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
5476 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
5420 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 5477 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
5421 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 5478 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
5422 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 5479 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
5423 <option value="Phospho (C)">Phospho (C)</option> 5480 <option value="Phospho (C)">Phospho (C)</option>
5424 <option value="Phospho (D)">Phospho (D)</option> 5481 <option value="Phospho (D)">Phospho (D)</option>
5429 <option value="Phospho (S)">Phospho (S)</option> 5486 <option value="Phospho (S)">Phospho (S)</option>
5430 <option value="Phospho (T)">Phospho (T)</option> 5487 <option value="Phospho (T)">Phospho (T)</option>
5431 <option value="Phospho (Y)">Phospho (Y)</option> 5488 <option value="Phospho (Y)">Phospho (Y)</option>
5432 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 5489 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
5433 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 5490 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
5491 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
5434 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 5492 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
5435 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 5493 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
5436 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 5494 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
5437 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 5495 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
5438 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 5496 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
5460 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 5518 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
5461 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 5519 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
5462 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 5520 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
5463 <option value="Piperidine (K)">Piperidine (K)</option> 5521 <option value="Piperidine (K)">Piperidine (K)</option>
5464 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 5522 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
5523 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
5465 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 5524 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
5466 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 5525 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
5467 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 5526 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
5468 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 5527 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
5469 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 5528 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
5537 <option value="QEQTGG (K)">QEQTGG (K)</option> 5596 <option value="QEQTGG (K)">QEQTGG (K)</option>
5538 <option value="QQQTGG (K)">QQQTGG (K)</option> 5597 <option value="QQQTGG (K)">QQQTGG (K)</option>
5539 <option value="QTGG (K)">QTGG (K)</option> 5598 <option value="QTGG (K)">QTGG (K)</option>
5540 <option value="Quinone (W)">Quinone (W)</option> 5599 <option value="Quinone (W)">Quinone (W)</option>
5541 <option value="Quinone (Y)">Quinone (Y)</option> 5600 <option value="Quinone (Y)">Quinone (Y)</option>
5601 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
5602 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
5603 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
5604 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
5605 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
5606 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
5607 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
5608 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
5609 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
5610 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
5611 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
5612 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
5613 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
5614 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
5615 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
5616 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
5617 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
5618 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
5619 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
5620 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
5542 <option value="Retinylidene (K)">Retinylidene (K)</option> 5621 <option value="Retinylidene (K)">Retinylidene (K)</option>
5543 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 5622 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
5544 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 5623 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
5545 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 5624 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
5546 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
5547 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
5548 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
5549 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
5550 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
5551 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
5552 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
5553 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
5554 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 5625 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
5555 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 5626 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
5556 <option value="Saligenin (H)">Saligenin (H)</option> 5627 <option value="Saligenin (H)">Saligenin (H)</option>
5557 <option value="Saligenin (K)">Saligenin (K)</option> 5628 <option value="Saligenin (K)">Saligenin (K)</option>
5558 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 5629 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
5576 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 5647 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
5577 <option value="serotonylation (Q)">serotonylation (Q)</option> 5648 <option value="serotonylation (Q)">serotonylation (Q)</option>
5578 <option value="shTMT (K)">shTMT (K)</option> 5649 <option value="shTMT (K)">shTMT (K)</option>
5579 <option value="shTMT (N-term)">shTMT (N-term)</option> 5650 <option value="shTMT (N-term)">shTMT (N-term)</option>
5580 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 5651 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
5652 <option value="shTMTpro (K)">shTMTpro (K)</option>
5653 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
5654 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
5581 <option value="SMA (K)">SMA (K)</option> 5655 <option value="SMA (K)">SMA (K)</option>
5582 <option value="SMA (N-term)">SMA (N-term)</option> 5656 <option value="SMA (N-term)">SMA (N-term)</option>
5583 <option value="spermidine (Q)">spermidine (Q)</option> 5657 <option value="spermidine (Q)">spermidine (Q)</option>
5584 <option value="spermine (Q)">spermine (Q)</option> 5658 <option value="spermine (Q)">spermine (Q)</option>
5585 <option value="SPITC (K)">SPITC (K)</option> 5659 <option value="SPITC (K)">SPITC (K)</option>
5751 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 5825 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
5752 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 5826 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
5753 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 5827 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
5754 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 5828 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
5755 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 5829 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
5756 <option value="Ub-amide (C)">Ub-amide (C)</option>
5757 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 5830 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
5758 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 5831 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
5759 <option value="Ub-VME (C)">Ub-VME (C)</option> 5832 <option value="Ub-VME (C)">Ub-VME (C)</option>
5760 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 5833 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
5761 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 5834 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
5946 <option value="ZGB (K)">ZGB (K)</option> 6019 <option value="ZGB (K)">ZGB (K)</option>
5947 <option value="ZGB (N-term)">ZGB (N-term)</option> 6020 <option value="ZGB (N-term)">ZGB (N-term)</option>
5948 <option value="ZQG (K)">ZQG (K)</option> 6021 <option value="ZQG (K)">ZQG (K)</option>
5949 <expand macro="list_string_san" name="variable_modifications"/> 6022 <expand macro="list_string_san" name="variable_modifications"/>
5950 </param> 6023 </param>
5951 <param argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/> 6024 <param argument="-minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment m/z" help=""/>
5952 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> 6025 <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
6026 <option value="TrypChymo">TrypChymo</option>
6027 <option value="Trypsin/P">Trypsin/P</option>
6028 <option value="V8-DE">V8-DE</option>
6029 <option value="V8-E">V8-E</option>
6030 <option value="Trypsin" selected="true">Trypsin</option>
6031 <option value="leukocyte elastase">leukocyte elastase</option>
6032 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6033 <option value="Arg-C">Arg-C</option>
6034 <option value="Arg-C/P">Arg-C/P</option>
6035 <option value="no cleavage">no cleavage</option>
6036 <option value="unspecific cleavage">unspecific cleavage</option>
6037 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6038 <option value="2-iodobenzoate">2-iodobenzoate</option>
6039 <option value="Lys-C">Lys-C</option>
6040 <option value="Lys-N">Lys-N</option>
6041 <option value="Chymotrypsin">Chymotrypsin</option>
5953 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 6042 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5954 <option value="CNBr">CNBr</option> 6043 <option value="CNBr">CNBr</option>
5955 <option value="Formic_acid">Formic_acid</option> 6044 <option value="Formic_acid">Formic_acid</option>
5956 <option value="Trypsin" selected="true">Trypsin</option> 6045 <option value="Asp-N">Asp-N</option>
5957 <option value="unspecific cleavage">unspecific cleavage</option> 6046 <option value="Asp-N/B">Asp-N/B</option>
5958 <option value="Lys-C">Lys-C</option> 6047 <option value="Asp-N_ambic">Asp-N_ambic</option>
5959 <option value="Lys-N">Lys-N</option>
5960 <option value="Lys-C/P">Lys-C/P</option> 6048 <option value="Lys-C/P">Lys-C/P</option>
5961 <option value="PepsinA">PepsinA</option> 6049 <option value="PepsinA">PepsinA</option>
5962 <option value="TrypChymo">TrypChymo</option>
5963 <option value="Trypsin/P">Trypsin/P</option>
5964 <option value="V8-DE">V8-DE</option>
5965 <option value="Asp-N/B">Asp-N/B</option>
5966 <option value="Asp-N_ambic">Asp-N_ambic</option>
5967 <option value="Chymotrypsin">Chymotrypsin</option>
5968 <option value="Arg-C/P">Arg-C/P</option>
5969 <option value="Arg-C">Arg-C</option>
5970 <option value="V8-E">V8-E</option>
5971 <option value="leukocyte elastase">leukocyte elastase</option>
5972 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5973 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5974 <option value="2-iodobenzoate">2-iodobenzoate</option>
5975 <option value="Asp-N">Asp-N</option>
5976 <expand macro="list_string_san" name="enzyme"/> 6050 <expand macro="list_string_san" name="enzyme"/>
5977 </param> 6051 </param>
5978 <param argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/> 6052 <param argument="-missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/>
5979 <param argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/> 6053 <param argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/>
5980 <param argument="-output_results" type="select" optional="true" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)"> 6054 <param argument="-output_results" type="select" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
5981 <option value="all" selected="true">all</option> 6055 <option value="all" selected="true">all</option>
5982 <option value="valid">valid</option> 6056 <option value="valid">valid</option>
5983 <option value="stochastic">stochastic</option> 6057 <option value="stochastic">stochastic</option>
5984 <expand macro="list_string_san" name="output_results"/> 6058 <expand macro="list_string_san" name="output_results"/>
5985 </param> 6059 </param>
5986 <param argument="-max_valid_expect" type="float" optional="true" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/> 6060 <param argument="-max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/>
5987 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/> 6061 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
5988 <section name="PeptideIndexing" title="" help="" expanded="false"> 6062 <section name="PeptideIndexing" title="" help="" expanded="false">
5989 <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)"> 6063 <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)">
5990 <expand macro="list_string_san" name="decoy_string"/> 6064 <expand macro="list_string_san" name="decoy_string"/>
5991 </param> 6065 </param>
5992 <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)"> 6066 <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)">
5993 <option value="prefix" selected="true">prefix</option> 6067 <option value="prefix" selected="true">prefix</option>
5994 <option value="suffix">suffix</option> 6068 <option value="suffix">suffix</option>
5995 <expand macro="list_string_san" name="decoy_string_position"/> 6069 <expand macro="list_string_san" name="decoy_string_position"/>
5996 </param> 6070 </param>
5997 <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=""> 6071 <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="">
5998 <option value="error">error</option> 6072 <option value="error">error</option>
5999 <option value="warn" selected="true">warn</option> 6073 <option value="warn" selected="true">warn</option>
6000 <option value="silent">silent</option> 6074 <option value="silent">silent</option>
6001 <expand macro="list_string_san" name="missing_decoy_action"/> 6075 <expand macro="list_string_san" name="missing_decoy_action"/>
6002 </param> 6076 </param>
6003 <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=""/> 6077 <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=""/>
6004 <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=""/> 6078 <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=""/>
6005 <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=""/> 6079 <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=""/>
6006 <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=""> 6080 <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="">
6007 <option value="error" selected="true">error</option> 6081 <option value="error" selected="true">error</option>
6008 <option value="warn">warn</option> 6082 <option value="warn">warn</option>
6009 <option value="remove">remove</option> 6083 <option value="remove">remove</option>
6010 <expand macro="list_string_san" name="unmatched_action"/> 6084 <expand macro="list_string_san" name="unmatched_action"/>
6011 </param> 6085 </param>
6012 <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'"/> 6086 <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'"/>
6013 <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"/> 6087 <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"/>
6014 <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"/> 6088 <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"/>
6089 <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=""/>
6015 <section name="enzyme" title="" help="" expanded="false"> 6090 <section name="enzyme" title="" help="" expanded="false">
6016 <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"> 6091 <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">
6017 <option value="auto" selected="true">auto</option> 6092 <option value="auto" selected="true">auto</option>
6018 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6019 <option value="CNBr">CNBr</option>
6020 <option value="Formic_acid">Formic_acid</option>
6021 <option value="Trypsin">Trypsin</option>
6022 <option value="Lys-C/P">Lys-C/P</option>
6023 <option value="PepsinA">PepsinA</option>
6024 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6025 <option value="2-iodobenzoate">2-iodobenzoate</option> 6093 <option value="2-iodobenzoate">2-iodobenzoate</option>
6026 <option value="iodosobenzoate">iodosobenzoate</option> 6094 <option value="iodosobenzoate">iodosobenzoate</option>
6027 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 6095 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6028 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 6096 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6029 <option value="Lys-C">Lys-C</option> 6097 <option value="Glu-C+P">Glu-C+P</option>
6030 <option value="Lys-N">Lys-N</option> 6098 <option value="Chymotrypsin">Chymotrypsin</option>
6031 <option value="Arg-C">Arg-C</option> 6099 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6032 <option value="leukocyte elastase">leukocyte elastase</option> 6100 <option value="CNBr">CNBr</option>
6101 <option value="Trypsin">Trypsin</option>
6102 <option value="unspecific cleavage">unspecific cleavage</option>
6033 <option value="proline endopeptidase">proline endopeptidase</option> 6103 <option value="proline endopeptidase">proline endopeptidase</option>
6034 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 6104 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6035 <option value="V8-DE">V8-DE</option> 6105 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6036 <option value="V8-E">V8-E</option>
6037 <option value="Arg-C/P">Arg-C/P</option>
6038 <option value="Asp-N">Asp-N</option>
6039 <option value="TrypChymo">TrypChymo</option> 6106 <option value="TrypChymo">TrypChymo</option>
6040 <option value="Trypsin/P">Trypsin/P</option> 6107 <option value="Trypsin/P">Trypsin/P</option>
6041 <option value="Glu-C+P">Glu-C+P</option> 6108 <option value="Lys-C/P">Lys-C/P</option>
6109 <option value="PepsinA">PepsinA</option>
6042 <option value="PepsinA + P">PepsinA + P</option> 6110 <option value="PepsinA + P">PepsinA + P</option>
6043 <option value="cyanogen-bromide">cyanogen-bromide</option> 6111 <option value="cyanogen-bromide">cyanogen-bromide</option>
6044 <option value="Clostripain/P">Clostripain/P</option> 6112 <option value="Clostripain/P">Clostripain/P</option>
6045 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 6113 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6046 <option value="no cleavage">no cleavage</option> 6114 <option value="no cleavage">no cleavage</option>
6047 <option value="unspecific cleavage">unspecific cleavage</option> 6115 <option value="Asp-N">Asp-N</option>
6048 <option value="Asp-N/B">Asp-N/B</option> 6116 <option value="Asp-N/B">Asp-N/B</option>
6049 <option value="Asp-N_ambic">Asp-N_ambic</option> 6117 <option value="Asp-N_ambic">Asp-N_ambic</option>
6050 <option value="Chymotrypsin">Chymotrypsin</option> 6118 <option value="Arg-C">Arg-C</option>
6119 <option value="Arg-C/P">Arg-C/P</option>
6120 <option value="V8-DE">V8-DE</option>
6121 <option value="V8-E">V8-E</option>
6122 <option value="leukocyte elastase">leukocyte elastase</option>
6123 <option value="Formic_acid">Formic_acid</option>
6124 <option value="Lys-C">Lys-C</option>
6125 <option value="Lys-N">Lys-N</option>
6051 <expand macro="list_string_san" name="name"/> 6126 <expand macro="list_string_san" name="name"/>
6052 </param> 6127 </param>
6053 <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)"> 6128 <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)">
6054 <option value="auto" selected="true">auto</option> 6129 <option value="auto" selected="true">auto</option>
6055 <option value="full">full</option> 6130 <option value="full">full</option>
6056 <option value="semi">semi</option> 6131 <option value="semi">semi</option>
6057 <option value="none">none</option> 6132 <option value="none">none</option>
6058 <expand macro="list_string_san" name="specificity"/> 6133 <expand macro="list_string_san" name="specificity"/>
6059 </param> 6134 </param>
6060 </section> 6135 </section>
6061 </section> 6136 </section>
6062 <expand macro="adv_opts_macro"> 6137 <expand macro="adv_opts_macro">
6063 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6138 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6064 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6139 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
6065 <expand macro="list_string_san" name="test"/> 6140 <expand macro="list_string_san" name="test"/>
6066 </param> 6141 </param>
6067 </expand> 6142 </expand>
6068 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6143 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6069 <option value="out_FLAG">out (Output file containing search results)</option> 6144 <option value="out_FLAG">out (Output file containing search results)</option>
6083 </data> 6158 </data>
6084 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6159 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6085 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6160 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6086 </data> 6161 </data>
6087 </outputs> 6162 </outputs>
6088 <tests><!-- TOPP_XTandemAdapter_1 --> 6163 <tests>
6164 <!-- TOPP_XTandemAdapter_1 -->
6089 <test expect_num_outputs="2"> 6165 <test expect_num_outputs="2">
6090 <section name="adv_opts"> 6166 <section name="adv_opts">
6091 <param name="force" value="false"/> 6167 <param name="force" value="false"/>
6092 <param name="test" value="true"/> 6168 <param name="test" value="true"/>
6093 </section> 6169 </section>
6094 <param name="in" value="spectra.mzML"/> 6170 <param name="in" value="spectra.mzML"/>
6095 <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6171 <output name="out" value="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6096 <param name="database" value="proteins.fasta"/> 6172 <param name="database" value="proteins.fasta"/>
6097 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> 6173 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6098 <param name="ignore_adapter_param" value="false"/> 6174 <param name="ignore_adapter_param" value="false"/>
6099 <param name="precursor_mass_tolerance" value="5.0"/> 6175 <param name="precursor_mass_tolerance" value="5.0"/>
6100 <param name="fragment_mass_tolerance" value="0.3"/> 6176 <param name="fragment_mass_tolerance" value="0.3"/>
6101 <param name="precursor_error_units" value="ppm"/> 6177 <param name="precursor_error_units" value="ppm"/>
6102 <param name="fragment_error_units" value="Da"/> 6178 <param name="fragment_error_units" value="Da"/>
6103 <param name="max_precursor_charge" value="0"/> 6179 <param name="max_precursor_charge" value="0"/>
6104 <param name="no_isotope_error" value="false"/> 6180 <param name="no_isotope_error" value="false"/>
6105 <param name="fixed_modifications"/>
6106 <param name="variable_modifications" value="Oxidation (M)"/> 6181 <param name="variable_modifications" value="Oxidation (M)"/>
6107 <param name="minimum_fragment_mz" value="150.0"/> 6182 <param name="minimum_fragment_mz" value="150.0"/>
6108 <param name="enzyme" value="Trypsin"/> 6183 <param name="enzyme" value="Trypsin"/>
6109 <param name="missed_cleavages" value="1"/> 6184 <param name="missed_cleavages" value="1"/>
6110 <param name="semi_cleavage" value="false"/> 6185 <param name="semi_cleavage" value="false"/>
6120 <param name="keep_unreferenced_proteins" value="false"/> 6195 <param name="keep_unreferenced_proteins" value="false"/>
6121 <param name="unmatched_action" value="error"/> 6196 <param name="unmatched_action" value="error"/>
6122 <param name="aaa_max" value="3"/> 6197 <param name="aaa_max" value="3"/>
6123 <param name="mismatches_max" value="0"/> 6198 <param name="mismatches_max" value="0"/>
6124 <param name="IL_equivalent" value="false"/> 6199 <param name="IL_equivalent" value="false"/>
6200 <param name="allow_nterm_protein_cleavage" value="true"/>
6125 <section name="enzyme"> 6201 <section name="enzyme">
6126 <param name="name" value="auto"/> 6202 <param name="name" value="auto"/>
6127 <param name="specificity" value="auto"/> 6203 <param name="specificity" value="auto"/>
6128 </section> 6204 </section>
6129 </section> 6205 </section>
6131 <output name="ctd_out" ftype="xml"> 6207 <output name="ctd_out" ftype="xml">
6132 <assert_contents> 6208 <assert_contents>
6133 <is_valid_xml/> 6209 <is_valid_xml/>
6134 </assert_contents> 6210 </assert_contents>
6135 </output> 6211 </output>
6212 <assert_stdout>
6213 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6214 </assert_stdout>
6136 </test> 6215 </test>
6137 <!-- TOPP_XTandemAdapter_2 --> 6216 <!-- TOPP_XTandemAdapter_2 -->
6138 <test expect_num_outputs="2"> 6217 <test expect_num_outputs="2">
6139 <section name="adv_opts"> 6218 <section name="adv_opts">
6140 <param name="force" value="false"/> 6219 <param name="force" value="false"/>
6141 <param name="test" value="true"/> 6220 <param name="test" value="true"/>
6142 </section> 6221 </section>
6143 <param name="in" value="spectra.mzML"/> 6222 <param name="in" value="spectra.mzML"/>
6144 <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6223 <output name="out" value="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6145 <param name="database" value="proteins.fasta"/> 6224 <param name="database" value="proteins.fasta"/>
6146 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> 6225 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6147 <param name="ignore_adapter_param" value="false"/> 6226 <param name="ignore_adapter_param" value="false"/>
6148 <param name="precursor_mass_tolerance" value="5.0"/> 6227 <param name="precursor_mass_tolerance" value="5.0"/>
6149 <param name="fragment_mass_tolerance" value="0.3"/> 6228 <param name="fragment_mass_tolerance" value="0.3"/>
6150 <param name="precursor_error_units" value="ppm"/> 6229 <param name="precursor_error_units" value="ppm"/>
6151 <param name="fragment_error_units" value="Da"/> 6230 <param name="fragment_error_units" value="Da"/>
6152 <param name="max_precursor_charge" value="0"/> 6231 <param name="max_precursor_charge" value="0"/>
6153 <param name="no_isotope_error" value="false"/> 6232 <param name="no_isotope_error" value="false"/>
6154 <param name="fixed_modifications"/>
6155 <param name="variable_modifications" value="Oxidation (M)"/> 6233 <param name="variable_modifications" value="Oxidation (M)"/>
6156 <param name="minimum_fragment_mz" value="150.0"/> 6234 <param name="minimum_fragment_mz" value="150.0"/>
6157 <param name="enzyme" value="Trypsin"/> 6235 <param name="enzyme" value="Trypsin"/>
6158 <param name="missed_cleavages" value="1"/> 6236 <param name="missed_cleavages" value="1"/>
6159 <param name="semi_cleavage" value="false"/> 6237 <param name="semi_cleavage" value="false"/>
6169 <param name="keep_unreferenced_proteins" value="false"/> 6247 <param name="keep_unreferenced_proteins" value="false"/>
6170 <param name="unmatched_action" value="error"/> 6248 <param name="unmatched_action" value="error"/>
6171 <param name="aaa_max" value="3"/> 6249 <param name="aaa_max" value="3"/>
6172 <param name="mismatches_max" value="0"/> 6250 <param name="mismatches_max" value="0"/>
6173 <param name="IL_equivalent" value="false"/> 6251 <param name="IL_equivalent" value="false"/>
6252 <param name="allow_nterm_protein_cleavage" value="true"/>
6174 <section name="enzyme"> 6253 <section name="enzyme">
6175 <param name="name" value="auto"/> 6254 <param name="name" value="auto"/>
6176 <param name="specificity" value="auto"/> 6255 <param name="specificity" value="auto"/>
6177 </section> 6256 </section>
6178 </section> 6257 </section>
6180 <output name="ctd_out" ftype="xml"> 6259 <output name="ctd_out" ftype="xml">
6181 <assert_contents> 6260 <assert_contents>
6182 <is_valid_xml/> 6261 <is_valid_xml/>
6183 </assert_contents> 6262 </assert_contents>
6184 </output> 6263 </output>
6264 <assert_stdout>
6265 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6266 </assert_stdout>
6185 </test> 6267 </test>
6186 <!-- TOPP_XTandemAdapter_3 --> 6268 <!-- TOPP_XTandemAdapter_3 -->
6187 <test expect_num_outputs="2"> 6269 <test expect_num_outputs="2">
6188 <section name="adv_opts"> 6270 <section name="adv_opts">
6189 <param name="force" value="false"/> 6271 <param name="force" value="false"/>
6190 <param name="test" value="true"/> 6272 <param name="test" value="true"/>
6191 </section> 6273 </section>
6192 <param name="in" value="spectra.mzML"/> 6274 <param name="in" value="spectra.mzML"/>
6193 <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6275 <output name="out" value="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6194 <param name="database" value="proteinslong.fasta"/> 6276 <param name="database" value="proteinslong.fasta"/>
6195 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> 6277 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6196 <param name="ignore_adapter_param" value="false"/> 6278 <param name="ignore_adapter_param" value="false"/>
6197 <param name="precursor_mass_tolerance" value="5.0"/> 6279 <param name="precursor_mass_tolerance" value="5.0"/>
6198 <param name="fragment_mass_tolerance" value="0.3"/> 6280 <param name="fragment_mass_tolerance" value="0.3"/>
6199 <param name="precursor_error_units" value="ppm"/> 6281 <param name="precursor_error_units" value="ppm"/>
6200 <param name="fragment_error_units" value="Da"/> 6282 <param name="fragment_error_units" value="Da"/>
6201 <param name="max_precursor_charge" value="0"/> 6283 <param name="max_precursor_charge" value="0"/>
6202 <param name="no_isotope_error" value="false"/> 6284 <param name="no_isotope_error" value="false"/>
6203 <param name="fixed_modifications"/>
6204 <param name="variable_modifications" value="Oxidation (M)"/> 6285 <param name="variable_modifications" value="Oxidation (M)"/>
6205 <param name="minimum_fragment_mz" value="150.0"/> 6286 <param name="minimum_fragment_mz" value="150.0"/>
6206 <param name="enzyme" value="Trypsin"/> 6287 <param name="enzyme" value="Trypsin"/>
6207 <param name="missed_cleavages" value="1"/> 6288 <param name="missed_cleavages" value="1"/>
6208 <param name="semi_cleavage" value="false"/> 6289 <param name="semi_cleavage" value="false"/>
6218 <param name="keep_unreferenced_proteins" value="false"/> 6299 <param name="keep_unreferenced_proteins" value="false"/>
6219 <param name="unmatched_action" value="error"/> 6300 <param name="unmatched_action" value="error"/>
6220 <param name="aaa_max" value="3"/> 6301 <param name="aaa_max" value="3"/>
6221 <param name="mismatches_max" value="0"/> 6302 <param name="mismatches_max" value="0"/>
6222 <param name="IL_equivalent" value="false"/> 6303 <param name="IL_equivalent" value="false"/>
6304 <param name="allow_nterm_protein_cleavage" value="true"/>
6223 <section name="enzyme"> 6305 <section name="enzyme">
6224 <param name="name" value="auto"/> 6306 <param name="name" value="auto"/>
6225 <param name="specificity" value="auto"/> 6307 <param name="specificity" value="auto"/>
6226 </section> 6308 </section>
6227 </section> 6309 </section>
6229 <output name="ctd_out" ftype="xml"> 6311 <output name="ctd_out" ftype="xml">
6230 <assert_contents> 6312 <assert_contents>
6231 <is_valid_xml/> 6313 <is_valid_xml/>
6232 </assert_contents> 6314 </assert_contents>
6233 </output> 6315 </output>
6316 <assert_stdout>
6317 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6318 </assert_stdout>
6234 </test> 6319 </test>
6235 </tests> 6320 </tests>
6236 <help><![CDATA[Annotates MS/MS spectra using X! Tandem. 6321 <help><![CDATA[Annotates MS/MS spectra using X! Tandem.
6237 6322
6238 6323
6239 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_XTandemAdapter.html]]></help> 6324 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XTandemAdapter.html]]></help>
6240 <expand macro="references"/> 6325 <expand macro="references"/>
6241 </tool> 6326 </tool>