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comparison LuciphorAdapter.xml @ 15:949086930a49 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 21:39:41 +0000
parents bf2bf60c8af2
children
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14:bf2bf60c8af2 15:949086930a49
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
4 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Modification site localisation using LuciPHOr2.</description> 4 <description>Modification site localisation using LuciPHOr2</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">LuciphorAdapter</token> 6 <token name="@EXECUTABLE@">LuciphorAdapter</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($in.ext)' &&
19 mkdir id && 18 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 mkdir out && 20 mkdir out &&
22 21
23 ## Main program call 22 ## Main program call
24 23
25 set -o pipefail && 24 set -o pipefail &&
41 <configfiles> 40 <configfiles>
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/> 45 <param argument="-in" type="data" format="mzml" label="Input spectrum file" help=" select mzml data sets(s)"/>
47 <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/> 46 <param argument="-id" type="data" format="idxml" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
48 <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method" help=""> 47 <param argument="-fragment_method" type="select" label="Fragmentation method" help="">
49 <option value="CID" selected="true">CID</option> 48 <option value="CID" selected="true">CID</option>
50 <option value="HCD">HCD</option> 49 <option value="HCD">HCD</option>
51 <expand macro="list_string_san" name="fragment_method"/> 50 <expand macro="list_string_san" name="fragment_method"/>
52 </param> 51 </param>
53 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/> 52 <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
54 <param argument="-fragment_error_units" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> 53 <param argument="-fragment_error_units" type="select" label="Unit of fragment mass tolerance" help="">
55 <option value="Da" selected="true">Da</option> 54 <option value="Da" selected="true">Da</option>
56 <option value="ppm">ppm</option> 55 <option value="ppm">ppm</option>
57 <expand macro="list_string_san" name="fragment_error_units"/> 56 <expand macro="list_string_san" name="fragment_error_units"/>
58 </param> 57 </param>
59 <param argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/> 58 <param argument="-min_mz" type="float" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
60 <param argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> 59 <param argument="-target_modifications" type="select" multiple="true" optional="false" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
61 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 60 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
62 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 61 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
63 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 62 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
64 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 63 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
65 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 64 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
66 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 65 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
67 <option value="2-succinyl (C)">2-succinyl (C)</option> 66 <option value="2-succinyl (C)">2-succinyl (C)</option>
68 <option value="2HPG (R)">2HPG (R)</option> 67 <option value="2HPG (R)">2HPG (R)</option>
69 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> 68 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
69 <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
70 <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
71 <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
72 <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
70 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> 73 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
71 <option value="3sulfo (N-term)">3sulfo (N-term)</option> 74 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
72 <option value="4-ONE (C)">4-ONE (C)</option> 75 <option value="4-ONE (C)">4-ONE (C)</option>
73 <option value="4-ONE (H)">4-ONE (H)</option> 76 <option value="4-ONE (H)">4-ONE (H)</option>
74 <option value="4-ONE (K)">4-ONE (K)</option> 77 <option value="4-ONE (K)">4-ONE (K)</option>
154 <option value="Ammonium (D)">Ammonium (D)</option> 157 <option value="Ammonium (D)">Ammonium (D)</option>
155 <option value="Ammonium (E)">Ammonium (E)</option> 158 <option value="Ammonium (E)">Ammonium (E)</option>
156 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> 159 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
157 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> 160 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
158 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> 161 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
162 <option value="Andro-H2O (C)">Andro-H2O (C)</option>
159 <option value="Archaeol (C)">Archaeol (C)</option> 163 <option value="Archaeol (C)">Archaeol (C)</option>
160 <option value="Arg (N-term)">Arg (N-term)</option> 164 <option value="Arg (N-term)">Arg (N-term)</option>
161 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option> 165 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
162 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option> 166 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
163 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option> 167 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
257 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option> 261 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
258 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option> 262 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
259 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> 263 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
260 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> 264 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
261 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> 265 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
266 <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
262 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> 267 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
263 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> 268 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
264 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> 269 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
265 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option> 270 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
266 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option> 271 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
289 <option value="BITC (C)">BITC (C)</option> 294 <option value="BITC (C)">BITC (C)</option>
290 <option value="BITC (K)">BITC (K)</option> 295 <option value="BITC (K)">BITC (K)</option>
291 <option value="BITC (N-term)">BITC (N-term)</option> 296 <option value="BITC (N-term)">BITC (N-term)</option>
292 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> 297 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
293 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> 298 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
294 <option value="Bodipy (C)">Bodipy (C)</option>
295 <option value="Brij35 (N-term)">Brij35 (N-term)</option> 299 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
296 <option value="Brij58 (N-term)">Brij58 (N-term)</option> 300 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
297 <option value="Bromo (F)">Bromo (F)</option> 301 <option value="Bromo (F)">Bromo (F)</option>
298 <option value="Bromo (H)">Bromo (H)</option> 302 <option value="Bromo (H)">Bromo (H)</option>
299 <option value="Bromo (W)">Bromo (W)</option> 303 <option value="Bromo (W)">Bromo (W)</option>
721 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option> 725 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
722 <option value="Dehydrated (S)">Dehydrated (S)</option> 726 <option value="Dehydrated (S)">Dehydrated (S)</option>
723 <option value="Dehydrated (T)">Dehydrated (T)</option> 727 <option value="Dehydrated (T)">Dehydrated (T)</option>
724 <option value="Dehydrated (Y)">Dehydrated (Y)</option> 728 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
725 <option value="Dehydro (C)">Dehydro (C)</option> 729 <option value="Dehydro (C)">Dehydro (C)</option>
730 <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
726 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> 731 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
727 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> 732 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
728 <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
729 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> 733 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
730 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> 734 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
731 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> 735 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
732 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option> 736 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
733 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option> 737 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
734 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option> 738 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
735 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> 739 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
736 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> 740 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
737 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> 741 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
738 <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
739 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> 742 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
740 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> 743 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
741 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> 744 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
742 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option> 745 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
743 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option> 746 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
745 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option> 748 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
746 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option> 749 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
747 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> 750 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
748 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> 751 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
749 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> 752 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
753 <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
750 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> 754 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
751 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> 755 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
752 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> 756 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
753 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option> 757 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
754 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option> 758 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
1317 <option value="Ethanolamine (D)">Ethanolamine (D)</option> 1321 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
1318 <option value="Ethanolamine (E)">Ethanolamine (E)</option> 1322 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
1319 <option value="Ethanolyl (C)">Ethanolyl (C)</option> 1323 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
1320 <option value="Ethanolyl (K)">Ethanolyl (K)</option> 1324 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
1321 <option value="Ethanolyl (R)">Ethanolyl (R)</option> 1325 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
1322 <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
1323 <option value="Ethyl (C-term)">Ethyl (C-term)</option> 1326 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
1324 <option value="Ethyl (D)">Ethyl (D)</option> 1327 <option value="Ethyl (D)">Ethyl (D)</option>
1325 <option value="Ethyl (E)">Ethyl (E)</option> 1328 <option value="Ethyl (E)">Ethyl (E)</option>
1326 <option value="Ethyl (K)">Ethyl (K)</option> 1329 <option value="Ethyl (K)">Ethyl (K)</option>
1327 <option value="Ethyl (N-term)">Ethyl (N-term)</option> 1330 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
1411 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option> 1414 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
1412 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option> 1415 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
1413 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option> 1416 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
1414 <option value="Glu (E)">Glu (E)</option> 1417 <option value="Glu (E)">Glu (E)</option>
1415 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> 1418 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
1419 <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
1416 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option> 1420 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
1417 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option> 1421 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
1418 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option> 1422 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
1419 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option> 1423 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
1420 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option> 1424 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
1425 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1429 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1426 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1430 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1427 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1431 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1428 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1432 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1429 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1433 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1430 <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>
1431 <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> 1434 <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>
1432 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1435 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1433 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1436 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
1434 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 1437 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
1435 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option> 1438 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
1449 <option value="Gluratylation (K)">Gluratylation (K)</option> 1452 <option value="Gluratylation (K)">Gluratylation (K)</option>
1450 <option value="Glutathione (C)">Glutathione (C)</option> 1453 <option value="Glutathione (C)">Glutathione (C)</option>
1451 <option value="Gly (K)">Gly (K)</option> 1454 <option value="Gly (K)">Gly (K)</option>
1452 <option value="Gly (S)">Gly (S)</option> 1455 <option value="Gly (S)">Gly (S)</option>
1453 <option value="Gly (T)">Gly (T)</option> 1456 <option value="Gly (T)">Gly (T)</option>
1457 <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
1454 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option> 1458 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
1455 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option> 1459 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
1456 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option> 1460 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
1457 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option> 1461 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
1458 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option> 1462 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
1839 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option> 1843 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
1840 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option> 1844 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
1841 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> 1845 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
1842 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> 1846 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
1843 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> 1847 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
1848 <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
1844 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> 1849 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
1845 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> 1850 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
1846 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> 1851 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
1847 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option> 1852 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
1848 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option> 1853 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
1850 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option> 1855 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
1851 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option> 1856 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
1852 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> 1857 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
1853 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> 1858 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
1854 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> 1859 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
1860 <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
1861 <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
1862 <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
1855 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> 1863 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
1856 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> 1864 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
1857 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> 1865 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
1858 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option> 1866 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
1859 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option> 1867 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
1905 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option> 1913 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
1906 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option> 1914 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
1907 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> 1915 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
1908 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> 1916 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
1909 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> 1917 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
1918 <option value="His+O(2) (H)">His+O(2) (H)</option>
1910 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option> 1919 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
1911 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option> 1920 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
1912 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option> 1921 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
1913 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option> 1922 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
1914 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option> 1923 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
2042 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option> 2051 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
2043 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option> 2052 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
2044 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> 2053 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
2045 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> 2054 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
2046 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> 2055 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
2056 <option value="Kdo (S)">Kdo (S)</option>
2057 <option value="Kdo (T)">Kdo (T)</option>
2047 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> 2058 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
2048 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> 2059 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
2049 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> 2060 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
2050 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> 2061 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
2051 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> 2062 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
2063 <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
2052 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> 2064 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
2053 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> 2065 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
2054 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> 2066 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
2055 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option> 2067 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
2056 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option> 2068 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
2131 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option> 2143 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
2132 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option> 2144 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
2133 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> 2145 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
2134 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> 2146 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
2135 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> 2147 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
2148 <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
2136 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> 2149 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
2137 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> 2150 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
2138 <option value="Lipoyl (K)">Lipoyl (K)</option> 2151 <option value="Lipoyl (K)">Lipoyl (K)</option>
2139 <option value="LRGG (K)">LRGG (K)</option> 2152 <option value="LRGG (K)">LRGG (K)</option>
2140 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> 2153 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
2141 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> 2154 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
2155 <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
2142 <option value="Lys (N-term)">Lys (N-term)</option> 2156 <option value="Lys (N-term)">Lys (N-term)</option>
2157 <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
2143 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option> 2158 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
2144 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option> 2159 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
2145 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option> 2160 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
2146 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option> 2161 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
2147 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option> 2162 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
2172 <option value="maleimide5 (C)">maleimide5 (C)</option> 2187 <option value="maleimide5 (C)">maleimide5 (C)</option>
2173 <option value="maleimide5 (K)">maleimide5 (K)</option> 2188 <option value="maleimide5 (K)">maleimide5 (K)</option>
2174 <option value="Malonyl (C)">Malonyl (C)</option> 2189 <option value="Malonyl (C)">Malonyl (C)</option>
2175 <option value="Malonyl (K)">Malonyl (K)</option> 2190 <option value="Malonyl (K)">Malonyl (K)</option>
2176 <option value="Malonyl (S)">Malonyl (S)</option> 2191 <option value="Malonyl (S)">Malonyl (S)</option>
2192 <option value="MBS+peptide (C)">MBS+peptide (C)</option>
2177 <option value="MDCC (C)">MDCC (C)</option> 2193 <option value="MDCC (C)">MDCC (C)</option>
2178 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> 2194 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
2179 <option value="Menadione (C)">Menadione (C)</option> 2195 <option value="Menadione (C)">Menadione (C)</option>
2180 <option value="Menadione (K)">Menadione (K)</option> 2196 <option value="Menadione (K)">Menadione (K)</option>
2181 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option> 2197 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
2183 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option> 2199 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
2184 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option> 2200 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
2185 <option value="MesitylOxide (H)">MesitylOxide (H)</option> 2201 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
2186 <option value="MesitylOxide (K)">MesitylOxide (K)</option> 2202 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
2187 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> 2203 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
2204 <option value="Met+O(2) (H)">Met+O(2) (H)</option>
2188 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option> 2205 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
2189 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option> 2206 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
2190 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option> 2207 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
2191 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option> 2208 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
2192 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option> 2209 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
2366 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option> 2383 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
2367 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option> 2384 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
2368 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> 2385 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
2369 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> 2386 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
2370 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> 2387 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
2371 <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
2372 <option value="NP40 (N-term)">NP40 (N-term)</option> 2388 <option value="NP40 (N-term)">NP40 (N-term)</option>
2373 <option value="NQIGG (K)">NQIGG (K)</option> 2389 <option value="NQIGG (K)">NQIGG (K)</option>
2374 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> 2390 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
2375 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option> 2391 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
2376 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option> 2392 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
2454 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option> 2470 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
2455 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option> 2471 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
2456 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option> 2472 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
2457 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option> 2473 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
2458 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option> 2474 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
2475 <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
2476 <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
2477 <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
2478 <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
2459 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> 2479 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
2460 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> 2480 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
2461 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> 2481 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
2462 <option value="Phospho (C)">Phospho (C)</option> 2482 <option value="Phospho (C)">Phospho (C)</option>
2463 <option value="Phospho (D)">Phospho (D)</option> 2483 <option value="Phospho (D)">Phospho (D)</option>
2468 <option value="Phospho (S)" selected="true">Phospho (S)</option> 2488 <option value="Phospho (S)" selected="true">Phospho (S)</option>
2469 <option value="Phospho (T)" selected="true">Phospho (T)</option> 2489 <option value="Phospho (T)" selected="true">Phospho (T)</option>
2470 <option value="Phospho (Y)" selected="true">Phospho (Y)</option> 2490 <option value="Phospho (Y)" selected="true">Phospho (Y)</option>
2471 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> 2491 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
2472 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> 2492 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
2493 <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
2473 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> 2494 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
2474 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> 2495 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
2475 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> 2496 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
2476 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option> 2497 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
2477 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option> 2498 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
2499 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option> 2520 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
2500 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option> 2521 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
2501 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> 2522 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
2502 <option value="Piperidine (K)">Piperidine (K)</option> 2523 <option value="Piperidine (K)">Piperidine (K)</option>
2503 <option value="Piperidine (N-term)">Piperidine (N-term)</option> 2524 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
2525 <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
2504 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option> 2526 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
2505 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option> 2527 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
2506 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option> 2528 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
2507 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option> 2529 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
2508 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option> 2530 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
2576 <option value="QEQTGG (K)">QEQTGG (K)</option> 2598 <option value="QEQTGG (K)">QEQTGG (K)</option>
2577 <option value="QQQTGG (K)">QQQTGG (K)</option> 2599 <option value="QQQTGG (K)">QQQTGG (K)</option>
2578 <option value="QTGG (K)">QTGG (K)</option> 2600 <option value="QTGG (K)">QTGG (K)</option>
2579 <option value="Quinone (W)">Quinone (W)</option> 2601 <option value="Quinone (W)">Quinone (W)</option>
2580 <option value="Quinone (Y)">Quinone (Y)</option> 2602 <option value="Quinone (Y)">Quinone (Y)</option>
2603 <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
2604 <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
2605 <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
2606 <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
2607 <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
2608 <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
2609 <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
2610 <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
2611 <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
2612 <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
2613 <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
2614 <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
2615 <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
2616 <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
2617 <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
2618 <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
2619 <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
2620 <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
2621 <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
2622 <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
2581 <option value="Retinylidene (K)">Retinylidene (K)</option> 2623 <option value="Retinylidene (K)">Retinylidene (K)</option>
2582 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> 2624 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
2583 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> 2625 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
2584 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> 2626 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
2585 <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
2586 <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
2587 <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
2588 <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
2589 <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
2590 <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
2591 <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
2592 <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
2593 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> 2627 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
2594 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> 2628 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
2595 <option value="Saligenin (H)">Saligenin (H)</option> 2629 <option value="Saligenin (H)">Saligenin (H)</option>
2596 <option value="Saligenin (K)">Saligenin (K)</option> 2630 <option value="Saligenin (K)">Saligenin (K)</option>
2597 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option> 2631 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
2615 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option> 2649 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
2616 <option value="serotonylation (Q)">serotonylation (Q)</option> 2650 <option value="serotonylation (Q)">serotonylation (Q)</option>
2617 <option value="shTMT (K)">shTMT (K)</option> 2651 <option value="shTMT (K)">shTMT (K)</option>
2618 <option value="shTMT (N-term)">shTMT (N-term)</option> 2652 <option value="shTMT (N-term)">shTMT (N-term)</option>
2619 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> 2653 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
2654 <option value="shTMTpro (K)">shTMTpro (K)</option>
2655 <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
2656 <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
2620 <option value="SMA (K)">SMA (K)</option> 2657 <option value="SMA (K)">SMA (K)</option>
2621 <option value="SMA (N-term)">SMA (N-term)</option> 2658 <option value="SMA (N-term)">SMA (N-term)</option>
2622 <option value="spermidine (Q)">spermidine (Q)</option> 2659 <option value="spermidine (Q)">spermidine (Q)</option>
2623 <option value="spermine (Q)">spermine (Q)</option> 2660 <option value="spermine (Q)">spermine (Q)</option>
2624 <option value="SPITC (K)">SPITC (K)</option> 2661 <option value="SPITC (K)">SPITC (K)</option>
2790 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option> 2827 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
2791 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option> 2828 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
2792 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option> 2829 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
2793 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option> 2830 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
2794 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option> 2831 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
2795 <option value="Ub-amide (C)">Ub-amide (C)</option>
2796 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> 2832 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
2797 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> 2833 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
2798 <option value="Ub-VME (C)">Ub-VME (C)</option> 2834 <option value="Ub-VME (C)">Ub-VME (C)</option>
2799 <option value="UgiJoullie (D)">UgiJoullie (D)</option> 2835 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
2800 <option value="UgiJoullie (E)">UgiJoullie (E)</option> 2836 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
2985 <option value="ZGB (K)">ZGB (K)</option> 3021 <option value="ZGB (K)">ZGB (K)</option>
2986 <option value="ZGB (N-term)">ZGB (N-term)</option> 3022 <option value="ZGB (N-term)">ZGB (N-term)</option>
2987 <option value="ZQG (K)">ZQG (K)</option> 3023 <option value="ZQG (K)">ZQG (K)</option>
2988 <expand macro="list_string_san" name="target_modifications"/> 3024 <expand macro="list_string_san" name="target_modifications"/>
2989 </param> 3025 </param>
2990 <param argument="-neutral_losses" type="text" optional="true" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 3026 <param argument="-neutral_losses" type="text" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
2991 <expand macro="list_string_val" name="neutral_losses"/> 3027 <expand macro="list_string_val" name="neutral_losses"/>
2992 <expand macro="list_string_san" name="neutral_losses"/> 3028 <expand macro="list_string_san" name="neutral_losses"/>
2993 </param> 3029 </param>
2994 <param argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/> 3030 <param argument="-decoy_mass" type="float" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
2995 <param argument="-decoy_neutral_losses" type="text" optional="true" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 3031 <param argument="-decoy_neutral_losses" type="text" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
2996 <expand macro="list_string_val" name="decoy_neutral_losses"/> 3032 <expand macro="list_string_val" name="decoy_neutral_losses"/>
2997 <expand macro="list_string_san" name="decoy_neutral_losses"/> 3033 <expand macro="list_string_san" name="decoy_neutral_losses"/>
2998 </param> 3034 </param>
2999 <param argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/> 3035 <param argument="-max_charge_state" type="integer" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
3000 <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/> 3036 <param argument="-max_peptide_length" type="integer" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
3001 <param argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/> 3037 <param argument="-max_num_perm" type="integer" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
3002 <param argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/> 3038 <param argument="-modeling_score_threshold" type="float" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
3003 <param argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/> 3039 <param argument="-scoring_threshold" type="float" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
3004 <param argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/> 3040 <param argument="-min_num_psms_model" type="integer" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
3005 <param argument="-run_mode" type="select" optional="true" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help=""> 3041 <param argument="-run_mode" type="select" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
3006 <option value="0" selected="true">0</option> 3042 <option value="0" selected="true">0</option>
3007 <option value="1">1</option> 3043 <option value="1">1</option>
3008 <expand macro="list_string_san" name="run_mode"/> 3044 <expand macro="list_string_san" name="run_mode"/>
3009 </param> 3045 </param>
3010 <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/> 3046 <param argument="-rt_tolerance" type="float" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
3011 <expand macro="adv_opts_macro"> 3047 <expand macro="adv_opts_macro">
3012 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 3048 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
3013 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 3049 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
3014 <expand macro="list_string_san" name="test"/> 3050 <expand macro="list_string_san" name="test"/>
3015 </param> 3051 </param>
3016 </expand> 3052 </expand>
3017 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 3053 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
3018 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 3054 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
3022 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 3058 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
3023 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 3059 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
3024 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 3060 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
3025 </data> 3061 </data>
3026 </outputs> 3062 </outputs>
3027 <tests><!-- TOPP_LuciphorAdapter_1 --> 3063 <tests>
3064 <!-- TOPP_LuciphorAdapter_1 -->
3028 <test expect_num_outputs="2"> 3065 <test expect_num_outputs="2">
3029 <section name="adv_opts"> 3066 <section name="adv_opts">
3030 <param name="force" value="false"/> 3067 <param name="force" value="false"/>
3031 <param name="test" value="true"/> 3068 <param name="test" value="true"/>
3032 </section> 3069 </section>
3033 <param name="in" value="LuciphorAdapter_1_input.mzML"/> 3070 <param name="in" value="LuciphorAdapter_1_input.mzML"/>
3034 <param name="id" value="LuciphorAdapter_1_input.idXML"/> 3071 <param name="id" value="LuciphorAdapter_1_input.idXML"/>
3035 <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 3072 <output name="out" value="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
3036 <param name="fragment_method" value="CID"/> 3073 <param name="fragment_method" value="CID"/>
3037 <param name="fragment_mass_tolerance" value="0.5"/> 3074 <param name="fragment_mass_tolerance" value="0.5"/>
3038 <param name="fragment_error_units" value="Da"/> 3075 <param name="fragment_error_units" value="Da"/>
3039 <param name="min_mz" value="150.0"/> 3076 <param name="min_mz" value="150.0"/>
3040 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> 3077 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
3053 <output name="ctd_out" ftype="xml"> 3090 <output name="ctd_out" ftype="xml">
3054 <assert_contents> 3091 <assert_contents>
3055 <is_valid_xml/> 3092 <is_valid_xml/>
3056 </assert_contents> 3093 </assert_contents>
3057 </output> 3094 </output>
3095 <assert_stdout>
3096 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
3097 </assert_stdout>
3058 </test> 3098 </test>
3059 </tests> 3099 </tests>
3060 <help><![CDATA[Modification site localisation using LuciPHOr2. 3100 <help><![CDATA[Modification site localisation using LuciPHOr2.
3061 3101
3062 3102
3063 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_LuciphorAdapter.html]]></help> 3103 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_LuciphorAdapter.html]]></help>
3064 <expand macro="references"/> 3104 <expand macro="references"/>
3065 </tool> 3105 </tool>