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comparison RNPxlSearch.xml @ 12:33e2670c3a18 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:45 +0000
parents 0f97ea098da0
children
comparison
equal deleted inserted replaced
11:0f97ea098da0 12:33e2670c3a18
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: [Utilities]--> 2 <!--Proposed Tool Section: [Cross-Linking]-->
4 <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra.</description> 4 <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">RNPxlSearch</token> 6 <token name="@EXECUTABLE@">RNPxlSearch</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir database && 18 mkdir database &&
20 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 19 cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
21 mkdir out && 20 mkdir out &&
22 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_tsv && 22 mkdir out_tsv &&
24 #end if 23 #end if
25 24
54 <configfiles> 53 <configfiles>
55 <inputs name="args_json" data_style="paths"/> 54 <inputs name="args_json" data_style="paths"/>
56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
57 </configfiles> 56 </configfiles>
58 <inputs> 57 <inputs>
59 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 58 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
60 <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> 59 <param argument="-database" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
61 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> 60 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
62 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/> 61 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/>
63 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> 62 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
64 <option value="ppm" selected="true">ppm</option> 63 <option value="ppm" selected="true">ppm</option>
65 <option value="Da">Da</option> 64 <option value="Da">Da</option>
66 <expand macro="list_string_san" name="mass_tolerance_unit"/> 65 <expand macro="list_string_san" name="mass_tolerance_unit"/>
67 </param> 66 </param>
68 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> 67 <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
69 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> 68 <param name="max_charge" argument="-precursor:max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help=""/>
70 <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 69 <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
71 <expand macro="list_integer_valsan" name="isotopes"/> 70 <expand macro="list_integer_valsan" name="isotopes"/>
72 </param> 71 </param>
73 </section> 72 </section>
74 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> 73 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
75 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> 74 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
76 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help=""> 75 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help="">
77 <option value="ppm" selected="true">ppm</option> 76 <option value="ppm" selected="true">ppm</option>
78 <option value="Da">Da</option> 77 <option value="Da">Da</option>
79 <expand macro="list_string_san" name="mass_tolerance_unit"/> 78 <expand macro="list_string_san" name="mass_tolerance_unit"/>
80 </param> 79 </param>
81 </section> 80 </section>
82 <section name="modifications" title="Modifications Options" help="" expanded="false"> 81 <section name="modifications" title="Modifications Options" help="" expanded="false">
83 <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> 82 <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
84 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 83 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
85 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 84 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
86 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 85 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
87 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 86 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
88 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 87 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
89 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 88 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
90 <option value="2-succinyl (C)">2-succinyl (C)</option> 89 <option value="2-succinyl (C)">2-succinyl (C)</option>
91 <option value="2HPG (R)">2HPG (R)</option> 90 <option value="2HPG (R)">2HPG (R)</option>
92 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 91 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
92 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
93 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
94 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
95 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
93 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 96 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
94 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 97 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
95 <option value="4-ONE (C)">4-ONE (C)</option> 98 <option value="4-ONE (C)">4-ONE (C)</option>
96 <option value="4-ONE (H)">4-ONE (H)</option> 99 <option value="4-ONE (H)">4-ONE (H)</option>
97 <option value="4-ONE (K)">4-ONE (K)</option> 100 <option value="4-ONE (K)">4-ONE (K)</option>
177 <option value="Ammonium (D)">Ammonium (D)</option> 180 <option value="Ammonium (D)">Ammonium (D)</option>
178 <option value="Ammonium (E)">Ammonium (E)</option> 181 <option value="Ammonium (E)">Ammonium (E)</option>
179 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 182 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
180 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 183 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
181 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 184 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
185 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
182 <option value="Archaeol (C)">Archaeol (C)</option> 186 <option value="Archaeol (C)">Archaeol (C)</option>
183 <option value="Arg (N-term)">Arg (N-term)</option> 187 <option value="Arg (N-term)">Arg (N-term)</option>
184 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 188 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
185 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 189 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
186 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 190 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
280 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 284 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
281 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 285 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
282 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 286 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
283 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 287 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
284 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 288 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
289 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
285 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 290 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
286 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 291 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
287 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 292 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
288 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 293 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
289 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 294 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
312 <option value="BITC (C)">BITC (C)</option> 317 <option value="BITC (C)">BITC (C)</option>
313 <option value="BITC (K)">BITC (K)</option> 318 <option value="BITC (K)">BITC (K)</option>
314 <option value="BITC (N-term)">BITC (N-term)</option> 319 <option value="BITC (N-term)">BITC (N-term)</option>
315 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 320 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
316 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 321 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
317 <option value="Bodipy (C)">Bodipy (C)</option>
318 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 322 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
319 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 323 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
320 <option value="Bromo (F)">Bromo (F)</option> 324 <option value="Bromo (F)">Bromo (F)</option>
321 <option value="Bromo (H)">Bromo (H)</option> 325 <option value="Bromo (H)">Bromo (H)</option>
322 <option value="Bromo (W)">Bromo (W)</option> 326 <option value="Bromo (W)">Bromo (W)</option>
744 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 748 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
745 <option value="Dehydrated (S)">Dehydrated (S)</option> 749 <option value="Dehydrated (S)">Dehydrated (S)</option>
746 <option value="Dehydrated (T)">Dehydrated (T)</option> 750 <option value="Dehydrated (T)">Dehydrated (T)</option>
747 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 751 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
748 <option value="Dehydro (C)">Dehydro (C)</option> 752 <option value="Dehydro (C)">Dehydro (C)</option>
753 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
749 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 754 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
750 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 755 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
751 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
752 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 756 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
753 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 757 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
754 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 758 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
755 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 759 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
756 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 760 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
757 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 761 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
758 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 762 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
759 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 763 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
760 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 764 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
761 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
762 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 765 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
763 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 766 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
764 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 767 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
765 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 768 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
766 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 769 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
768 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 771 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
769 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 772 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
770 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 773 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
771 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 774 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
772 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 775 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
776 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
773 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 777 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
774 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 778 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
775 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 779 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
776 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 780 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
777 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 781 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
1340 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 1344 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
1341 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 1345 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
1342 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 1346 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
1343 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 1347 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
1344 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 1348 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
1345 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
1346 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 1349 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
1347 <option value="Ethyl (D)">Ethyl (D)</option> 1350 <option value="Ethyl (D)">Ethyl (D)</option>
1348 <option value="Ethyl (E)">Ethyl (E)</option> 1351 <option value="Ethyl (E)">Ethyl (E)</option>
1349 <option value="Ethyl (K)">Ethyl (K)</option> 1352 <option value="Ethyl (K)">Ethyl (K)</option>
1350 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 1353 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
1434 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 1437 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
1435 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 1438 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
1436 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 1439 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
1437 <option value="Glu (E)">Glu (E)</option> 1440 <option value="Glu (E)">Glu (E)</option>
1438 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 1441 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
1442 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
1439 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 1443 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
1440 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 1444 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
1441 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 1445 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
1442 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 1446 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
1443 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 1447 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
1448 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1452 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1449 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1453 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1450 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1454 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1451 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1455 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1452 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1456 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1453 <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>
1454 <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> 1457 <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>
1455 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1458 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1456 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1459 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
1457 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 1460 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
1458 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 1461 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
1472 <option value="Gluratylation (K)">Gluratylation (K)</option> 1475 <option value="Gluratylation (K)">Gluratylation (K)</option>
1473 <option value="Glutathione (C)">Glutathione (C)</option> 1476 <option value="Glutathione (C)">Glutathione (C)</option>
1474 <option value="Gly (K)">Gly (K)</option> 1477 <option value="Gly (K)">Gly (K)</option>
1475 <option value="Gly (S)">Gly (S)</option> 1478 <option value="Gly (S)">Gly (S)</option>
1476 <option value="Gly (T)">Gly (T)</option> 1479 <option value="Gly (T)">Gly (T)</option>
1480 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
1477 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 1481 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
1478 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 1482 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
1479 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 1483 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
1480 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 1484 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
1481 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 1485 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
1862 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 1866 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
1863 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 1867 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
1864 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 1868 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
1865 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 1869 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
1866 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 1870 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
1871 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
1867 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 1872 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
1868 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 1873 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
1869 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 1874 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
1870 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 1875 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
1871 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 1876 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
1873 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 1878 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
1874 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 1879 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
1875 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 1880 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
1876 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 1881 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
1877 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 1882 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
1883 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
1884 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
1885 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
1878 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 1886 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
1879 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 1887 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
1880 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 1888 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
1881 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 1889 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
1882 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 1890 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
1928 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 1936 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
1929 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 1937 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
1930 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 1938 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
1931 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 1939 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
1932 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 1940 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
1941 <option value="His+O(2) (H)">His+O(2) (H)</option>
1933 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 1942 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
1934 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 1943 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
1935 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 1944 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
1936 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 1945 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
1937 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 1946 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
2065 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 2074 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
2066 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 2075 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
2067 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 2076 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
2068 <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) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
2069 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 2078 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
2079 <option value="Kdo (S)">Kdo (S)</option>
2080 <option value="Kdo (T)">Kdo (T)</option>
2070 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 2081 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
2071 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 2082 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
2072 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 2083 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
2073 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 2084 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
2074 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 2085 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
2086 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
2075 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 2087 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
2076 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 2088 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
2077 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 2089 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
2078 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 2090 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
2079 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 2091 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
2154 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 2166 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
2155 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 2167 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
2156 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 2168 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
2157 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 2169 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
2158 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 2170 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
2171 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
2159 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 2172 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
2160 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 2173 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
2161 <option value="Lipoyl (K)">Lipoyl (K)</option> 2174 <option value="Lipoyl (K)">Lipoyl (K)</option>
2162 <option value="LRGG (K)">LRGG (K)</option> 2175 <option value="LRGG (K)">LRGG (K)</option>
2163 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 2176 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
2164 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 2177 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
2178 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
2165 <option value="Lys (N-term)">Lys (N-term)</option> 2179 <option value="Lys (N-term)">Lys (N-term)</option>
2180 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
2166 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 2181 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
2167 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 2182 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
2168 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 2183 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
2169 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 2184 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
2170 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 2185 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
2195 <option value="maleimide5 (C)">maleimide5 (C)</option> 2210 <option value="maleimide5 (C)">maleimide5 (C)</option>
2196 <option value="maleimide5 (K)">maleimide5 (K)</option> 2211 <option value="maleimide5 (K)">maleimide5 (K)</option>
2197 <option value="Malonyl (C)">Malonyl (C)</option> 2212 <option value="Malonyl (C)">Malonyl (C)</option>
2198 <option value="Malonyl (K)">Malonyl (K)</option> 2213 <option value="Malonyl (K)">Malonyl (K)</option>
2199 <option value="Malonyl (S)">Malonyl (S)</option> 2214 <option value="Malonyl (S)">Malonyl (S)</option>
2215 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
2200 <option value="MDCC (C)">MDCC (C)</option> 2216 <option value="MDCC (C)">MDCC (C)</option>
2201 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 2217 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
2202 <option value="Menadione (C)">Menadione (C)</option> 2218 <option value="Menadione (C)">Menadione (C)</option>
2203 <option value="Menadione (K)">Menadione (K)</option> 2219 <option value="Menadione (K)">Menadione (K)</option>
2204 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 2220 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
2206 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 2222 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
2207 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 2223 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
2208 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 2224 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
2209 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 2225 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
2210 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 2226 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
2227 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
2211 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 2228 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
2212 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 2229 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
2213 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 2230 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
2214 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 2231 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
2215 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 2232 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
2389 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 2406 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
2390 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 2407 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
2391 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 2408 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
2392 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 2409 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
2393 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 2410 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
2394 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
2395 <option value="NP40 (N-term)">NP40 (N-term)</option> 2411 <option value="NP40 (N-term)">NP40 (N-term)</option>
2396 <option value="NQIGG (K)">NQIGG (K)</option> 2412 <option value="NQIGG (K)">NQIGG (K)</option>
2397 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 2413 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
2398 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 2414 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
2399 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 2415 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
2477 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 2493 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
2478 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 2494 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
2479 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 2495 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
2480 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 2496 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
2481 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 2497 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
2498 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
2499 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
2500 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
2501 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
2482 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 2502 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
2483 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 2503 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
2484 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 2504 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
2485 <option value="Phospho (C)">Phospho (C)</option> 2505 <option value="Phospho (C)">Phospho (C)</option>
2486 <option value="Phospho (D)">Phospho (D)</option> 2506 <option value="Phospho (D)">Phospho (D)</option>
2491 <option value="Phospho (S)">Phospho (S)</option> 2511 <option value="Phospho (S)">Phospho (S)</option>
2492 <option value="Phospho (T)">Phospho (T)</option> 2512 <option value="Phospho (T)">Phospho (T)</option>
2493 <option value="Phospho (Y)">Phospho (Y)</option> 2513 <option value="Phospho (Y)">Phospho (Y)</option>
2494 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 2514 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
2495 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 2515 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
2516 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
2496 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 2517 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
2497 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 2518 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
2498 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 2519 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
2499 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 2520 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
2500 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 2521 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
2522 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 2543 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
2523 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 2544 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
2524 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 2545 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
2525 <option value="Piperidine (K)">Piperidine (K)</option> 2546 <option value="Piperidine (K)">Piperidine (K)</option>
2526 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 2547 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
2548 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
2527 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 2549 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
2528 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 2550 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
2529 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 2551 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
2530 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 2552 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
2531 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 2553 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
2599 <option value="QEQTGG (K)">QEQTGG (K)</option> 2621 <option value="QEQTGG (K)">QEQTGG (K)</option>
2600 <option value="QQQTGG (K)">QQQTGG (K)</option> 2622 <option value="QQQTGG (K)">QQQTGG (K)</option>
2601 <option value="QTGG (K)">QTGG (K)</option> 2623 <option value="QTGG (K)">QTGG (K)</option>
2602 <option value="Quinone (W)">Quinone (W)</option> 2624 <option value="Quinone (W)">Quinone (W)</option>
2603 <option value="Quinone (Y)">Quinone (Y)</option> 2625 <option value="Quinone (Y)">Quinone (Y)</option>
2626 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
2627 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
2628 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
2629 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
2630 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
2631 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
2632 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
2633 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
2634 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
2635 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
2636 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
2637 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
2638 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
2639 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
2640 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
2641 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
2642 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
2643 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
2644 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
2645 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
2604 <option value="Retinylidene (K)">Retinylidene (K)</option> 2646 <option value="Retinylidene (K)">Retinylidene (K)</option>
2605 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 2647 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
2606 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 2648 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
2607 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 2649 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
2608 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
2609 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
2610 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
2611 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
2612 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
2613 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
2614 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
2615 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
2616 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 2650 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
2617 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 2651 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
2618 <option value="Saligenin (H)">Saligenin (H)</option> 2652 <option value="Saligenin (H)">Saligenin (H)</option>
2619 <option value="Saligenin (K)">Saligenin (K)</option> 2653 <option value="Saligenin (K)">Saligenin (K)</option>
2620 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 2654 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
2638 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 2672 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
2639 <option value="serotonylation (Q)">serotonylation (Q)</option> 2673 <option value="serotonylation (Q)">serotonylation (Q)</option>
2640 <option value="shTMT (K)">shTMT (K)</option> 2674 <option value="shTMT (K)">shTMT (K)</option>
2641 <option value="shTMT (N-term)">shTMT (N-term)</option> 2675 <option value="shTMT (N-term)">shTMT (N-term)</option>
2642 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 2676 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
2677 <option value="shTMTpro (K)">shTMTpro (K)</option>
2678 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
2679 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
2643 <option value="SMA (K)">SMA (K)</option> 2680 <option value="SMA (K)">SMA (K)</option>
2644 <option value="SMA (N-term)">SMA (N-term)</option> 2681 <option value="SMA (N-term)">SMA (N-term)</option>
2645 <option value="spermidine (Q)">spermidine (Q)</option> 2682 <option value="spermidine (Q)">spermidine (Q)</option>
2646 <option value="spermine (Q)">spermine (Q)</option> 2683 <option value="spermine (Q)">spermine (Q)</option>
2647 <option value="SPITC (K)">SPITC (K)</option> 2684 <option value="SPITC (K)">SPITC (K)</option>
2813 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 2850 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
2814 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 2851 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
2815 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 2852 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
2816 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 2853 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
2817 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 2854 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
2818 <option value="Ub-amide (C)">Ub-amide (C)</option>
2819 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 2855 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
2820 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 2856 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
2821 <option value="Ub-VME (C)">Ub-VME (C)</option> 2857 <option value="Ub-VME (C)">Ub-VME (C)</option>
2822 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 2858 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
2823 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 2859 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
3008 <option value="ZGB (K)">ZGB (K)</option> 3044 <option value="ZGB (K)">ZGB (K)</option>
3009 <option value="ZGB (N-term)">ZGB (N-term)</option> 3045 <option value="ZGB (N-term)">ZGB (N-term)</option>
3010 <option value="ZQG (K)">ZQG (K)</option> 3046 <option value="ZQG (K)">ZQG (K)</option>
3011 <expand macro="list_string_san" name="fixed"/> 3047 <expand macro="list_string_san" name="fixed"/>
3012 </param> 3048 </param>
3013 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> 3049 <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
3014 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3050 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3015 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3051 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3016 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3052 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3017 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3053 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3018 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3054 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
3019 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 3055 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
3020 <option value="2-succinyl (C)">2-succinyl (C)</option> 3056 <option value="2-succinyl (C)">2-succinyl (C)</option>
3021 <option value="2HPG (R)">2HPG (R)</option> 3057 <option value="2HPG (R)">2HPG (R)</option>
3022 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 3058 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
3059 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
3060 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
3061 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
3062 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
3023 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 3063 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
3024 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 3064 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
3025 <option value="4-ONE (C)">4-ONE (C)</option> 3065 <option value="4-ONE (C)">4-ONE (C)</option>
3026 <option value="4-ONE (H)">4-ONE (H)</option> 3066 <option value="4-ONE (H)">4-ONE (H)</option>
3027 <option value="4-ONE (K)">4-ONE (K)</option> 3067 <option value="4-ONE (K)">4-ONE (K)</option>
3107 <option value="Ammonium (D)">Ammonium (D)</option> 3147 <option value="Ammonium (D)">Ammonium (D)</option>
3108 <option value="Ammonium (E)">Ammonium (E)</option> 3148 <option value="Ammonium (E)">Ammonium (E)</option>
3109 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 3149 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
3110 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 3150 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
3111 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 3151 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
3152 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
3112 <option value="Archaeol (C)">Archaeol (C)</option> 3153 <option value="Archaeol (C)">Archaeol (C)</option>
3113 <option value="Arg (N-term)">Arg (N-term)</option> 3154 <option value="Arg (N-term)">Arg (N-term)</option>
3114 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 3155 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
3115 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 3156 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
3116 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 3157 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
3210 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 3251 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
3211 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 3252 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
3212 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 3253 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
3213 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 3254 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
3214 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 3255 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
3256 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
3215 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 3257 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
3216 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 3258 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
3217 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 3259 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
3218 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 3260 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
3219 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 3261 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
3242 <option value="BITC (C)">BITC (C)</option> 3284 <option value="BITC (C)">BITC (C)</option>
3243 <option value="BITC (K)">BITC (K)</option> 3285 <option value="BITC (K)">BITC (K)</option>
3244 <option value="BITC (N-term)">BITC (N-term)</option> 3286 <option value="BITC (N-term)">BITC (N-term)</option>
3245 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 3287 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
3246 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 3288 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
3247 <option value="Bodipy (C)">Bodipy (C)</option>
3248 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 3289 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
3249 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 3290 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
3250 <option value="Bromo (F)">Bromo (F)</option> 3291 <option value="Bromo (F)">Bromo (F)</option>
3251 <option value="Bromo (H)">Bromo (H)</option> 3292 <option value="Bromo (H)">Bromo (H)</option>
3252 <option value="Bromo (W)">Bromo (W)</option> 3293 <option value="Bromo (W)">Bromo (W)</option>
3674 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 3715 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
3675 <option value="Dehydrated (S)">Dehydrated (S)</option> 3716 <option value="Dehydrated (S)">Dehydrated (S)</option>
3676 <option value="Dehydrated (T)">Dehydrated (T)</option> 3717 <option value="Dehydrated (T)">Dehydrated (T)</option>
3677 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 3718 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
3678 <option value="Dehydro (C)">Dehydro (C)</option> 3719 <option value="Dehydro (C)">Dehydro (C)</option>
3720 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
3679 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 3721 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
3680 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 3722 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
3681 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
3682 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 3723 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
3683 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 3724 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
3684 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 3725 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
3685 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 3726 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
3686 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 3727 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
3687 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 3728 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
3688 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 3729 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
3689 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 3730 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
3690 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 3731 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
3691 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
3692 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 3732 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
3693 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 3733 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
3694 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 3734 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
3695 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 3735 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
3696 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 3736 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
3698 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 3738 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
3699 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 3739 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
3700 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 3740 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
3701 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 3741 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
3702 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 3742 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
3743 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
3703 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 3744 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
3704 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 3745 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
3705 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 3746 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
3706 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 3747 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
3707 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 3748 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
4270 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 4311 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
4271 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 4312 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
4272 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 4313 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
4273 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 4314 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
4274 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 4315 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
4275 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
4276 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 4316 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
4277 <option value="Ethyl (D)">Ethyl (D)</option> 4317 <option value="Ethyl (D)">Ethyl (D)</option>
4278 <option value="Ethyl (E)">Ethyl (E)</option> 4318 <option value="Ethyl (E)">Ethyl (E)</option>
4279 <option value="Ethyl (K)">Ethyl (K)</option> 4319 <option value="Ethyl (K)">Ethyl (K)</option>
4280 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 4320 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
4364 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 4404 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
4365 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 4405 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
4366 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 4406 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
4367 <option value="Glu (E)">Glu (E)</option> 4407 <option value="Glu (E)">Glu (E)</option>
4368 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 4408 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
4409 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
4369 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 4410 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
4370 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 4411 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
4371 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 4412 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
4372 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 4413 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
4373 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 4414 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
4378 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4419 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4379 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4420 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4380 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4421 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4381 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4422 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4382 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4423 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4383 <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>
4384 <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> 4424 <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>
4385 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4425 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4386 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4426 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
4387 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 4427 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
4388 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 4428 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
4402 <option value="Gluratylation (K)">Gluratylation (K)</option> 4442 <option value="Gluratylation (K)">Gluratylation (K)</option>
4403 <option value="Glutathione (C)">Glutathione (C)</option> 4443 <option value="Glutathione (C)">Glutathione (C)</option>
4404 <option value="Gly (K)">Gly (K)</option> 4444 <option value="Gly (K)">Gly (K)</option>
4405 <option value="Gly (S)">Gly (S)</option> 4445 <option value="Gly (S)">Gly (S)</option>
4406 <option value="Gly (T)">Gly (T)</option> 4446 <option value="Gly (T)">Gly (T)</option>
4447 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
4407 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 4448 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
4408 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 4449 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
4409 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 4450 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
4410 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 4451 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
4411 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 4452 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
4792 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 4833 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
4793 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 4834 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
4794 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 4835 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
4795 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 4836 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
4796 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 4837 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
4838 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
4797 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 4839 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
4798 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 4840 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
4799 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 4841 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
4800 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 4842 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
4801 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 4843 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
4803 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 4845 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
4804 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 4846 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
4805 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 4847 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
4806 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 4848 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
4807 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 4849 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
4850 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
4851 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
4852 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
4808 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 4853 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
4809 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 4854 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
4810 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 4855 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
4811 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 4856 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
4812 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 4857 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
4858 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 4903 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
4859 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 4904 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
4860 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 4905 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
4861 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 4906 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
4862 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 4907 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
4908 <option value="His+O(2) (H)">His+O(2) (H)</option>
4863 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 4909 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
4864 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 4910 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
4865 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 4911 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
4866 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 4912 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
4867 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 4913 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
4995 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 5041 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
4996 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 5042 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
4997 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 5043 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
4998 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 5044 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
4999 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 5045 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
5046 <option value="Kdo (S)">Kdo (S)</option>
5047 <option value="Kdo (T)">Kdo (T)</option>
5000 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 5048 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
5001 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 5049 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
5002 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 5050 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
5003 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 5051 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
5004 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 5052 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
5053 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
5005 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 5054 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
5006 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 5055 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
5007 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 5056 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
5008 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 5057 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
5009 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 5058 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
5084 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 5133 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
5085 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 5134 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
5086 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 5135 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
5087 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 5136 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
5088 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 5137 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
5138 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
5089 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 5139 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
5090 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 5140 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
5091 <option value="Lipoyl (K)">Lipoyl (K)</option> 5141 <option value="Lipoyl (K)">Lipoyl (K)</option>
5092 <option value="LRGG (K)">LRGG (K)</option> 5142 <option value="LRGG (K)">LRGG (K)</option>
5093 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 5143 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
5094 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 5144 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
5145 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
5095 <option value="Lys (N-term)">Lys (N-term)</option> 5146 <option value="Lys (N-term)">Lys (N-term)</option>
5147 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
5096 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 5148 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
5097 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 5149 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
5098 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 5150 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
5099 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 5151 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
5100 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 5152 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
5125 <option value="maleimide5 (C)">maleimide5 (C)</option> 5177 <option value="maleimide5 (C)">maleimide5 (C)</option>
5126 <option value="maleimide5 (K)">maleimide5 (K)</option> 5178 <option value="maleimide5 (K)">maleimide5 (K)</option>
5127 <option value="Malonyl (C)">Malonyl (C)</option> 5179 <option value="Malonyl (C)">Malonyl (C)</option>
5128 <option value="Malonyl (K)">Malonyl (K)</option> 5180 <option value="Malonyl (K)">Malonyl (K)</option>
5129 <option value="Malonyl (S)">Malonyl (S)</option> 5181 <option value="Malonyl (S)">Malonyl (S)</option>
5182 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
5130 <option value="MDCC (C)">MDCC (C)</option> 5183 <option value="MDCC (C)">MDCC (C)</option>
5131 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 5184 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
5132 <option value="Menadione (C)">Menadione (C)</option> 5185 <option value="Menadione (C)">Menadione (C)</option>
5133 <option value="Menadione (K)">Menadione (K)</option> 5186 <option value="Menadione (K)">Menadione (K)</option>
5134 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 5187 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
5136 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 5189 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
5137 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 5190 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
5138 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 5191 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
5139 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 5192 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
5140 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 5193 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
5194 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
5141 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 5195 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
5142 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 5196 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
5143 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 5197 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
5144 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 5198 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
5145 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 5199 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
5319 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 5373 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
5320 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 5374 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
5321 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 5375 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
5322 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 5376 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
5323 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 5377 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
5324 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
5325 <option value="NP40 (N-term)">NP40 (N-term)</option> 5378 <option value="NP40 (N-term)">NP40 (N-term)</option>
5326 <option value="NQIGG (K)">NQIGG (K)</option> 5379 <option value="NQIGG (K)">NQIGG (K)</option>
5327 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 5380 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
5328 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 5381 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
5329 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 5382 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
5407 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 5460 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
5408 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 5461 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
5409 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 5462 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
5410 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 5463 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
5411 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 5464 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
5465 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
5466 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
5467 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
5468 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
5412 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 5469 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
5413 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 5470 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
5414 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 5471 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
5415 <option value="Phospho (C)">Phospho (C)</option> 5472 <option value="Phospho (C)">Phospho (C)</option>
5416 <option value="Phospho (D)">Phospho (D)</option> 5473 <option value="Phospho (D)">Phospho (D)</option>
5421 <option value="Phospho (S)">Phospho (S)</option> 5478 <option value="Phospho (S)">Phospho (S)</option>
5422 <option value="Phospho (T)">Phospho (T)</option> 5479 <option value="Phospho (T)">Phospho (T)</option>
5423 <option value="Phospho (Y)">Phospho (Y)</option> 5480 <option value="Phospho (Y)">Phospho (Y)</option>
5424 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 5481 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
5425 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 5482 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
5483 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
5426 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 5484 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
5427 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 5485 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
5428 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 5486 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
5429 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 5487 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
5430 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 5488 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
5452 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 5510 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
5453 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 5511 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
5454 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 5512 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
5455 <option value="Piperidine (K)">Piperidine (K)</option> 5513 <option value="Piperidine (K)">Piperidine (K)</option>
5456 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 5514 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
5515 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
5457 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 5516 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
5458 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 5517 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
5459 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 5518 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
5460 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 5519 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
5461 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 5520 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
5529 <option value="QEQTGG (K)">QEQTGG (K)</option> 5588 <option value="QEQTGG (K)">QEQTGG (K)</option>
5530 <option value="QQQTGG (K)">QQQTGG (K)</option> 5589 <option value="QQQTGG (K)">QQQTGG (K)</option>
5531 <option value="QTGG (K)">QTGG (K)</option> 5590 <option value="QTGG (K)">QTGG (K)</option>
5532 <option value="Quinone (W)">Quinone (W)</option> 5591 <option value="Quinone (W)">Quinone (W)</option>
5533 <option value="Quinone (Y)">Quinone (Y)</option> 5592 <option value="Quinone (Y)">Quinone (Y)</option>
5593 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
5594 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
5595 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
5596 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
5597 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
5598 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
5599 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
5600 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
5601 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
5602 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
5603 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
5604 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
5605 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
5606 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
5607 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
5608 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
5609 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
5610 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
5611 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
5612 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
5534 <option value="Retinylidene (K)">Retinylidene (K)</option> 5613 <option value="Retinylidene (K)">Retinylidene (K)</option>
5535 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 5614 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
5536 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 5615 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
5537 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 5616 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
5538 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
5539 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
5540 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
5541 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
5542 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
5543 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
5544 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
5545 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
5546 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 5617 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
5547 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 5618 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
5548 <option value="Saligenin (H)">Saligenin (H)</option> 5619 <option value="Saligenin (H)">Saligenin (H)</option>
5549 <option value="Saligenin (K)">Saligenin (K)</option> 5620 <option value="Saligenin (K)">Saligenin (K)</option>
5550 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 5621 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
5568 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 5639 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
5569 <option value="serotonylation (Q)">serotonylation (Q)</option> 5640 <option value="serotonylation (Q)">serotonylation (Q)</option>
5570 <option value="shTMT (K)">shTMT (K)</option> 5641 <option value="shTMT (K)">shTMT (K)</option>
5571 <option value="shTMT (N-term)">shTMT (N-term)</option> 5642 <option value="shTMT (N-term)">shTMT (N-term)</option>
5572 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 5643 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
5644 <option value="shTMTpro (K)">shTMTpro (K)</option>
5645 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
5646 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
5573 <option value="SMA (K)">SMA (K)</option> 5647 <option value="SMA (K)">SMA (K)</option>
5574 <option value="SMA (N-term)">SMA (N-term)</option> 5648 <option value="SMA (N-term)">SMA (N-term)</option>
5575 <option value="spermidine (Q)">spermidine (Q)</option> 5649 <option value="spermidine (Q)">spermidine (Q)</option>
5576 <option value="spermine (Q)">spermine (Q)</option> 5650 <option value="spermine (Q)">spermine (Q)</option>
5577 <option value="SPITC (K)">SPITC (K)</option> 5651 <option value="SPITC (K)">SPITC (K)</option>
5743 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 5817 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
5744 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 5818 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
5745 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 5819 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
5746 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 5820 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
5747 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 5821 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
5748 <option value="Ub-amide (C)">Ub-amide (C)</option>
5749 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 5822 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
5750 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 5823 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
5751 <option value="Ub-VME (C)">Ub-VME (C)</option> 5824 <option value="Ub-VME (C)">Ub-VME (C)</option>
5752 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 5825 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
5753 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 5826 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
5938 <option value="ZGB (K)">ZGB (K)</option> 6011 <option value="ZGB (K)">ZGB (K)</option>
5939 <option value="ZGB (N-term)">ZGB (N-term)</option> 6012 <option value="ZGB (N-term)">ZGB (N-term)</option>
5940 <option value="ZQG (K)">ZQG (K)</option> 6013 <option value="ZQG (K)">ZQG (K)</option>
5941 <expand macro="list_string_san" name="variable"/> 6014 <expand macro="list_string_san" name="variable"/>
5942 </param> 6015 </param>
5943 <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> 6016 <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
5944 </section> 6017 </section>
5945 <section name="peptide" title="Peptide Options" help="" expanded="false"> 6018 <section name="peptide" title="Peptide Options" help="" expanded="false">
5946 <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> 6019 <param name="min_size" argument="-peptide:min_size" type="integer" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
5947 <param name="max_size" argument="-peptide:max_size" type="integer" optional="true" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/> 6020 <param name="max_size" argument="-peptide:max_size" type="integer" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/>
5948 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> 6021 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/>
5949 <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> 6022 <param name="enzyme" argument="-peptide:enzyme" type="select" label="The enzyme used for peptide digestion" help="">
6023 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6024 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6025 <option value="2-iodobenzoate">2-iodobenzoate</option>
6026 <option value="iodosobenzoate">iodosobenzoate</option>
6027 <option value="Lys-C/P">Lys-C/P</option>
5950 <option value="PepsinA">PepsinA</option> 6028 <option value="PepsinA">PepsinA</option>
5951 <option value="TrypChymo">TrypChymo</option>
5952 <option value="Trypsin/P">Trypsin/P</option>
5953 <option value="Trypsin" selected="true">Trypsin</option> 6029 <option value="Trypsin" selected="true">Trypsin</option>
5954 <option value="Lys-N">Lys-N</option> 6030 <option value="Chymotrypsin">Chymotrypsin</option>
5955 <option value="Lys-C/P">Lys-C/P</option> 6031 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5956 <option value="Clostripain/P">Clostripain/P</option> 6032 <option value="CNBr">CNBr</option>
5957 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
5958 <option value="no cleavage">no cleavage</option>
5959 <option value="unspecific cleavage">unspecific cleavage</option>
5960 <option value="Arg-C/P">Arg-C/P</option>
5961 <option value="Asp-N">Asp-N</option>
5962 <option value="Asp-N/B">Asp-N/B</option>
5963 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 6033 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
5964 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 6034 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
5965 <option value="Glu-C+P">Glu-C+P</option> 6035 <option value="Glu-C+P">Glu-C+P</option>
5966 <option value="PepsinA + P">PepsinA + P</option> 6036 <option value="PepsinA + P">PepsinA + P</option>
5967 <option value="cyanogen-bromide">cyanogen-bromide</option> 6037 <option value="cyanogen-bromide">cyanogen-bromide</option>
5968 <option value="Asp-N_ambic">Asp-N_ambic</option>
5969 <option value="Chymotrypsin">Chymotrypsin</option>
5970 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5971 <option value="Arg-C">Arg-C</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="iodosobenzoate">iodosobenzoate</option>
5976 <option value="CNBr">CNBr</option>
5977 <option value="Formic_acid">Formic_acid</option> 6038 <option value="Formic_acid">Formic_acid</option>
5978 <option value="Lys-C">Lys-C</option> 6039 <option value="Lys-C">Lys-C</option>
6040 <option value="Lys-N">Lys-N</option>
6041 <option value="Arg-C">Arg-C</option>
6042 <option value="Arg-C/P">Arg-C/P</option>
5979 <option value="V8-DE">V8-DE</option> 6043 <option value="V8-DE">V8-DE</option>
5980 <option value="V8-E">V8-E</option> 6044 <option value="V8-E">V8-E</option>
6045 <option value="Asp-N">Asp-N</option>
6046 <option value="Asp-N/B">Asp-N/B</option>
6047 <option value="Asp-N_ambic">Asp-N_ambic</option>
5981 <option value="leukocyte elastase">leukocyte elastase</option> 6048 <option value="leukocyte elastase">leukocyte elastase</option>
5982 <option value="proline endopeptidase">proline endopeptidase</option> 6049 <option value="proline endopeptidase">proline endopeptidase</option>
6050 <option value="TrypChymo">TrypChymo</option>
6051 <option value="Trypsin/P">Trypsin/P</option>
6052 <option value="Clostripain/P">Clostripain/P</option>
6053 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6054 <option value="no cleavage">no cleavage</option>
6055 <option value="unspecific cleavage">unspecific cleavage</option>
5983 <expand macro="list_string_san" name="enzyme"/> 6056 <expand macro="list_string_san" name="enzyme"/>
5984 </param> 6057 </param>
5985 </section> 6058 </section>
5986 <section name="report" title="Reporting Options" help="" expanded="false"> 6059 <section name="report" title="Reporting Options" help="" expanded="false">
5987 <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> 6060 <param name="top_hits" argument="-report:top_hits" type="integer" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
5988 </section> 6061 </section>
5989 <section name="RNPxl" title="RNPxl Options" help="" expanded="false"> 6062 <section name="RNPxl" title="RNPxl Options" help="" expanded="false">
5990 <param name="length" argument="-RNPxl:length" type="integer" optional="true" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/> 6063 <param name="length" argument="-RNPxl:length" type="integer" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/>
5991 <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)"> 6064 <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)">
5992 <expand macro="list_string_san" name="sequence"/> 6065 <expand macro="list_string_san" name="sequence"/>
5993 </param> 6066 </param>
5994 <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" optional="true" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6067 <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)">
5995 <expand macro="list_string_val" name="target_nucleotides"/> 6068 <expand macro="list_string_val" name="target_nucleotides"/>
5996 <expand macro="list_string_san" name="target_nucleotides"/> 6069 <expand macro="list_string_san" name="target_nucleotides"/>
5997 </param> 6070 </param>
5998 <param name="nt_groups" argument="-RNPxl:nt_groups" type="text" optional="true" value="" label="Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate" help="e.g.: AU CG) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6071 <param name="nt_groups" argument="-RNPxl:nt_groups" type="text" optional="true" value="" label="Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate" help="e.g.: AU CG) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
5999 <expand macro="list_string_val" name="nt_groups"/> 6072 <expand macro="list_string_val" name="nt_groups"/>
6000 <expand macro="list_string_san" name="nt_groups"/> 6073 <expand macro="list_string_san" name="nt_groups"/>
6001 </param> 6074 </param>
6002 <param name="mapping" argument="-RNPxl:mapping" type="text" optional="true" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6075 <param name="mapping" argument="-RNPxl:mapping" type="text" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6003 <expand macro="list_string_val" name="mapping"/> 6076 <expand macro="list_string_val" name="mapping"/>
6004 <expand macro="list_string_san" name="mapping"/> 6077 <expand macro="list_string_san" name="mapping"/>
6005 </param> 6078 </param>
6006 <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" optional="true" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links"> 6079 <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links">
6007 <expand macro="list_string_san" name="can_cross_link"/> 6080 <expand macro="list_string_san" name="can_cross_link"/>
6008 </param> 6081 </param>
6009 <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" optional="true" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6082 <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6010 <expand macro="list_string_val" name="fragment_adducts"/> 6083 <expand macro="list_string_val" name="fragment_adducts"/>
6011 <expand macro="list_string_san" name="fragment_adducts"/> 6084 <expand macro="list_string_san" name="fragment_adducts"/>
6012 </param> 6085 </param>
6013 <param name="modifications" argument="-RNPxl:modifications" type="text" optional="true" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6086 <param name="modifications" argument="-RNPxl:modifications" type="text" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6014 <expand macro="list_string_val" name="modifications"/> 6087 <expand macro="list_string_val" name="modifications"/>
6015 <expand macro="list_string_san" name="modifications"/> 6088 <expand macro="list_string_san" name="modifications"/>
6016 </param> 6089 </param>
6017 <param name="scoring" argument="-RNPxl:scoring" type="select" optional="true" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help=""> 6090 <param name="scoring" argument="-RNPxl:scoring" type="select" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
6018 <option value="fast" selected="true">fast</option> 6091 <option value="fast" selected="true">fast</option>
6019 <option value="slow">slow</option> 6092 <option value="slow">slow</option>
6020 <expand macro="list_string_san" name="scoring"/> 6093 <expand macro="list_string_san" name="scoring"/>
6021 </param> 6094 </param>
6022 <param name="decoys" argument="-RNPxl:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate decoy sequences and spectra" help=""/> 6095 <param name="decoys" argument="-RNPxl:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate decoy sequences and spectra" help=""/>
6023 <param name="CysteineAdduct" argument="-RNPxl:CysteineAdduct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the +152 adduct is expected" help=""/> 6096 <param name="CysteineAdduct" argument="-RNPxl:CysteineAdduct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the +152 adduct is expected" help=""/>
6024 <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/> 6097 <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/>
6025 <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/> 6098 <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/>
6026 <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/> 6099 <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/>
6027 <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" optional="true" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/> 6100 <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/>
6028 <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/> 6101 <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/>
6029 </section> 6102 </section>
6030 <expand macro="adv_opts_macro"> 6103 <expand macro="adv_opts_macro">
6031 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6104 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6032 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6105 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
6033 <expand macro="list_string_san" name="test"/> 6106 <expand macro="list_string_san" name="test"/>
6034 </param> 6107 </param>
6035 </expand> 6108 </expand>
6036 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6037 <option value="out_tsv_FLAG">out_tsv (tsv output file)</option> 6110 <option value="out_tsv_FLAG">out_tsv (tsv output file)</option>
6045 </data> 6118 </data>
6046 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6047 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6048 </data> 6121 </data>
6049 </outputs> 6122 </outputs>
6050 <tests><!-- TOPP_RNPxlSearch_1 --> 6123 <tests>
6124 <!-- TOPP_RNPxlSearch_1 -->
6051 <test expect_num_outputs="2"> 6125 <test expect_num_outputs="2">
6052 <section name="adv_opts"> 6126 <section name="adv_opts">
6053 <param name="force" value="false"/> 6127 <param name="force" value="false"/>
6054 <param name="test" value="true"/> 6128 <param name="test" value="true"/>
6055 </section> 6129 </section>
6056 <param name="in" value="RNPxlSearch_1_input.mzML"/> 6130 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6057 <param name="database" value="RNPxlSearch_1_input.fasta"/> 6131 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6058 <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6132 <output name="out" value="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6059 <section name="precursor"> 6133 <section name="precursor">
6060 <param name="mass_tolerance" value="20.0"/> 6134 <param name="mass_tolerance" value="20.0"/>
6061 <param name="mass_tolerance_unit" value="ppm"/> 6135 <param name="mass_tolerance_unit" value="ppm"/>
6062 <param name="min_charge" value="2"/> 6136 <param name="min_charge" value="2"/>
6063 <param name="max_charge" value="5"/> 6137 <param name="max_charge" value="5"/>
6066 <section name="fragment"> 6140 <section name="fragment">
6067 <param name="mass_tolerance" value="20.0"/> 6141 <param name="mass_tolerance" value="20.0"/>
6068 <param name="mass_tolerance_unit" value="ppm"/> 6142 <param name="mass_tolerance_unit" value="ppm"/>
6069 </section> 6143 </section>
6070 <section name="modifications"> 6144 <section name="modifications">
6071 <param name="fixed"/>
6072 <param name="variable" value="Oxidation (M)"/> 6145 <param name="variable" value="Oxidation (M)"/>
6073 <param name="variable_max_per_peptide" value="2"/> 6146 <param name="variable_max_per_peptide" value="2"/>
6074 </section> 6147 </section>
6075 <section name="peptide"> 6148 <section name="peptide">
6076 <param name="min_size" value="6"/> 6149 <param name="min_size" value="6"/>
6083 </section> 6156 </section>
6084 <section name="RNPxl"> 6157 <section name="RNPxl">
6085 <param name="length" value="2"/> 6158 <param name="length" value="2"/>
6086 <param name="sequence" value="GUA"/> 6159 <param name="sequence" value="GUA"/>
6087 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/> 6160 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6088 <param name="nt_groups" value=""/>
6089 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/> 6161 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6090 <param name="can_cross_link" value="U"/> 6162 <param name="can_cross_link" value="U"/>
6091 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/> 6163 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6092 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/> 6164 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6093 <param name="scoring" value="fast"/> 6165 <param name="scoring" value="fast"/>
6103 <output name="ctd_out" ftype="xml"> 6175 <output name="ctd_out" ftype="xml">
6104 <assert_contents> 6176 <assert_contents>
6105 <is_valid_xml/> 6177 <is_valid_xml/>
6106 </assert_contents> 6178 </assert_contents>
6107 </output> 6179 </output>
6180 <assert_stdout>
6181 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6182 </assert_stdout>
6108 </test> 6183 </test>
6109 <!-- TOPP_RNPxlSearch_2 --> 6184 <!-- TOPP_RNPxlSearch_2 -->
6110 <test expect_num_outputs="2"> 6185 <test expect_num_outputs="2">
6111 <section name="adv_opts"> 6186 <section name="adv_opts">
6112 <param name="force" value="false"/> 6187 <param name="force" value="false"/>
6113 <param name="test" value="true"/> 6188 <param name="test" value="true"/>
6114 </section> 6189 </section>
6115 <param name="in" value="RNPxlSearch_1_input.mzML"/> 6190 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6116 <param name="database" value="RNPxlSearch_1_input.fasta"/> 6191 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6117 <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6192 <output name="out" value="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6118 <section name="precursor"> 6193 <section name="precursor">
6119 <param name="mass_tolerance" value="20.0"/> 6194 <param name="mass_tolerance" value="20.0"/>
6120 <param name="mass_tolerance_unit" value="ppm"/> 6195 <param name="mass_tolerance_unit" value="ppm"/>
6121 <param name="min_charge" value="2"/> 6196 <param name="min_charge" value="2"/>
6122 <param name="max_charge" value="5"/> 6197 <param name="max_charge" value="5"/>
6125 <section name="fragment"> 6200 <section name="fragment">
6126 <param name="mass_tolerance" value="20.0"/> 6201 <param name="mass_tolerance" value="20.0"/>
6127 <param name="mass_tolerance_unit" value="ppm"/> 6202 <param name="mass_tolerance_unit" value="ppm"/>
6128 </section> 6203 </section>
6129 <section name="modifications"> 6204 <section name="modifications">
6130 <param name="fixed"/>
6131 <param name="variable" value="Oxidation (M)"/> 6205 <param name="variable" value="Oxidation (M)"/>
6132 <param name="variable_max_per_peptide" value="2"/> 6206 <param name="variable_max_per_peptide" value="2"/>
6133 </section> 6207 </section>
6134 <section name="peptide"> 6208 <section name="peptide">
6135 <param name="min_size" value="6"/> 6209 <param name="min_size" value="6"/>
6142 </section> 6216 </section>
6143 <section name="RNPxl"> 6217 <section name="RNPxl">
6144 <param name="length" value="2"/> 6218 <param name="length" value="2"/>
6145 <param name="sequence" value="GUA"/> 6219 <param name="sequence" value="GUA"/>
6146 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/> 6220 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6147 <param name="nt_groups" value=""/>
6148 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/> 6221 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6149 <param name="can_cross_link" value="U"/> 6222 <param name="can_cross_link" value="U"/>
6150 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/> 6223 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6151 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/> 6224 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6152 <param name="scoring" value="fast"/> 6225 <param name="scoring" value="fast"/>
6162 <output name="ctd_out" ftype="xml"> 6235 <output name="ctd_out" ftype="xml">
6163 <assert_contents> 6236 <assert_contents>
6164 <is_valid_xml/> 6237 <is_valid_xml/>
6165 </assert_contents> 6238 </assert_contents>
6166 </output> 6239 </output>
6240 <assert_stdout>
6241 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6242 </assert_stdout>
6167 </test> 6243 </test>
6168 <!-- TOPP_RNPxlSearch_3 --> 6244 <!-- TOPP_RNPxlSearch_3 -->
6169 <test expect_num_outputs="3"> 6245 <test expect_num_outputs="3">
6170 <section name="adv_opts"> 6246 <section name="adv_opts">
6171 <param name="force" value="false"/> 6247 <param name="force" value="false"/>
6172 <param name="test" value="true"/> 6248 <param name="test" value="true"/>
6173 </section> 6249 </section>
6174 <param name="in" value="RNPxlSearch_1_input.mzML"/> 6250 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6175 <param name="database" value="RNPxlSearch_1_input.fasta"/> 6251 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6176 <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6252 <output name="out" value="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6177 <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 6253 <output name="out_tsv" value="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6178 <section name="precursor"> 6254 <section name="precursor">
6179 <param name="mass_tolerance" value="10.0"/> 6255 <param name="mass_tolerance" value="10.0"/>
6180 <param name="mass_tolerance_unit" value="ppm"/> 6256 <param name="mass_tolerance_unit" value="ppm"/>
6181 <param name="min_charge" value="2"/> 6257 <param name="min_charge" value="2"/>
6182 <param name="max_charge" value="5"/> 6258 <param name="max_charge" value="5"/>
6185 <section name="fragment"> 6261 <section name="fragment">
6186 <param name="mass_tolerance" value="10.0"/> 6262 <param name="mass_tolerance" value="10.0"/>
6187 <param name="mass_tolerance_unit" value="ppm"/> 6263 <param name="mass_tolerance_unit" value="ppm"/>
6188 </section> 6264 </section>
6189 <section name="modifications"> 6265 <section name="modifications">
6190 <param name="fixed"/>
6191 <param name="variable"/>
6192 <param name="variable_max_per_peptide" value="2"/> 6266 <param name="variable_max_per_peptide" value="2"/>
6193 </section> 6267 </section>
6194 <section name="peptide"> 6268 <section name="peptide">
6195 <param name="min_size" value="6"/> 6269 <param name="min_size" value="6"/>
6196 <param name="max_size" value="1000000"/> 6270 <param name="max_size" value="1000000"/>
6202 </section> 6276 </section>
6203 <section name="RNPxl"> 6277 <section name="RNPxl">
6204 <param name="length" value="2"/> 6278 <param name="length" value="2"/>
6205 <param name="sequence" value=""/> 6279 <param name="sequence" value=""/>
6206 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/> 6280 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6207 <param name="nt_groups" value=""/>
6208 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/> 6281 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6209 <param name="can_cross_link" value="U"/> 6282 <param name="can_cross_link" value="U"/>
6210 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/> 6283 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6211 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/> 6284 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6212 <param name="scoring" value="fast"/> 6285 <param name="scoring" value="fast"/>
6222 <output name="ctd_out" ftype="xml"> 6295 <output name="ctd_out" ftype="xml">
6223 <assert_contents> 6296 <assert_contents>
6224 <is_valid_xml/> 6297 <is_valid_xml/>
6225 </assert_contents> 6298 </assert_contents>
6226 </output> 6299 </output>
6300 <assert_stdout>
6301 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6302 </assert_stdout>
6227 </test> 6303 </test>
6228 <!-- TOPP_RNPxlSearch_4 --> 6304 <!-- TOPP_RNPxlSearch_4 -->
6229 <test expect_num_outputs="3"> 6305 <test expect_num_outputs="3">
6230 <section name="adv_opts"> 6306 <section name="adv_opts">
6231 <param name="force" value="false"/> 6307 <param name="force" value="false"/>
6232 <param name="test" value="true"/> 6308 <param name="test" value="true"/>
6233 </section> 6309 </section>
6234 <param name="in" value="RNPxlSearch_1_input.mzML"/> 6310 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6235 <param name="database" value="RNPxlSearch_1_input.fasta"/> 6311 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6236 <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 6312 <output name="out" value="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6237 <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 6313 <output name="out_tsv" value="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6238 <section name="precursor"> 6314 <section name="precursor">
6239 <param name="mass_tolerance" value="10.0"/> 6315 <param name="mass_tolerance" value="10.0"/>
6240 <param name="mass_tolerance_unit" value="ppm"/> 6316 <param name="mass_tolerance_unit" value="ppm"/>
6241 <param name="min_charge" value="2"/> 6317 <param name="min_charge" value="2"/>
6242 <param name="max_charge" value="5"/> 6318 <param name="max_charge" value="5"/>
6245 <section name="fragment"> 6321 <section name="fragment">
6246 <param name="mass_tolerance" value="10.0"/> 6322 <param name="mass_tolerance" value="10.0"/>
6247 <param name="mass_tolerance_unit" value="ppm"/> 6323 <param name="mass_tolerance_unit" value="ppm"/>
6248 </section> 6324 </section>
6249 <section name="modifications"> 6325 <section name="modifications">
6250 <param name="fixed"/>
6251 <param name="variable"/>
6252 <param name="variable_max_per_peptide" value="2"/> 6326 <param name="variable_max_per_peptide" value="2"/>
6253 </section> 6327 </section>
6254 <section name="peptide"> 6328 <section name="peptide">
6255 <param name="min_size" value="6"/> 6329 <param name="min_size" value="6"/>
6256 <param name="max_size" value="1000000"/> 6330 <param name="max_size" value="1000000"/>
6262 </section> 6336 </section>
6263 <section name="RNPxl"> 6337 <section name="RNPxl">
6264 <param name="length" value="2"/> 6338 <param name="length" value="2"/>
6265 <param name="sequence" value=""/> 6339 <param name="sequence" value=""/>
6266 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/> 6340 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6267 <param name="nt_groups" value=""/>
6268 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/> 6341 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6269 <param name="can_cross_link" value="U"/> 6342 <param name="can_cross_link" value="U"/>
6270 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/> 6343 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6271 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/> 6344 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6272 <param name="scoring" value="fast"/> 6345 <param name="scoring" value="fast"/>
6282 <output name="ctd_out" ftype="xml"> 6355 <output name="ctd_out" ftype="xml">
6283 <assert_contents> 6356 <assert_contents>
6284 <is_valid_xml/> 6357 <is_valid_xml/>
6285 </assert_contents> 6358 </assert_contents>
6286 </output> 6359 </output>
6360 <assert_stdout>
6361 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
6362 </assert_stdout>
6287 </test> 6363 </test>
6288 </tests> 6364 </tests>
6289 <help><![CDATA[Annotate RNA/DNA-peptide cross-links in MS/MS spectra. 6365 <help><![CDATA[Annotate RNA/DNA-peptide cross-links in MS/MS spectra.
6290 6366
6291 6367
6292 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlSearch.html]]></help> 6368 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlSearch.html]]></help>
6293 <expand macro="references"/> 6369 <expand macro="references"/>
6294 </tool> 6370 </tool>