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OpenMS workflow, triple dimethyl labelled quantification, Thermo Q Exactive, 15/11/2015
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.0.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="31" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="41" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="true" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-2900" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="720" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="15" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="ConsensusID" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1580" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file" required="true" advanced="false" supported_formats="*.idXML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.idXML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="rt_delta" value="0.1" type="double" description="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_delta" value="0.1" type="double" description="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="algorithm" value="best" type="string" description="Algorithm used for consensus scoring.#br#* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.#br#* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.#br#* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.#br#* average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.#br#* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types." required="false" advanced="false" restrictions="PEPMatrix,PEPIons,best,average,ranks" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="filter" description="Options for filtering peptide hits"> | |
| <ITEM name="considered_hits" value="0" type="int" description="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="min_support" value="0" type="double" description="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="count_empty" value="false" type="string" description="Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="PEPIons" description="PEPIons algorithm parameters"> | |
| <ITEM name="mass_tolerance" value="0.5" type="double" description="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides ." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="min_shared" value="2" type="int" description="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)." required="false" advanced="false" restrictions="1:" /> | |
| </NODE> | |
| <NODE name="PEPMatrix" description="PEPMatrix algorithm parameters"> | |
| <ITEM name="matrix" value="identity" type="string" description="Substitution matrix to use for alignment-based similarity scoring" required="false" advanced="false" restrictions="identity,PAM30MS" /> | |
| <ITEM name="penalty" value="5" type="int" description="Alignment gap penalty (the same value is used for gap opening and extension)" required="false" advanced="false" restrictions="1:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1200" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDMerger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1380" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files separated by blanks" required="true" advanced="false" supported_formats="*.idXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="add_to" value="" type="input-file" description="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each protein/peptide identification (meta value: file_origin)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="pepxml_protxml" value="false" type="string" description="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="16" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1800" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins." required="false" advanced="false" /> | |
| <ITEM name="missing_decoy_action" value="warn" type="string" description="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)" required="false" advanced="false" restrictions="error,warn" /> | |
| <ITEM name="prefix" value="true" type="string" description="If set, protein accessions in the database contain 'decoy_string' as prefix." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_proteins" value="true" type="string" description="If set, add target/decoy information to proteins (as well as peptides)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_sequence" value="true" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_description" value="true" type="string" description="If set, the protein description is stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's. AAA's are 'B', 'Z' and 'X'" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="IL_equivalent" value="false" type="string" description="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="enzyme" description="The enzyme determines valid cleavage sites; cleavage specificity determines to what extent validity is enforced."> | |
| <ITEM name="name" value="Trypsin/P" type="string" description="Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)." required="false" advanced="false" restrictions="Trypsin,Trypsin/P" /> | |
| <ITEM name="specificity" value="none" type="string" description="Specificity of the enzyme.#br# 'full': both internal cleavage sites must match.#br# 'semi': one of two internal cleavage sites must match.#br# 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2640" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="800" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins." required="false" advanced="false" /> | |
| <ITEM name="missing_decoy_action" value="warn" type="string" description="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)" required="false" advanced="false" restrictions="error,warn" /> | |
| <ITEM name="prefix" value="true" type="string" description="If set, protein accessions in the database contain 'decoy_string' as prefix." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_proteins" value="true" type="string" description="If set, add target/decoy information to proteins (as well as peptides)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_sequence" value="true" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_description" value="true" type="string" description="If set, the protein description is stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's. AAA's are 'B', 'Z' and 'X'" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="IL_equivalent" value="false" type="string" description="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="enzyme" description="The enzyme determines valid cleavage sites; cleavage specificity determines to what extent validity is enforced."> | |
| <ITEM name="name" value="Trypsin/P" type="string" description="Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)." required="false" advanced="false" restrictions="Trypsin,Trypsin/P" /> | |
| <ITEM name="specificity" value="none" type="string" description="Specificity of the enzyme.#br# 'full': both internal cleavage sites must match.#br# 'semi': one of two internal cleavage sites must match.#br# 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="800" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins." required="false" advanced="false" /> | |
| <ITEM name="missing_decoy_action" value="warn" type="string" description="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)" required="false" advanced="false" restrictions="error,warn" /> | |
| <ITEM name="prefix" value="true" type="string" description="If set, protein accessions in the database contain 'decoy_string' as prefix." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_proteins" value="true" type="string" description="If set, add target/decoy information to proteins (as well as peptides)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_sequence" value="true" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_description" value="true" type="string" description="If set, the protein description is stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's. AAA's are 'B', 'Z' and 'X'" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="IL_equivalent" value="false" type="string" description="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="enzyme" description="The enzyme determines valid cleavage sites; cleavage specificity determines to what extent validity is enforced."> | |
| <ITEM name="name" value="Trypsin/P" type="string" description="Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)." required="false" advanced="false" restrictions="Trypsin,Trypsin/P" /> | |
| <ITEM name="specificity" value="none" type="string" description="Specificity of the enzyme.#br# 'full': both internal cleavage sites must match.#br# 'semi': one of two internal cleavage sites must match.#br# 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2160" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="800" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins." required="false" advanced="false" /> | |
| <ITEM name="missing_decoy_action" value="warn" type="string" description="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)" required="false" advanced="false" restrictions="error,warn" /> | |
| <ITEM name="prefix" value="true" type="string" description="If set, protein accessions in the database contain 'decoy_string' as prefix." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_proteins" value="true" type="string" description="If set, add target/decoy information to proteins (as well as peptides)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_sequence" value="true" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_description" value="true" type="string" description="If set, the protein description is stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's. AAA's are 'B', 'Z' and 'X'" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="IL_equivalent" value="false" type="string" description="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="enzyme" description="The enzyme determines valid cleavage sites; cleavage specificity determines to what extent validity is enforced."> | |
| <ITEM name="name" value="Trypsin/P" type="string" description="Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)." required="false" advanced="false" restrictions="Trypsin,Trypsin/P" /> | |
| <ITEM name="specificity" value="none" type="string" description="Specificity of the enzyme.#br# 'full': both internal cleavage sites must match.#br# 'semi': one of two internal cleavage sites must match.#br# 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDPosteriorErrorProbability" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2640" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1000" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out_plot" value="" type="output-file" description="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="split_charge" value="false" type="string" description="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="top_hits_only" value="false" type="string" description="If set only the top hits of every PeptideIdentification will be used" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fdr_for_targets_smaller" value="0.05" type="double" description="Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." required="false" advanced="true" /> | |
| <ITEM name="ignore_bad_data" value="false" type="string" description="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="prob_correct" value="false" type="string" description="If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="fit_algorithm" description="Algorithm parameter subsection"> | |
| <ITEM name="number_of_bins" value="100" type="int" description="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" required="false" advanced="true" /> | |
| <ITEM name="incorrectly_assigned" value="Gumbel" type="string" description="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." required="false" advanced="true" restrictions="Gumbel,Gauss" /> | |
| <ITEM name="max_nr_iterations" value="1000" type="int" description="Bounds the number of iterations for the EM algorithm when convergence is slow." required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDPosteriorErrorProbability" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1000" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out_plot" value="" type="output-file" description="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="split_charge" value="false" type="string" description="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="top_hits_only" value="false" type="string" description="If set only the top hits of every PeptideIdentification will be used" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fdr_for_targets_smaller" value="0.05" type="double" description="Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." required="false" advanced="true" /> | |
| <ITEM name="ignore_bad_data" value="false" type="string" description="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="prob_correct" value="false" type="string" description="If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="fit_algorithm" description="Algorithm parameter subsection"> | |
| <ITEM name="number_of_bins" value="100" type="int" description="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" required="false" advanced="true" /> | |
| <ITEM name="incorrectly_assigned" value="Gumbel" type="string" description="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." required="false" advanced="true" restrictions="Gumbel,Gauss" /> | |
| <ITEM name="max_nr_iterations" value="1000" type="int" description="Bounds the number of iterations for the EM algorithm when convergence is slow." required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDPosteriorErrorProbability" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2160" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1000" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out_plot" value="" type="output-file" description="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="split_charge" value="false" type="string" description="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="top_hits_only" value="false" type="string" description="If set only the top hits of every PeptideIdentification will be used" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fdr_for_targets_smaller" value="0.05" type="double" description="Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." required="false" advanced="true" /> | |
| <ITEM name="ignore_bad_data" value="false" type="string" description="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="prob_correct" value="false" type="string" description="If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="fit_algorithm" description="Algorithm parameter subsection"> | |
| <ITEM name="number_of_bins" value="100" type="int" description="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" required="false" advanced="true" /> | |
| <ITEM name="incorrectly_assigned" value="Gumbel" type="string" description="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." required="false" advanced="true" restrictions="Gumbel,Gauss" /> | |
| <ITEM name="max_nr_iterations" value="1000" type="int" description="Bounds the number of iterations for the EM algorithm when convergence is slow." required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="20" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2220" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="min_length" value="0" type="int" description="Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="max_length" value="0" type="int" description="Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length < min_length, max_length will be ignored." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="min_charge" value="1" type="int" description="Keep only peptide hits for tandem spectra with charge greater or equal this value." required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="var_mods" value="false" type="string" description="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once per PSM, only one instance is kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_protein_hits" value="false" type="string" description="Proteins not referenced by a peptide are retained in the ids." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_decoys" value="false" type="string" description="Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="delete_unreferenced_peptide_hits" value="false" type="string" description="Peptides not referenced by any protein are deleted in the ids. Usually used in combination with 'score:prot' or 'thresh:prot'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="precursor" description="Filtering by precursor RT or m/z"> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract." required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="Mass-to-charge range to extract." required="false" advanced="false" /> | |
| <ITEM name="allow_missing" value="false" type="string" description="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="score" description="Filtering by peptide/protein score. To enable any of the filters below, just change their default value. All active filters will be applied in order."> | |
| <ITEM name="pep" value="0.01" type="double" description="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="double" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only instances also present in a whitelist file can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="by_seq_only" value="false" type="string" description="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that are not referencing at least one of the provided protein accession are removed.#br#Only proteins of the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only instances not present in a blacklist file can pass)"> | |
| <ITEM name="peptides" value="" type="input-file" description="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out. Use with blacklist:ignore_modification flag to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare blacklisted peptides by sequence only.#br#" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." required="false" advanced="false" restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="mz" description="Filtering by mz"> | |
| <ITEM name="error" value="-1" type="double" description="Filtering by deviation to theoretical mass (disabled for negative values)." required="false" advanced="false" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Absolute or relative error." required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins"> | |
| <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n>0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="strict" value="false" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="n_to_m_peptide_hits" value=":" type="string" description="peptide hit rank range to extracts" required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="21" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FidoAdapter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2800" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2420" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input: identification results" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output: identification results with scored/grouped proteins" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fido_executable" value="C:/Program Files/Fido/Fido.exe" type="input-file" description="Path to the Fido executable to use; may be empty if the executable is globally available." required="true" advanced="false" /> | |
| <ITEM name="fidocp_executable" value="C:/Program Files/Fido/FidoChooseParameters.exe" type="input-file" description="Path to the FidoChooseParameters executable to use; may be empty if the executable is globally available." required="true" advanced="false" /> | |
| <ITEM name="prob_param" value="Posterior Probability_score" type="string" description="Read the peptide probability from this user parameter ('UserParam') in the input file, instead of from the 'score' field, if available. (Use e.g. for search results that were processed with the TOPP tools IDPosteriorErrorProbability followed by FalseDiscoveryRate.)" required="false" advanced="false" /> | |
| <ITEM name="separate_runs" value="false" type="string" description="Process multiple protein identification runs in the input separately, don't merge them. Merging results in loss of descriptive information of the single protein identification runs." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_zero_group" value="false" type="string" description="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="greedy_group_resolution" value="true" type="string" description="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities. Also adds the resolved ambiguity groups to output." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_cleanup" value="false" type="string" description="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="all_PSMs" value="false" type="string" description="Consider all PSMs of each peptide, instead of only the best one" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="group_level" value="false" type="string" description="Perform inference on protein group level (instead of individual protein level). This will lead to higher probabilities for (bigger) protein groups." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="accuracy" value="" type="string" description="Accuracy level of start parameters. There is a trade-off between accuracy and runtime. Empty uses the default ('best')." required="false" advanced="true" restrictions=",best,relaxed,sloppy" /> | |
| <ITEM name="log2_states" value="0" type="int" description="Binary logarithm of the max. number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="log2_states_precalc" value="0" type="int" description="Like 'log2_states', but allows to set a separate limit for the precalculation" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="prob" description="Probability values for running Fido directly, i.e. without parameter estimation (in which case other settings, except 'log2_states', are ignored)"> | |
| <ITEM name="protein" value="0" type="double" description="Protein prior probability ('gamma' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide" value="0" type="double" description="Peptide emission probability ('alpha' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="spurious" value="0" type="double" description="Spurious peptide identification probability ('beta' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="17" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2800" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2040" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="18" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDMerger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2800" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2220" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files separated by blanks" required="true" advanced="false" supported_formats="*.idXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="add_to" value="" type="input-file" description="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each protein/peptide identification (meta value: file_origin)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="pepxml_protxml" value="false" type="string" description="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="22" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2800" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2620" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file containing a search against a concatenated sequence database. Either specify '-in' alone or 'in_target' together with 'in_decoy' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_target" value="" type="input-file" description="Identification input file containing a search against a target-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_decoy" value="" type="input-file" description="Identification input file containing a search against a decoy-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Identification output with annotated FDR" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="proteins_only" value="true" type="string" description="If set only the FDR on protein level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set only the FDR on peptide (PSM) level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm"> | |
| <ITEM name="no_qvalues" value="false" type="string" description="If 'true' strict FDRs will be calculated instead of q-values (the default)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_all_hits" value="false" type="string" description="If 'true' not only the first hit, but all are used (peptides only)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="split_charge_variants" value="false" type="string" description="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="treat_runs_separately" value="false" type="string" description="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="23" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2800" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2820" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="min_length" value="0" type="int" description="Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="max_length" value="0" type="int" description="Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length < min_length, max_length will be ignored." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="min_charge" value="1" type="int" description="Keep only peptide hits for tandem spectra with charge greater or equal this value." required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="var_mods" value="false" type="string" description="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once per PSM, only one instance is kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_protein_hits" value="false" type="string" description="Proteins not referenced by a peptide are retained in the ids." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_decoys" value="false" type="string" description="Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="delete_unreferenced_peptide_hits" value="false" type="string" description="Peptides not referenced by any protein are deleted in the ids. Usually used in combination with 'score:prot' or 'thresh:prot'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="precursor" description="Filtering by precursor RT or m/z"> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract." required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="Mass-to-charge range to extract." required="false" advanced="false" /> | |
| <ITEM name="allow_missing" value="false" type="string" description="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="score" description="Filtering by peptide/protein score. To enable any of the filters below, just change their default value. All active filters will be applied in order."> | |
| <ITEM name="pep" value="0" type="double" description="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0.01" type="double" description="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="double" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only instances also present in a whitelist file can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="by_seq_only" value="false" type="string" description="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that are not referencing at least one of the provided protein accession are removed.#br#Only proteins of the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only instances not present in a blacklist file can pass)"> | |
| <ITEM name="peptides" value="" type="input-file" description="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out. Use with blacklist:ignore_modification flag to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare blacklisted peptides by sequence only.#br#" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." required="false" advanced="false" restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="mz" description="Filtering by mz"> | |
| <ITEM name="error" value="-1" type="double" description="Filtering by deviation to theoretical mass (disabled for negative values)." required="false" advanced="false" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Absolute or relative error." required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins"> | |
| <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n>0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="strict" value="false" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="n_to_m_peptide_hits" value=":" type="string" description="peptide hit rank range to extracts" required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="MSGFPlusAdapter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2640" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="580" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file (MS-GF+ parameter '-s')" required="true" advanced="false" supported_formats="*.mzML,*.mzXML,*.mgf,*.ms2" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="mzid_out" value="" type="output-file" description="Alternative output file (MS-GF+ parameter '-o')#br#Either 'out' or 'mzid_out' are required. They can be used together." required="false" advanced="false" supported_formats="*.mzid" /> | |
| <ITEM name="executable" value="C:/Program Files/MSGFPlus/MSGFPlus.jar" type="input-file" description="MS-GF+ .jar file, e.g. 'c:\program files\MSGFPlus.jar'" required="true" advanced="false" /> | |
| <ITEM name="database" value="" type="input-file" description="Protein sequence database (FASTA file; MS-GF+ parameter '-d'). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'." required="true" advanced="false" supported_formats="*.FASTA" /> | |
| <ITEM name="add_decoys" value="false" type="string" description="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda'). This allows the calculation of FDRs, but should only be used if the database does not already contain decoys." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="precursor_mass_tolerance" value="10" type="double" description="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" /> | |
| <ITEM name="precursor_error_units" value="ppm" type="string" description="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="isotope_error_range" value="0,0" type="string" description="Range of allowed isotope peak errors (MS-GF+ parameter '-ti'). Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2." required="false" advanced="false" /> | |
| <ITEM name="fragment_method" value="from_spectrum" type="string" description="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" required="false" advanced="false" restrictions="from_spectrum,CID,ETD,HCD" /> | |
| <ITEM name="instrument" value="Q_Exactive" type="string" description="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" required="false" advanced="false" restrictions="low_res,high_res,TOF,Q_Exactive" /> | |
| <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" required="false" advanced="false" restrictions="unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage" /> | |
| <ITEM name="protocol" value="none" type="string" description="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" required="false" advanced="false" restrictions="none,phospho,iTRAQ,iTRAQ_phospho,TMT" /> | |
| <ITEM name="tryptic" value="fully" type="string" description="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" required="false" advanced="false" restrictions="non,semi,fully" /> | |
| <ITEM name="min_precursor_charge" value="2" type="int" description="Minimum precursor ion charge (MS-GF+ parameter '-minCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_precursor_charge" value="4" type="int" description="Maximum precursor ion charge (MS-GF+ parameter '-maxCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="min_peptide_length" value="7" type="int" description="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_peptide_length" value="40" type="int" description="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="matches_per_spec" value="1" type="int" description="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="add_features" value="true" type="string" description="Output additional features - needed e.g. by Percolator (default: basic scores only; MS-GF+ parameter '-addFeatures')" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="max_mods" value="3" type="int" description="Maximum number of modifications per peptide. If this value is large, the search may take very long." required="false" advanced="false" restrictions="0:" /> | |
| <ITEMLIST name="fixed_modifications" type="string" description="Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| <LISTITEM value="Carbamidomethyl (C)"/> | |
| <LISTITEM value="Dimethyl (K)"/> | |
| <LISTITEM value="Dimethyl (N-term)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEM name="legacy_conversion" value="true" type="string" description="Use the indirect conversion of MS-GF+ results to idXML via export to TSV. Try this only if the default conversion takes too long or uses too much memory." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="java_memory" value="3500" type="int" description="Maximum Java heap size (in MB)" required="false" advanced="false" /> | |
| <ITEM name="java_permgen" value="0" type="int" description="Maximum Java permanent generation space (in MB); only for Java 7 and below" required="false" advanced="true" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="3" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="true" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="MSGFPlusAdapter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="580" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file (MS-GF+ parameter '-s')" required="true" advanced="false" supported_formats="*.mzML,*.mzXML,*.mgf,*.ms2" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="mzid_out" value="" type="output-file" description="Alternative output file (MS-GF+ parameter '-o')#br#Either 'out' or 'mzid_out' are required. They can be used together." required="false" advanced="false" supported_formats="*.mzid" /> | |
| <ITEM name="executable" value="C:/Program Files/MSGFPlus/MSGFPlus.jar" type="input-file" description="MS-GF+ .jar file, e.g. 'c:\program files\MSGFPlus.jar'" required="true" advanced="false" /> | |
| <ITEM name="database" value="" type="input-file" description="Protein sequence database (FASTA file; MS-GF+ parameter '-d'). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'." required="true" advanced="false" supported_formats="*.FASTA" /> | |
| <ITEM name="add_decoys" value="false" type="string" description="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda'). This allows the calculation of FDRs, but should only be used if the database does not already contain decoys." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="precursor_mass_tolerance" value="10" type="double" description="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" /> | |
| <ITEM name="precursor_error_units" value="ppm" type="string" description="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="isotope_error_range" value="0,0" type="string" description="Range of allowed isotope peak errors (MS-GF+ parameter '-ti'). Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2." required="false" advanced="false" /> | |
| <ITEM name="fragment_method" value="from_spectrum" type="string" description="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" required="false" advanced="false" restrictions="from_spectrum,CID,ETD,HCD" /> | |
| <ITEM name="instrument" value="Q_Exactive" type="string" description="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" required="false" advanced="false" restrictions="low_res,high_res,TOF,Q_Exactive" /> | |
| <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" required="false" advanced="false" restrictions="unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage" /> | |
| <ITEM name="protocol" value="none" type="string" description="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" required="false" advanced="false" restrictions="none,phospho,iTRAQ,iTRAQ_phospho,TMT" /> | |
| <ITEM name="tryptic" value="fully" type="string" description="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" required="false" advanced="false" restrictions="non,semi,fully" /> | |
| <ITEM name="min_precursor_charge" value="2" type="int" description="Minimum precursor ion charge (MS-GF+ parameter '-minCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_precursor_charge" value="4" type="int" description="Maximum precursor ion charge (MS-GF+ parameter '-maxCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="min_peptide_length" value="7" type="int" description="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_peptide_length" value="40" type="int" description="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="matches_per_spec" value="1" type="int" description="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="add_features" value="true" type="string" description="Output additional features - needed e.g. by Percolator (default: basic scores only; MS-GF+ parameter '-addFeatures')" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="max_mods" value="3" type="int" description="Maximum number of modifications per peptide. If this value is large, the search may take very long." required="false" advanced="false" restrictions="0:" /> | |
| <ITEMLIST name="fixed_modifications" type="string" description="Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| <LISTITEM value="Carbamidomethyl (C)"/> | |
| <LISTITEM value="Dimethyl:2H(4) (K)"/> | |
| <LISTITEM value="Dimethyl:2H(4) (N-term)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEM name="legacy_conversion" value="true" type="string" description="Use the indirect conversion of MS-GF+ results to idXML via export to TSV. Try this only if the default conversion takes too long or uses too much memory." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="java_memory" value="3500" type="int" description="Maximum Java heap size (in MB)" required="false" advanced="false" /> | |
| <ITEM name="java_permgen" value="0" type="int" description="Maximum Java permanent generation space (in MB); only for Java 7 and below" required="false" advanced="true" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="3" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="true" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="MSGFPlusAdapter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2160" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="580" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file (MS-GF+ parameter '-s')" required="true" advanced="false" supported_formats="*.mzML,*.mzXML,*.mgf,*.ms2" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="mzid_out" value="" type="output-file" description="Alternative output file (MS-GF+ parameter '-o')#br#Either 'out' or 'mzid_out' are required. They can be used together." required="false" advanced="false" supported_formats="*.mzid" /> | |
| <ITEM name="executable" value="C:/Program Files/MSGFPlus/MSGFPlus.jar" type="input-file" description="MS-GF+ .jar file, e.g. 'c:\program files\MSGFPlus.jar'" required="true" advanced="false" /> | |
| <ITEM name="database" value="" type="input-file" description="Protein sequence database (FASTA file; MS-GF+ parameter '-d'). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'." required="true" advanced="false" supported_formats="*.FASTA" /> | |
| <ITEM name="add_decoys" value="false" type="string" description="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda'). This allows the calculation of FDRs, but should only be used if the database does not already contain decoys." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="precursor_mass_tolerance" value="10" type="double" description="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" /> | |
| <ITEM name="precursor_error_units" value="ppm" type="string" description="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="isotope_error_range" value="0,0" type="string" description="Range of allowed isotope peak errors (MS-GF+ parameter '-ti'). Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2." required="false" advanced="false" /> | |
| <ITEM name="fragment_method" value="from_spectrum" type="string" description="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" required="false" advanced="false" restrictions="from_spectrum,CID,ETD,HCD" /> | |
| <ITEM name="instrument" value="Q_Exactive" type="string" description="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" required="false" advanced="false" restrictions="low_res,high_res,TOF,Q_Exactive" /> | |
| <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" required="false" advanced="false" restrictions="unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage" /> | |
| <ITEM name="protocol" value="none" type="string" description="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" required="false" advanced="false" restrictions="none,phospho,iTRAQ,iTRAQ_phospho,TMT" /> | |
| <ITEM name="tryptic" value="fully" type="string" description="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" required="false" advanced="false" restrictions="non,semi,fully" /> | |
| <ITEM name="min_precursor_charge" value="2" type="int" description="Minimum precursor ion charge (MS-GF+ parameter '-minCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_precursor_charge" value="4" type="int" description="Maximum precursor ion charge (MS-GF+ parameter '-maxCharge')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="min_peptide_length" value="7" type="int" description="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="max_peptide_length" value="40" type="int" description="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="matches_per_spec" value="1" type="int" description="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="add_features" value="true" type="string" description="Output additional features - needed e.g. by Percolator (default: basic scores only; MS-GF+ parameter '-addFeatures')" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="max_mods" value="3" type="int" description="Maximum number of modifications per peptide. If this value is large, the search may take very long." required="false" advanced="false" restrictions="0:" /> | |
| <ITEMLIST name="fixed_modifications" type="string" description="Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| <LISTITEM value="Carbamidomethyl (C)"/> | |
| <LISTITEM value="Dimethyl:2H(6)13C(2) (K)"/> | |
| <LISTITEM value="Dimethyl:2H(6)13C(2) (N-term)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) 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(N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP 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(T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEM name="legacy_conversion" value="true" type="string" description="Use the indirect conversion of MS-GF+ results to idXML via export to TSV. Try this only if the default conversion takes too long or uses too much memory." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="java_memory" value="3500" type="int" description="Maximum Java heap size (in MB)" required="false" advanced="false" /> | |
| <ITEM name="java_permgen" value="0" type="int" description="Maximum Java permanent generation space (in MB); only for Java 7 and below" required="false" advanced="true" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="3" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="true" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="19" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2000" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file containing a search against a concatenated sequence database. Either specify '-in' alone or 'in_target' together with 'in_decoy' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_target" value="" type="input-file" description="Identification input file containing a search against a target-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_decoy" value="" type="input-file" description="Identification input file containing a search against a decoy-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Identification output with annotated FDR" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="proteins_only" value="false" type="string" description="If set only the FDR on protein level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="true" type="string" description="If set only the FDR on peptide (PSM) level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm"> | |
| <ITEM name="no_qvalues" value="false" type="string" description="If 'true' strict FDRs will be calculated instead of q-values (the default)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_all_hits" value="false" type="string" description="If 'true' not only the first hit, but all are used (peptides only)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="split_charge_variants" value="false" type="string" description="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="treat_runs_separately" value="false" type="string" description="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-2120" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-100" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FeatureFinderMultiplex" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1860" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="output-file" description="Optional output file containing the individual peptide features in 'out'." required="false" advanced="true" supported_formats="*.featureXML" /> | |
| <ITEM name="out_mzq" value="" type="output-file" description="Optional output file of MzQuantML." required="false" advanced="true" supported_formats="*.mzq" /> | |
| <ITEM name="out_debug" value="" type="string" description="Directory for debug output." required="false" advanced="true" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="3" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]" type="string" description="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10] ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC#br#[Dimethyl0][Dimethyl6] ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL" required="false" advanced="false" /> | |
| <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." required="false" advanced="false" /> | |
| <ITEM name="isotopes_per_peptide" value="3:6" type="string" description="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " required="false" advanced="true" /> | |
| <ITEM name="rt_typical" value="50" type="double" description="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_min" value="3" type="double" description="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="15" type="double" description="m/z tolerance for search of peak patterns." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_unit" value="ppm" type="string" description="Unit of the 'mz_tolerance' parameter." required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="intensity_cutoff" value="10" type="double" description="Lower bound for the intensity of isotopic peaks." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide_similarity" value="0.6" type="double" description="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="averagine_similarity" value="0.5" type="double" description="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="averagine_similarity_scaling" value="0.75" type="double" description="Let x denote this scaling factor, and p the averagine similarity parameter. For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)" required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="missed_cleavages" value="2" type="int" description="Maximum number of missed cleavages due to incomplete digestion." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="knock_out" value="false" type="string" description="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'algorithm:labels'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="double" description="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="double" description="Label:2H(4) | H(-4) 2H(4) | unimod #481" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="double" description="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl0" value="28.0313" type="double" description="Dimethyl | H(4) C(2) | unimod #36" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl4" value="32.056407" type="double" description="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl6" value="34.063117" type="double" description="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl8" value="36.07567" type="double" description="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL0" value="105.021464" type="double" description="ICPL | H(3) C(6) N O | unimod #365" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL4" value="109.046571" type="double" description="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL6" value="111.041593" type="double" description="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL10" value="115.0667" type="double" description="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="HighResPrecursorMassCorrector" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-2400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file (centroided data)" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out_csv" value="" type="output-file" description="Optional csv output file containing columns: precursor rt, uncorrected mz, corrected mz, delta mz#br#" required="false" advanced="false" supported_formats="*.csv" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="feature" description="Use features for precursor mass correction."> | |
| <ITEM name="in" value="" type="input-file" description="features used to correct precursor masses." required="false" advanced="false" supported_formats="*.featureXML" /> | |
| <ITEM name="mz_tolerance" value="40" type="double" description="The precursor mass tolerance. Used to determine matching to feature mass traces." required="false" advanced="false" /> | |
| <ITEM name="mz_tolerance_unit" value="ppm" type="string" description="Unit of precursor mass tolerance" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="rt_tolerance" value="15" type="double" description="Additional retention time tolerance added to feature boundaries." required="false" advanced="false" /> | |
| <ITEM name="max_trace" value="3" type="int" description="Maximum isotopic trace considered in matching a precursor to a feature." required="false" advanced="true" /> | |
| <ITEM name="believe_charge" value="false" type="string" description="Whether precursor charge is assumed correct." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_original" value="false" type="string" description="Whether a copy of the precusor and MS2 should be made (true) or if the original should be discarded (false)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="assign_all_matching" value="false" type="string" description="Whether a precursor should be corrected to all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original)." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="nearest_peak" description="Use nearest MS1 peak for precursor mass correction."> | |
| <ITEM name="mz_tolerance" value="0" type="double" description="The precursor mass tolerance. Used to determine matching to next MS1 peak." required="false" advanced="false" /> | |
| <ITEM name="mz_tolerance_unit" value="ppm" type="string" description="Unit of precursor mass tolerance" required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="24" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1860" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2220" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="input-file" description="Protein/peptide identifications file" required="true" advanced="false" supported_formats="*.mzid,*.idXML" /> | |
| <ITEM name="in" value="" type="input-file" description="Feature map/consensus map file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file (the format depends on the input file format)." required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="rt_tolerance" value="50" type="double" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="20" type="double" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." required="false" advanced="false" restrictions="ppm,Da" /> | |
| <ITEM name="mz_reference" value="precursor" type="string" description="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" required="false" advanced="false" restrictions="precursor,peptide" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="feature" description="Additional options for featureXML input"> | |
| <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_centroid_mz" value="false" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Additional options for consensusXML input"> | |
| <ITEM name="use_subelements" value="true" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_ids_with_subelements" value="false" type="string" description="Store the map index of the sub-feature in the peptide ID." required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="25" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2480" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract" required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract (applies to ALL ms levels!)" required="false" advanced="false" /> | |
| <ITEM name="pc_mz" value=":" type="string" description="MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag." required="false" advanced="false" /> | |
| <ITEM name="int" value=":" type="string" description="Intensity range to extract" required="false" advanced="false" /> | |
| <ITEM name="sort" value="false" type="string" description="Sorts the output according to RT and m/z." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="peak_options" description="Peak data options"> | |
| <ITEM name="sn" value="0" type="double" description="Write peaks with S/N > 'sn' values only" required="false" advanced="false" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract" required="false" advanced="false"> | |
| <LISTITEM value="1"/> | |
| <LISTITEM value="2"/> | |
| <LISTITEM value="3"/> | |
| </ITEMLIST> | |
| <ITEM name="sort_peaks" value="false" type="string" description="Sorts the peaks according to m/z" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="mz_precision" value="64" type="string" description="Store base64 encoded m/z data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="int_precision" value="32" type="string" description="Store base64 encoded intensity data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="indexed_file" value="false" type="string" description="Whether to add an index to the file when writing" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="numpress" description="Numpress compression for peak data"> | |
| <ITEM name="masstime" value="none" type="string" description="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="masstime_error" value="0.0001" type="double" description="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| <ITEM name="intensity" value="none" type="string" description="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="intensity_error" value="0.0001" type="double" description="Maximal allowable error in intensity dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="spectra" description="Remove spectra or select spectra (removing all others) with certain properties"> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="remove_activation" value="" type="string" description="Remove MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="remove_collision_energy" value=":" type="string" description="Remove MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="remove_isolation_window_width" value=":" type="string" description="Remove MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Retain MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="select_collision_energy" value=":" type="string" description="Select MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_isolation_window_width" value=":" type="string" description="Select MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_polarity" value="" type="string" description="Retain MSn scans with a certain scan polarity" required="false" advanced="false" restrictions="unknown,positive,negative" /> | |
| </NODE> | |
| <NODE name="feature" description="Feature data options"> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Consensus feature data options"> | |
| <ITEMLIST name="map" type="int" description="Maps to be extracted from a consensus" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="blackorwhitelist" description="Black or white listing of of MS2 spectra by consensus features"> | |
| <ITEM name="blacklist" value="true" type="string" description="True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept" required="false" advanced="false" restrictions="false,true" /> | |
| <ITEM name="file" value="" type="input-file" description="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.#br#If consensus:blackorwhitelist:maps is specified, only these will be used.#br#" required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEMLIST name="maps" type="int" description="Maps used for black/white list filtering" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="rt" value="60" type="double" description="Retention tolerance [s] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.01" type="double" description="m/z tolerance [Th] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="use_ppm_tolerance" value="false" type="string" description="If ppm tolerance should be used. Otherwise Da are used." required="false" advanced="false" restrictions="false,true" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="f_and_c" description="Feature & Consensus data options"> | |
| <ITEM name="charge" value=":" type="string" description="Charge range to extract" required="false" advanced="false" /> | |
| <ITEM name="size" value=":" type="string" description="Size range to extract" required="false" advanced="false" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="id" description="ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="Remove features with id clashes (different sequences mapped to one feature)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="keep_best_score_id" value="false" type="string" description="in case of multiple peptide identifications, keep only the id with best score" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="Remove features with annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="true" type="string" description="Remove features without annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="true" type="string" description="Remove unassigned peptide identifications" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="blacklist" value="" type="input-file" description="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'id:rt' and 'id:mz' options.#br#This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rt" value="0.1" type="double" description="Retention tolerance [s] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.001" type="double" description="m/z tolerance [Th] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="blacklist_imperfect" value="false" type="string" description="Allow for mismatching precursor positions (see 'id:blacklist')" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="algorithm" description="S/N algorithm section"> | |
| <NODE name="SignalToNoise" description=""> | |
| <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" /> | |
| <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" /> | |
| <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" /> | |
| <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> | |
| <ITEM name="write_log_messages" value="true" type="string" description="Write out log messages in case of sparse windows or median in rightmost histogram bin" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="26" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2680" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="27" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="2860" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files separated by blank" required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML"> | |
| </ITEMLIST> | |
| <ITEM name="in_type" value="" type="string" description="Input file type (default: determined from file extension or content)" required="false" advanced="false" restrictions="mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" /> | |
| <ITEM name="annotate_file_origin" value="true" type="string" description="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="raw" description="Flags for non-featureXML input/output"> | |
| <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="rt_custom" type="double" description="List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="rt_filename" value="false" type="string" description="If this flag is set FileMerger tries to guess the rt of the file name.#br#This option is useful for merging DTA file, which should contain the string#br#'rt' directly followed by a floating point number:#br#i.e. my_spectrum_rt2795.15.dta" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ms_level" value="2" type="int" description="This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra." required="false" advanced="false" /> | |
| <ITEM name="user_ms_level" value="false" type="string" description="If this flag is set, the MS level given above is used" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="29" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="3260" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.idXML" /> | |
| <ITEM name="protein_groups" value="" type="input-file" description="Protein inference results for the identification runs that were used to annotate the input (e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).#br#Information about indistinguishable proteins will be used for protein quantification." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file for protein abundances" required="false" advanced="false" supported_formats="*.csv" /> | |
| <ITEM name="peptide_out" value="" type="output-file" description="Output file for peptide abundances" required="false" advanced="false" supported_formats="*.csv" /> | |
| <ITEM name="top" value="0" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="average" value="sum" type="string" description="Averaging method used to compute protein abundances from peptide abundances" required="false" advanced="false" restrictions="median,mean,weighted_mean,sum" /> | |
| <ITEM name="include_all" value="true" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ratios" value="true" type="string" description="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ..." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ratiosSILAC" value="false" type="string" description="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps (and identification results comprising multiple runs)"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" required="false" advanced="false" /> | |
| <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" required="false" advanced="false" restrictions="none,double,escape" /> | |
| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="28" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDConflictResolver" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="3060" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file (data annotated with identifications)" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file (data with one peptide identification per feature)" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="30" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="3440" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="13/14" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="14/15" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/16" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="15/16" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/7" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/8" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/9" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/10" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="10/13" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="8/11" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/12" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="11/13" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="12/13" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="17/18" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="18/21" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="15" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="16/17" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="16" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="21/22" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="17" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="22/23" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="18" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/4" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="database" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="19" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/7" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="20" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/5" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="database" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="21" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/8" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="22" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/6" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="database" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="23" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="6/9" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="24" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="16/19" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="25" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="19/20" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="26" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/3" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out_features" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="feature:in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="27" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/3" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="28" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/4" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="29" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/5" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="30" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/6" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="protein_groups" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="40" description=""> | |
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| <ITEM name="" value="1/2" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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