openms_cometadapter: CometAdapter.xml comparison

comparison CometAdapter.xml @ 9:df0c77da6c87 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:35:36 +0000
parents	e75929491905
children

comparison

equal deleted inserted replaced

-:e75929491905
+:df0c77da6c87
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-<description>Annotates MS/MS spectra using Comet.</description>
+<description>Annotates MS/MS spectra using Comet</description>
 <macros>
 <token name="@EXECUTABLE@">CometAdapter</token>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 @EXT_FOO@
 #import re
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
 mkdir pin_out &&
 #end if
 #if $default_params_file:
 mkdir default_params_file &&
-ln -s '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' &&
+cp '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' &&
 #end if
 ## Main program call
 set -o pipefail &&
 <configfiles>
 <inputs name="args_json" data_style="paths"/>
 <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
 </configfiles>
 <inputs>
-<param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
+<param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
-<param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
+<param argument="-database" type="data" format="fasta" label="FASTA file" help=" select fasta data sets(s)"/>
 <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
-<param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
+<param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
-<param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
+<param argument="-precursor_error_units" type="select" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
 <option value="amu">amu</option>
 <option value="ppm" selected="true">ppm</option>
 <option value="Da">Da</option>
 <expand macro="list_string_san" name="precursor_error_units"/>
 </param>
-<param argument="-isotope_error" type="select" optional="true" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
+<param argument="-isotope_error" type="select" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
 <option value="off" selected="true">off</option>
 <option value="0/1">0/1</option>
 <option value="0/1/2">0/1/2</option>
 <option value="0/1/2/3">0/1/2/3</option>
 <option value="-8/-4/0/4/8">-8/-4/0/4/8</option>
 <option value="-1/0/1/2/3">-1/0/1/2/3</option>
 <expand macro="list_string_san" name="isotope_error"/>
 </param>
-<param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
+<param argument="-fragment_mass_tolerance" type="float" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
-<param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help="">
+<param argument="-fragment_error_units" type="select" label="Fragment monoisotopic mass error units" help="">
 <option value="Da" selected="true">Da</option>
 <expand macro="list_string_san" name="fragment_error_units"/>
 </param>
-<param argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
+<param argument="-fragment_bin_offset" type="float" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
-<param argument="-instrument" type="select" optional="true" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
+<param argument="-instrument" type="select" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
 <option value="low_res">low_res</option>
 <option value="high_res" selected="true">high_res</option>
 <expand macro="list_string_san" name="instrument"/>
 </param>
-<param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
+<param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+<option value="Asp-N">Asp-N</option>
+<option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+<option value="Trypsin" selected="true">Trypsin</option>
+<option value="Arg-C">Arg-C</option>
+<option value="no cleavage">no cleavage</option>
+<option value="unspecific cleavage">unspecific cleavage</option>
+<option value="Chymotrypsin">Chymotrypsin</option>
 <option value="CNBr">CNBr</option>
 <option value="Lys-C">Lys-C</option>
-<option value="Trypsin" selected="true">Trypsin</option>
-<option value="Arg-C">Arg-C</option>
-<option value="Chymotrypsin">Chymotrypsin</option>
-<option value="Asp-N">Asp-N</option>
-<option value="unspecific cleavage">unspecific cleavage</option>
 <option value="Lys-N">Lys-N</option>
 <option value="PepsinA">PepsinA</option>
 <option value="Trypsin/P">Trypsin/P</option>
-<option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
 <expand macro="list_string_san" name="enzyme"/>
 </param>
-<param argument="-num_enzyme_termini" type="select" optional="true" label="Specify the termini where the cleavage rule has to match" help="">
+<param argument="-num_enzyme_termini" type="select" label="Specify the termini where the cleavage rule has to match" help="">
 <option value="semi">semi</option>
 <option value="fully" selected="true">fully</option>
 <option value="C-term unspecific">C-term unspecific</option>
 <option value="N-term unspecific">N-term unspecific</option>
 <expand macro="list_string_san" name="num_enzyme_termini"/>
 </param>
-<param argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
+<param argument="-missed_cleavages" type="integer" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
-<param argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
+<param argument="-min_peptide_length" type="integer" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
-<param argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
+<param argument="-max_peptide_length" type="integer" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
-<param argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/>
+<param argument="-num_hits" type="integer" value="1" label="Number of peptide hits (PSMs) per spectrum in output file" help=""/>
-<param argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
+<param argument="-precursor_charge" type="text" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
 <expand macro="list_string_san" name="precursor_charge"/>
 </param>
-<param argument="-override_charge" type="select" optional="true" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
+<param argument="-override_charge" type="select" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
 <option value="keep any known">keep any known</option>
 <option value="ignore known">ignore known</option>
 <option value="ignore outside range">ignore outside range</option>
 <option value="keep known search unknown" selected="true">keep known search unknown</option>
 <expand macro="list_string_san" name="override_charge"/>
 </param>
-<param argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
+<param argument="-ms_level" type="integer" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
-<param argument="-activation_method" type="select" optional="true" label="If not ALL, only searches spectra of the given method" help="">
+<param argument="-activation_method" type="select" label="If not ALL, only searches spectra of the given method" help="">
 <option value="ALL" selected="true">ALL</option>
 <option value="CID">CID</option>
 <option value="ECD">ECD</option>
 <option value="ETD">ETD</option>
 <option value="PQD">PQD</option>
 <option value="HCD">HCD</option>
 <option value="IRMPD">IRMPD</option>
 <expand macro="list_string_san" name="activation_method"/>
 </param>
-<param argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
+<param argument="-max_fragment_charge" type="integer" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
 <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/>
-<param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+<param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
 <option value="2-succinyl (C)">2-succinyl (C)</option>
 <option value="2HPG (R)">2HPG (R)</option>
 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+<option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+<option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+<option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+<option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
 <option value="4-ONE (C)">4-ONE (C)</option>
 <option value="4-ONE (H)">4-ONE (H)</option>
 <option value="4-ONE (K)">4-ONE (K)</option>
 <option value="Ammonium (D)">Ammonium (D)</option>
 <option value="Ammonium (E)">Ammonium (E)</option>
 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+<option value="Andro-H2O (C)">Andro-H2O (C)</option>
 <option value="Archaeol (C)">Archaeol (C)</option>
 <option value="Arg (N-term)">Arg (N-term)</option>
 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+<option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
 <option value="BITC (C)">BITC (C)</option>
 <option value="BITC (K)">BITC (K)</option>
 <option value="BITC (N-term)">BITC (N-term)</option>
 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-<option value="Bodipy (C)">Bodipy (C)</option>
 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
 <option value="Bromo (F)">Bromo (F)</option>
 <option value="Bromo (H)">Bromo (H)</option>
 <option value="Bromo (W)">Bromo (W)</option>
 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
 <option value="Dehydrated (S)">Dehydrated (S)</option>
 <option value="Dehydrated (T)">Dehydrated (T)</option>
 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
 <option value="Dehydro (C)">Dehydro (C)</option>
+<option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-<option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-<option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+<option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-<option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
 <option value="Ethyl (D)">Ethyl (D)</option>
 <option value="Ethyl (E)">Ethyl (E)</option>
 <option value="Ethyl (K)">Ethyl (K)</option>
 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
 <option value="Glu (E)">Glu (E)</option>
 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+<option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-<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>
 <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>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
 <option value="Gluratylation (K)">Gluratylation (K)</option>
 <option value="Glutathione (C)">Glutathione (C)</option>
 <option value="Gly (K)">Gly (K)</option>
 <option value="Gly (S)">Gly (S)</option>
 <option value="Gly (T)">Gly (T)</option>
+<option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+<option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+<option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+<option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+<option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+<option value="His+O(2) (H)">His+O(2) (H)</option>
 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+<option value="Kdo (S)">Kdo (S)</option>
+<option value="Kdo (T)">Kdo (T)</option>
 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+<option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+<option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
 <option value="Lipoyl (K)">Lipoyl (K)</option>
 <option value="LRGG (K)">LRGG (K)</option>
 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+<option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
 <option value="Lys (N-term)">Lys (N-term)</option>
+<option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
 <option value="maleimide5 (C)">maleimide5 (C)</option>
 <option value="maleimide5 (K)">maleimide5 (K)</option>
 <option value="Malonyl (C)">Malonyl (C)</option>
 <option value="Malonyl (K)">Malonyl (K)</option>
 <option value="Malonyl (S)">Malonyl (S)</option>
+<option value="MBS+peptide (C)">MBS+peptide (C)</option>
 <option value="MDCC (C)">MDCC (C)</option>
 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
 <option value="Menadione (C)">Menadione (C)</option>
 <option value="Menadione (K)">Menadione (K)</option>
 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+<option value="Met+O(2) (H)">Met+O(2) (H)</option>
 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-<option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
 <option value="NP40 (N-term)">NP40 (N-term)</option>
 <option value="NQIGG (K)">NQIGG (K)</option>
 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+<option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+<option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+<option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+<option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
 <option value="Phospho (C)">Phospho (C)</option>
 <option value="Phospho (D)">Phospho (D)</option>
 <option value="Phospho (S)">Phospho (S)</option>
 <option value="Phospho (T)">Phospho (T)</option>
 <option value="Phospho (Y)">Phospho (Y)</option>
 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+<option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
 <option value="Piperidine (K)">Piperidine (K)</option>
 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+<option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
 <option value="QEQTGG (K)">QEQTGG (K)</option>
 <option value="QQQTGG (K)">QQQTGG (K)</option>
 <option value="QTGG (K)">QTGG (K)</option>
 <option value="Quinone (W)">Quinone (W)</option>
 <option value="Quinone (Y)">Quinone (Y)</option>
+<option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+<option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+<option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+<option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+<option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+<option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+<option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+<option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+<option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+<option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+<option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+<option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+<option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+<option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+<option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+<option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+<option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+<option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+<option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+<option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
 <option value="Retinylidene (K)">Retinylidene (K)</option>
 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-<option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-<option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-<option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-<option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-<option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-<option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-<option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-<option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
 <option value="Saligenin (H)">Saligenin (H)</option>
 <option value="Saligenin (K)">Saligenin (K)</option>
 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
 <option value="serotonylation (Q)">serotonylation (Q)</option>
 <option value="shTMT (K)">shTMT (K)</option>
 <option value="shTMT (N-term)">shTMT (N-term)</option>
 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+<option value="shTMTpro (K)">shTMTpro (K)</option>
+<option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+<option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
 <option value="SMA (K)">SMA (K)</option>
 <option value="SMA (N-term)">SMA (N-term)</option>
 <option value="spermidine (Q)">spermidine (Q)</option>
 <option value="spermine (Q)">spermine (Q)</option>
 <option value="SPITC (K)">SPITC (K)</option>
 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-<option value="Ub-amide (C)">Ub-amide (C)</option>
 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
 <option value="Ub-VME (C)">Ub-VME (C)</option>
 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
 <option value="ZGB (K)">ZGB (K)</option>
 <option value="ZGB (N-term)">ZGB (N-term)</option>
 <option value="ZQG (K)">ZQG (K)</option>
 <expand macro="list_string_san" name="fixed_modifications"/>
 </param>
-<param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+<param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
 <option value="2-succinyl (C)">2-succinyl (C)</option>
 <option value="2HPG (R)">2HPG (R)</option>
 <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+<option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+<option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+<option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+<option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
 <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
 <option value="3sulfo (N-term)">3sulfo (N-term)</option>
 <option value="4-ONE (C)">4-ONE (C)</option>
 <option value="4-ONE (H)">4-ONE (H)</option>
 <option value="4-ONE (K)">4-ONE (K)</option>
 <option value="Ammonium (D)">Ammonium (D)</option>
 <option value="Ammonium (E)">Ammonium (E)</option>
 <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
 <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
 <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+<option value="Andro-H2O (C)">Andro-H2O (C)</option>
 <option value="Archaeol (C)">Archaeol (C)</option>
 <option value="Arg (N-term)">Arg (N-term)</option>
 <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
 <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
 <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
 <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+<option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
 <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
 <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
 <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
 <option value="BITC (C)">BITC (C)</option>
 <option value="BITC (K)">BITC (K)</option>
 <option value="BITC (N-term)">BITC (N-term)</option>
 <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
 <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-<option value="Bodipy (C)">Bodipy (C)</option>
 <option value="Brij35 (N-term)">Brij35 (N-term)</option>
 <option value="Brij58 (N-term)">Brij58 (N-term)</option>
 <option value="Bromo (F)">Bromo (F)</option>
 <option value="Bromo (H)">Bromo (H)</option>
 <option value="Bromo (W)">Bromo (W)</option>
 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
 <option value="Dehydrated (S)">Dehydrated (S)</option>
 <option value="Dehydrated (T)">Dehydrated (T)</option>
 <option value="Dehydrated (Y)">Dehydrated (Y)</option>
 <option value="Dehydro (C)">Dehydro (C)</option>
+<option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
 <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
 <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-<option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
 <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
 <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
 <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
 <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
 <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
 <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-<option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
 <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
 <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
 <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
 <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
 <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
 <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+<option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
 <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
 <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
 <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
 <option value="Ethanolyl (C)">Ethanolyl (C)</option>
 <option value="Ethanolyl (K)">Ethanolyl (K)</option>
 <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-<option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
 <option value="Ethyl (C-term)">Ethyl (C-term)</option>
 <option value="Ethyl (D)">Ethyl (D)</option>
 <option value="Ethyl (E)">Ethyl (E)</option>
 <option value="Ethyl (K)">Ethyl (K)</option>
 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
 <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
 <option value="Glu (E)">Glu (E)</option>
 <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+<option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
 <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-<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>
 <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>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
 <option value="Gluratylation (K)">Gluratylation (K)</option>
 <option value="Glutathione (C)">Glutathione (C)</option>
 <option value="Gly (K)">Gly (K)</option>
 <option value="Gly (S)">Gly (S)</option>
 <option value="Gly (T)">Gly (T)</option>
+<option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
 <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
 <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
 <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
 <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+<option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
 <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
 <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
 <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
 <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
 <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+<option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+<option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+<option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
 <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
 <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
 <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
 <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
 <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
 <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+<option value="His+O(2) (H)">His+O(2) (H)</option>
 <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+<option value="Kdo (S)">Kdo (S)</option>
+<option value="Kdo (T)">Kdo (T)</option>
 <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
 <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
 <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
 <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
 <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+<option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
 <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
 <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
 <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
 <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
 <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
 <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+<option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
 <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
 <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
 <option value="Lipoyl (K)">Lipoyl (K)</option>
 <option value="LRGG (K)">LRGG (K)</option>
 <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
 <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+<option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
 <option value="Lys (N-term)">Lys (N-term)</option>
+<option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
 <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
 <option value="maleimide5 (C)">maleimide5 (C)</option>
 <option value="maleimide5 (K)">maleimide5 (K)</option>
 <option value="Malonyl (C)">Malonyl (C)</option>
 <option value="Malonyl (K)">Malonyl (K)</option>
 <option value="Malonyl (S)">Malonyl (S)</option>
+<option value="MBS+peptide (C)">MBS+peptide (C)</option>
 <option value="MDCC (C)">MDCC (C)</option>
 <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
 <option value="Menadione (C)">Menadione (C)</option>
 <option value="Menadione (K)">Menadione (K)</option>
 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
 <option value="MesitylOxide (H)">MesitylOxide (H)</option>
 <option value="MesitylOxide (K)">MesitylOxide (K)</option>
 <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+<option value="Met+O(2) (H)">Met+O(2) (H)</option>
 <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
 <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
 <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
 <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-<option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
 <option value="NP40 (N-term)">NP40 (N-term)</option>
 <option value="NQIGG (K)">NQIGG (K)</option>
 <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
 <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+<option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+<option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+<option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+<option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
 <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
 <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
 <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
 <option value="Phospho (C)">Phospho (C)</option>
 <option value="Phospho (D)">Phospho (D)</option>
 <option value="Phospho (S)">Phospho (S)</option>
 <option value="Phospho (T)">Phospho (T)</option>
 <option value="Phospho (Y)">Phospho (Y)</option>
 <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
 <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+<option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
 <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
 <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
 <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
 <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
 <option value="Piperidine (K)">Piperidine (K)</option>
 <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+<option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
 <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
 <option value="QEQTGG (K)">QEQTGG (K)</option>
 <option value="QQQTGG (K)">QQQTGG (K)</option>
 <option value="QTGG (K)">QTGG (K)</option>
 <option value="Quinone (W)">Quinone (W)</option>
 <option value="Quinone (Y)">Quinone (Y)</option>
+<option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+<option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+<option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+<option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+<option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+<option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+<option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+<option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+<option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+<option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+<option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+<option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+<option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+<option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+<option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+<option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+<option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+<option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+<option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+<option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
 <option value="Retinylidene (K)">Retinylidene (K)</option>
 <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
 <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
 <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-<option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-<option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-<option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-<option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-<option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-<option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-<option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-<option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
 <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
 <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
 <option value="Saligenin (H)">Saligenin (H)</option>
 <option value="Saligenin (K)">Saligenin (K)</option>
 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
 <option value="serotonylation (Q)">serotonylation (Q)</option>
 <option value="shTMT (K)">shTMT (K)</option>
 <option value="shTMT (N-term)">shTMT (N-term)</option>
 <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+<option value="shTMTpro (K)">shTMTpro (K)</option>
+<option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+<option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
 <option value="SMA (K)">SMA (K)</option>
 <option value="SMA (N-term)">SMA (N-term)</option>
 <option value="spermidine (Q)">spermidine (Q)</option>
 <option value="spermine (Q)">spermine (Q)</option>
 <option value="SPITC (K)">SPITC (K)</option>
 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-<option value="Ub-amide (C)">Ub-amide (C)</option>
 <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
 <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
 <option value="Ub-VME (C)">Ub-VME (C)</option>
 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
 <section name="PeptideIndexing" title="" help="" expanded="false">
 <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
 <expand macro="list_string_san" name="decoy_string"/>
 </param>
-<param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+<param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
 <option value="prefix" selected="true">prefix</option>
 <option value="suffix">suffix</option>
 <expand macro="list_string_san" name="decoy_string_position"/>
 </param>
-<param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+<param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
 <option value="error">error</option>
 <option value="warn" selected="true">warn</option>
 <option value="silent">silent</option>
 <expand macro="list_string_san" name="missing_decoy_action"/>
 </param>
 <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
 <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
 <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-<param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+<param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
 <option value="error" selected="true">error</option>
 <option value="warn">warn</option>
 <option value="remove">remove</option>
 <expand macro="list_string_san" name="unmatched_action"/>
 </param>
-<param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+<param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-<param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+<param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
 <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+<param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
 <section name="enzyme" title="" help="" expanded="false">
-<param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+<param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
 <option value="auto" selected="true">auto</option>
+<option value="Arg-C">Arg-C</option>
+<option value="Arg-C/P">Arg-C/P</option>
+<option value="Asp-N">Asp-N</option>
+<option value="Asp-N/B">Asp-N/B</option>
+<option value="Asp-N_ambic">Asp-N_ambic</option>
 <option value="Trypsin">Trypsin</option>
+<option value="Chymotrypsin">Chymotrypsin</option>
+<option value="Chymotrypsin/P">Chymotrypsin/P</option>
+<option value="CNBr">CNBr</option>
+<option value="Formic_acid">Formic_acid</option>
 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
 <option value="Glu-C+P">Glu-C+P</option>
 <option value="PepsinA + P">PepsinA + P</option>
 <option value="cyanogen-bromide">cyanogen-bromide</option>
 <option value="Clostripain/P">Clostripain/P</option>
 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
 <option value="no cleavage">no cleavage</option>
+<option value="unspecific cleavage">unspecific cleavage</option>
+<option value="TrypChymo">TrypChymo</option>
+<option value="Trypsin/P">Trypsin/P</option>
+<option value="V8-DE">V8-DE</option>
+<option value="V8-E">V8-E</option>
+<option value="leukocyte elastase">leukocyte elastase</option>
 <option value="proline endopeptidase">proline endopeptidase</option>
 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
 <option value="2-iodobenzoate">2-iodobenzoate</option>
 <option value="iodosobenzoate">iodosobenzoate</option>
 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-<option value="Trypsin/P">Trypsin/P</option>
+<option value="Lys-C">Lys-C</option>
-<option value="V8-DE">V8-DE</option>
-<option value="V8-E">V8-E</option>
-<option value="leukocyte elastase">leukocyte elastase</option>
-<option value="PepsinA">PepsinA</option>
-<option value="TrypChymo">TrypChymo</option>
-<option value="Asp-N">Asp-N</option>
-<option value="unspecific cleavage">unspecific cleavage</option>
-<option value="Asp-N/B">Asp-N/B</option>
-<option value="Asp-N_ambic">Asp-N_ambic</option>
-<option value="Chymotrypsin">Chymotrypsin</option>
-<option value="Chymotrypsin/P">Chymotrypsin/P</option>
-<option value="CNBr">CNBr</option>
-<option value="Arg-C/P">Arg-C/P</option>
 <option value="Lys-N">Lys-N</option>
 <option value="Lys-C/P">Lys-C/P</option>
-<option value="Formic_acid">Formic_acid</option>
+<option value="PepsinA">PepsinA</option>
-<option value="Lys-C">Lys-C</option>
-<option value="Arg-C">Arg-C</option>
 <expand macro="list_string_san" name="name"/>
 </param>
-<param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+<param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
 <option value="auto" selected="true">auto</option>
 <option value="full">full</option>
 <option value="semi">semi</option>
 <option value="none">none</option>
 <expand macro="list_string_san" name="specificity"/>
 <param argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/>
 <param argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/>
 <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/>
 <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/>
 <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help="">
+<option value="Asp-N">Asp-N</option>
+<option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+<option value="Trypsin">Trypsin</option>
+<option value="Arg-C">Arg-C</option>
+<option value="no cleavage">no cleavage</option>
+<option value="unspecific cleavage">unspecific cleavage</option>
+<option value="Chymotrypsin">Chymotrypsin</option>
 <option value="CNBr">CNBr</option>
 <option value="Lys-C">Lys-C</option>
-<option value="Trypsin">Trypsin</option>
-<option value="Arg-C">Arg-C</option>
-<option value="Chymotrypsin">Chymotrypsin</option>
-<option value="Asp-N">Asp-N</option>
-<option value="unspecific cleavage">unspecific cleavage</option>
 <option value="Lys-N">Lys-N</option>
 <option value="PepsinA">PepsinA</option>
 <option value="Trypsin/P">Trypsin/P</option>
-<option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
 <expand macro="list_string_san" name="second_enzyme"/>
 </param>
-<param argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help="">
+<param argument="-digest_mass_range" type="text" value="600:5000" label="MH+ peptide mass range to analyze" help="">
 <expand macro="list_string_san" name="digest_mass_range"/>
 </param>
-<param argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
+<param argument="-max_precursor_charge" type="integer" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
-<param argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
+<param argument="-spectrum_batch_size" type="integer" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
-<param argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+<param argument="-mass_offsets" type="text" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
 <expand macro="list_float_valsan" name="mass_offsets"/>
 </param>
-<param argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
+<param argument="-minimum_peaks" type="integer" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
-<param argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
+<param argument="-minimum_intensity" type="float" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
-<param argument="-remove_precursor_peak" type="select" optional="true" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
+<param argument="-remove_precursor_peak" type="select" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
 <option value="no" selected="true">no</option>
 <option value="yes">yes</option>
 <option value="charge_reduced">charge_reduced</option>
 <option value="phosphate_loss">phosphate_loss</option>
 <expand macro="list_string_san" name="remove_precursor_peak"/>
 </param>
-<param argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
+<param argument="-remove_precursor_tolerance" type="float" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
-<param argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
+<param argument="-clear_mz_range" type="text" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
 <expand macro="list_string_san" name="clear_mz_range"/>
 </param>
-<param argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
+<param argument="-max_variable_mods_in_peptide" type="integer" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
 <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/>
 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-<param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+<param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
 <expand macro="list_string_san" name="test"/>
 </param>
 </expand>
 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
 <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option>
 </data>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
 </data>
 </outputs>
-<tests><!-- TOPP_CometAdapter_1 -->
+<tests>
+<!-- TOPP_CometAdapter_1 -->
 <test expect_num_outputs="3">
 <section name="adv_opts">
 <param name="use_A_ions" value="false"/>
 <param name="use_B_ions" value="true"/>
 <param name="use_C_ions" value="false"/>
 <param name="use_X_ions" value="false"/>
 <param name="use_Y_ions" value="true"/>
 <param name="use_Z_ions" value="false"/>
 <param name="use_NL_ions" value="false"/>
-<param name="second_enzyme"/>
 <param name="digest_mass_range" value="600:5000"/>
 <param name="max_precursor_charge" value="5"/>
 <param name="spectrum_batch_size" value="1000"/>
 <param name="mass_offsets" value="0.0"/>
 <param name="minimum_peaks" value="10"/>
 <param name="require_variable_mod" value="false"/>
 <param name="force" value="true"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="spectra_comet.mzML"/>
-<output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="database" value="proteins.fasta"/>
-<output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+<output name="pin_out" value="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
 <param name="precursor_mass_tolerance" value="3.0"/>
 <param name="precursor_error_units" value="ppm"/>
 <param name="isotope_error" value="off"/>
 <param name="fragment_mass_tolerance" value="0.50025"/>
 <param name="fragment_error_units" value="Da"/>
 <param name="override_charge" value="keep any known"/>
 <param name="ms_level" value="2"/>
 <param name="activation_method" value="ALL"/>
 <param name="max_fragment_charge" value="3"/>
 <param name="clip_nterm_methionine" value="false"/>
-<param name="fixed_modifications"/>
-<param name="variable_modifications"/>
-<param name="binary_modifications" value=""/>
 <param name="reindex" value="true"/>
 <section name="PeptideIndexing">
 <param name="decoy_string" value=""/>
 <param name="decoy_string_position" value="prefix"/>
 <param name="missing_decoy_action" value="warn"/>
 <param name="keep_unreferenced_proteins" value="false"/>
 <param name="unmatched_action" value="error"/>
 <param name="aaa_max" value="3"/>
 <param name="mismatches_max" value="0"/>
 <param name="IL_equivalent" value="false"/>
+<param name="allow_nterm_protein_cleavage" value="true"/>
 <section name="enzyme">
 <param name="name" value="auto"/>
 <param name="specificity" value="auto"/>
 </section>
 </section>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_CometAdapter_2 -->
 <test expect_num_outputs="3">
 <section name="adv_opts">
 <param name="use_A_ions" value="false"/>
 <param name="use_C_ions" value="false"/>
 <param name="use_X_ions" value="false"/>
 <param name="use_Y_ions" value="true"/>
 <param name="use_Z_ions" value="false"/>
 <param name="use_NL_ions" value="false"/>
-<param name="second_enzyme"/>
 <param name="digest_mass_range" value="600:5000"/>
 <param name="max_precursor_charge" value="5"/>
 <param name="spectrum_batch_size" value="1000"/>
 <param name="mass_offsets" value="0.0"/>
 <param name="minimum_peaks" value="10"/>
 <param name="require_variable_mod" value="false"/>
 <param name="force" value="true"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="CometAdapter_2_prepared.mzML"/>
-<output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="database" value="CometAdapter_2_in.fasta"/>
-<output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+<output name="pin_out" value="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
 <param name="precursor_mass_tolerance" value="3.0"/>
 <param name="precursor_error_units" value="Da"/>
 <param name="isotope_error" value="off"/>
 <param name="fragment_mass_tolerance" value="0.50025"/>
 <param name="fragment_error_units" value="Da"/>
 <param name="override_charge" value="keep any known"/>
 <param name="ms_level" value="2"/>
 <param name="activation_method" value="ALL"/>
 <param name="max_fragment_charge" value="3"/>
 <param name="clip_nterm_methionine" value="false"/>
-<param name="fixed_modifications"/>
-<param name="variable_modifications"/>
-<param name="binary_modifications" value=""/>
 <param name="reindex" value="true"/>
 <section name="PeptideIndexing">
 <param name="decoy_string" value=""/>
 <param name="decoy_string_position" value="prefix"/>
 <param name="missing_decoy_action" value="warn"/>
 <param name="keep_unreferenced_proteins" value="false"/>
 <param name="unmatched_action" value="error"/>
 <param name="aaa_max" value="3"/>
 <param name="mismatches_max" value="0"/>
 <param name="IL_equivalent" value="false"/>
+<param name="allow_nterm_protein_cleavage" value="true"/>
 <section name="enzyme">
 <param name="name" value="auto"/>
 <param name="specificity" value="auto"/>
 </section>
 </section>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_CometAdapter_3 -->
 <test expect_num_outputs="3">
 <section name="adv_opts">
 <param name="use_A_ions" value="false"/>
 <param name="use_C_ions" value="false"/>
 <param name="use_X_ions" value="false"/>
 <param name="use_Y_ions" value="true"/>
 <param name="use_Z_ions" value="false"/>
 <param name="use_NL_ions" value="false"/>
-<param name="second_enzyme"/>
 <param name="digest_mass_range" value="600:5000"/>
 <param name="max_precursor_charge" value="5"/>
 <param name="spectrum_batch_size" value="20000"/>
 <param name="mass_offsets" value="0.0"/>
 <param name="minimum_peaks" value="10"/>
 <param name="require_variable_mod" value="false"/>
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="CometAdapter_3.mzML"/>
-<output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="database" value="CometAdapter_3.fasta"/>
-<output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+<output name="pin_out" value="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
 <param name="precursor_mass_tolerance" value="5.0"/>
 <param name="precursor_error_units" value="ppm"/>
 <param name="isotope_error" value="off"/>
 <param name="fragment_mass_tolerance" value="0.01"/>
 <param name="fragment_error_units" value="Da"/>
 <param name="activation_method" value="ALL"/>
 <param name="max_fragment_charge" value="3"/>
 <param name="clip_nterm_methionine" value="false"/>
 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/>
-<param name="binary_modifications" value=""/>
 <param name="reindex" value="true"/>
 <section name="PeptideIndexing">
 <param name="decoy_string" value=""/>
 <param name="decoy_string_position" value="prefix"/>
 <param name="missing_decoy_action" value="warn"/>
 <param name="keep_unreferenced_proteins" value="false"/>
 <param name="unmatched_action" value="error"/>
 <param name="aaa_max" value="3"/>
 <param name="mismatches_max" value="0"/>
 <param name="IL_equivalent" value="false"/>
+<param name="allow_nterm_protein_cleavage" value="true"/>
 <section name="enzyme">
 <param name="name" value="auto"/>
 <param name="specificity" value="auto"/>
 </section>
 </section>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_CometAdapter_4 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="use_A_ions" value="false"/>
 <param name="use_C_ions" value="false"/>
 <param name="use_X_ions" value="false"/>
 <param name="use_Y_ions" value="true"/>
 <param name="use_Z_ions" value="false"/>
 <param name="use_NL_ions" value="false"/>
-<param name="second_enzyme"/>
 <param name="digest_mass_range" value="600:1200"/>
 <param name="max_precursor_charge" value="5"/>
 <param name="spectrum_batch_size" value="20000"/>
 <param name="mass_offsets" value="0.0"/>
 <param name="minimum_peaks" value="10"/>
 <param name="require_variable_mod" value="false"/>
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
-<output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
 <param name="precursor_mass_tolerance" value="5.0"/>
 <param name="precursor_error_units" value="ppm"/>
 <param name="isotope_error" value="off"/>
 <param name="fragment_mass_tolerance" value="0.01"/>
 <param name="activation_method" value="ALL"/>
 <param name="max_fragment_charge" value="3"/>
 <param name="clip_nterm_methionine" value="false"/>
 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
-<param name="binary_modifications" value=""/>
 <param name="reindex" value="true"/>
 <section name="PeptideIndexing">
 <param name="decoy_string" value=""/>
 <param name="decoy_string_position" value="prefix"/>
 <param name="missing_decoy_action" value="warn"/>
 <param name="keep_unreferenced_proteins" value="false"/>
 <param name="unmatched_action" value="error"/>
 <param name="aaa_max" value="3"/>
 <param name="mismatches_max" value="0"/>
 <param name="IL_equivalent" value="false"/>
+<param name="allow_nterm_protein_cleavage" value="true"/>
 <section name="enzyme">
 <param name="name" value="auto"/>
 <param name="specificity" value="auto"/>
 </section>
 </section>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 </tests>
 <help><![CDATA[Annotates MS/MS spectra using Comet.
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CometAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CometAdapter.html]]></help>
 <expand macro="references"/>
 </tool>

Mercurial > repos > galaxyp > openms_cometadapter

comparison CometAdapter.xml @ 9:df0c77da6c87 draft default tip