Created
July 23, 2017 10:30
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OpenMS workflow, label free quantification, Mascot, Thermo Q Exactive, 23/07/2017
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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="2.2.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="25" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="27" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> | |
| <html><head><meta name="qrichtext" content="1" /><style type="text/css"> | |
| p, li { white-space: pre-wrap; } | |
| </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p></body></html>]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <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="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="-100" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-140" 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="2" 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="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"> | |
| <LISTITEM value="../../proteome-databases-OpenMS/uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms-plus-shuffled.fasta"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-440" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="220" type="double" description="" required="false" advanced="false" /> | |
| </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="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="-100" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="220" 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="full" 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="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="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="440" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fwd_in" value="" type="input-file" description="Identification input to estimate FDR, forward run." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rev_in" value="" type="input-file" description="Identification input to estimate FDR, decoy run." 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, the FDR of the proteins only is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set, the FDR of the peptides only 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="q_value" value="true" type="string" description="If 'true', the q-values will be calculated instead of the FDRs" 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 set to '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 set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." required="false" advanced="false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If set to 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="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="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="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="620" 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="0.05" 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="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"> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM10.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM11.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM12.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM13.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM14.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM15.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM16.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM7.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM8.mzML"/> | |
| <LISTITEM value="../../Ann-Kathrin/OpenMS/AM9.mzML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="80" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-360" type="double" description="" required="false" advanced="false" /> | |
| </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="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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="460" 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="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="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="10" 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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="640" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </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="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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="860" 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="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> | |
| </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="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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1060" 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="Fido" 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="FidoChooseParameters" 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="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="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="13" 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="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="460" 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="40" 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="40" 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="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="Additional options for featureXML input"> | |
| <ITEM name="use_centroid_rt" value="true" 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="true" 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="false" 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="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="FeatureLinkerUnlabeledQT" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1040" 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="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." 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="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="100" type="double" description="Maximum allowed difference in RT in seconds" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="double" description="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="RT distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="10" type="double" description="Maximum allowed difference in m/z (unit defined by 'unit')" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="double" description="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="m/z distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="double" description="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="double" description="Distances based on relative intensity are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </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="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="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1220" 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="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="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="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1400" 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="false" 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="false" 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="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="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="24" 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="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1600" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" 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="MapAlignerPoseClustering" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="640" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files to align (all must have the same file type)" required="true" advanced="false" supported_formats="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="out" type="output-file" description="Output files (same file type as 'in'). Either this option or 'trafo_out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="trafo_out" type="output-file" description="Transformation output files. Either this option or 'out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.trafoXML"> | |
| </ITEMLIST> | |
| <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="reference" description="Options to define a reference file (use either 'file' or 'index', not both)"> | |
| <ITEM name="file" value="" type="input-file" description="File to use as reference (same file format as input files required)" required="false" advanced="false" supported_formats="*.mzML,*.featureXML" /> | |
| <ITEM name="index" value="0" type="int" description="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." required="false" advanced="false" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="max_num_peaks_considered" value="1000" type="int" description="The maximal number of peaks/features to be considered per map. To use all, set to '-1'." required="false" advanced="false" restrictions="-1:" /> | |
| <NODE name="superimposer" description=""> | |
| <ITEM name="mz_pair_max_distance" value="0.5" type="double" description="Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_pair_distance_fraction" value="0.1" type="double" description="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). " required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="num_used_points" value="2000" type="int" description="Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1." required="false" advanced="false" restrictions="-1:" /> | |
| <ITEM name="scaling_bucket_size" value="0.005" type="double" description="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="shift_bucket_size" value="3" type="double" description="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="max_shift" value="1000" type="double" description="Maximal shift which is considered during histogramming (in seconds). This applies for both directions." required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="max_scaling" value="2" type="double" description="Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this." required="false" advanced="true" restrictions="1:" /> | |
| <ITEM name="dump_buckets" value="" type="string" description="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically." required="false" advanced="true" /> | |
| <ITEM name="dump_pairs" value="" type="string" description="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically." required="false" advanced="true" /> | |
| </NODE> | |
| <NODE name="pairfinder" description=""> | |
| <ITEM name="second_nearest_gap" value="2" type="double" description="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself." required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="100" type="double" description="Never pair features with a larger RT distance (in seconds)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="double" description="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final RT distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="10" type="double" description="Never pair features with larger m/z distance (unit defined by 'unit')" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="double" description="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final m/z distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)"> | |
| <ITEM name="exponent" value="1" type="double" description="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="double" description="Final intensity distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="15" 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="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="840" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="16" 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="480" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="460" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="21" 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="460" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1040" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="17" 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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1220" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fwd_in" value="" type="input-file" description="Identification input to estimate FDR, forward run." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rev_in" value="" type="input-file" description="Identification input to estimate FDR, decoy run." 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, the FDR of the proteins only is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set, the FDR of the peptides only 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="q_value" value="true" type="string" description="If 'true', the q-values will be calculated instead of the FDRs" 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 set to '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 set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." required="false" advanced="false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If set to 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="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="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="-260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1400" 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="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="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-160" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="LC-MS dataset in centroid or profile mode" 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="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="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="labels" value="" 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="25" 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="10" 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="1000" type="double" description="Lower bound for the intensity of isotopic peaks." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide_similarity" value="0.5" 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="-1:1" /> | |
| <ITEM name="averagine_similarity" value="0.3" 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="-1:1" /> | |
| <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="0" 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" /> | |
| <ITEM name="averagine_type" value="peptide" type="string" description="The type of averagine to use, currently RNA, DNA or peptide" required="false" advanced="false" restrictions="RNA,peptide,DNA" /> | |
| </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="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="ConsensusMapNormalizer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="260" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1400" 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="*.consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="algorithm_type" value="median" type="string" description="The normalization algorithm that is applied." required="false" advanced="false" restrictions="robust_regression,median,quantile" /> | |
| <ITEM name="ratio_threshold" value="0.67" type="double" description="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers." required="false" advanced="false" restrictions="0.001:1" /> | |
| <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="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="MascotAdapterOnline" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-100" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="20" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file in mzML format.#br#" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file in idXML format.#br#" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="keep_protein_links" value="false" type="string" description="The Mascot response file usually returns incomplete/wrong protein hits, so re-indexing the peptide hits is required. To avoid confusion why there are so few protein hits and force re-indexing, no proteins should be reported. To see the original (wrong) list, enable this flag." required="false" advanced="true" 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="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="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="Mascot_parameters" description="Mascot parameters used for searching"> | |
| <ITEM name="database" value="" type="string" description="Name of the sequence database" required="false" advanced="false" /> | |
| <ITEM name="search_type" value="MIS" type="string" description="Name of the search type for the query" required="false" advanced="true" restrictions="MIS,SQ,PMF" /> | |
| <ITEM name="enzyme" value="trypsin" type="string" description="The enzyme descriptor to the enzyme used for digestion. (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)." required="false" advanced="false" /> | |
| <ITEM name="instrument" value="Q_Exactive" type="string" description="Instrument definition which specifies the fragmentation rules" required="false" advanced="false" /> | |
| <ITEM name="missed_cleavages" value="1" type="int" description="Number of missed cleavages allowed for the enzyme" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="precursor_mass_tolerance" value="20" type="double" description="Tolerance of the precursor peaks" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="precursor_error_units" value="ppm" type="string" description="Units of the precursor mass tolerance" required="false" advanced="false" restrictions="%,ppm,mmu,Da" /> | |
| <ITEM name="fragment_mass_tolerance" value="0.3" type="double" description="Tolerance of the peaks in the fragment spectrum" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="fragment_error_units" value="Da" type="string" description="Units of the fragment peaks tolerance" required="false" advanced="false" restrictions="mmu,Da" /> | |
| <ITEM name="charges" value="1,2,3,4,5" type="string" description="Charge states to consider, given as a comma separated list of integers (only used for spectra without precursor charge information)" required="false" advanced="false" /> | |
| <ITEM name="taxonomy" value="All entries" type="string" description="Taxonomy specification of the sequences" required="false" advanced="false" /> | |
| <ITEMLIST name="fixed_modifications" type="string" description="List of fixed modifications, according to UniMod definitions." required="false" advanced="false" restrictions="15N-oxobutanoic (N-term C),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),ADP-Ribosyl (T),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),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-tyramide (Y),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21330 (K),Biotin:Thermo-21330 (N-term),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (X),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (X),Biotin:Thermo-33033-H (X),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Brij35 (N-term),Brij58 (N-term),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),CUSTOM0 (A),CUSTOM0 (C),CUSTOM0 (C-term),CUSTOM0 (D),CUSTOM0 (E),CUSTOM0 (F),CUSTOM0 (G),CUSTOM0 (H),CUSTOM0 (I),CUSTOM0 (K),CUSTOM0 (L),CUSTOM0 (M),CUSTOM0 (N),CUSTOM0 (N-term),CUSTOM0 (P),CUSTOM0 (Q),CUSTOM0 (R),CUSTOM0 (S),CUSTOM0 (T),CUSTOM0 (V),CUSTOM0 (W),CUSTOM0 (Y),CUSTOM1 (A),CUSTOM1 (C),CUSTOM1 (C-term),CUSTOM1 (D),CUSTOM1 (E),CUSTOM1 (F),CUSTOM1 (G),CUSTOM1 (H),CUSTOM1 (I),CUSTOM1 (K),CUSTOM1 (L),CUSTOM1 (M),CUSTOM1 (N),CUSTOM1 (N-term),CUSTOM1 (P),CUSTOM1 (Q),CUSTOM1 (R),CUSTOM1 (S),CUSTOM1 (T),CUSTOM1 (V),CUSTOM1 (W),CUSTOM1 (Y),CUSTOM2 (A),CUSTOM2 (C),CUSTOM2 (C-term),CUSTOM2 (D),CUSTOM2 (E),CUSTOM2 (F),CUSTOM2 (G),CUSTOM2 (H),CUSTOM2 (I),CUSTOM2 (K),CUSTOM2 (L),CUSTOM2 (M),CUSTOM2 (N),CUSTOM2 (N-term),CUSTOM2 (P),CUSTOM2 (Q),CUSTOM2 (R),CUSTOM2 (S),CUSTOM2 (T),CUSTOM2 (V),CUSTOM2 (W),CUSTOM2 (Y),CUSTOM3 (A),CUSTOM3 (C),CUSTOM3 (C-term),CUSTOM3 (D),CUSTOM3 (E),CUSTOM3 (F),CUSTOM3 (G),CUSTOM3 (H),CUSTOM3 (I),CUSTOM3 (K),CUSTOM3 (L),CUSTOM3 (M),CUSTOM3 (N),CUSTOM3 (N-term),CUSTOM3 (P),CUSTOM3 (Q),CUSTOM3 (R),CUSTOM3 (S),CUSTOM3 (T),CUSTOM3 (V),CUSTOM3 (W),CUSTOM3 (Y),CUSTOM4 (A),CUSTOM4 (C),CUSTOM4 (C-term),CUSTOM4 (D),CUSTOM4 (E),CUSTOM4 (F),CUSTOM4 (G),CUSTOM4 (H),CUSTOM4 (I),CUSTOM4 (K),CUSTOM4 (L),CUSTOM4 (M),CUSTOM4 (N),CUSTOM4 (N-term),CUSTOM4 (P),CUSTOM4 (Q),CUSTOM4 (R),CUSTOM4 (S),CUSTOM4 (T),CUSTOM4 (V),CUSTOM4 (W),CUSTOM4 (Y),CUSTOM5 (A),CUSTOM5 (C),CUSTOM5 (C-term),CUSTOM5 (D),CUSTOM5 (E),CUSTOM5 (F),CUSTOM5 (G),CUSTOM5 (H),CUSTOM5 (I),CUSTOM5 (K),CUSTOM5 (L),CUSTOM5 (M),CUSTOM5 (N),CUSTOM5 (N-term),CUSTOM5 (P),CUSTOM5 (Q),CUSTOM5 (R),CUSTOM5 (S),CUSTOM5 (T),CUSTOM5 (V),CUSTOM5 (W),CUSTOM5 (Y),CUSTOM6 (A),CUSTOM6 (C),CUSTOM6 (C-term),CUSTOM6 (D),CUSTOM6 (E),CUSTOM6 (F),CUSTOM6 (G),CUSTOM6 (H),CUSTOM6 (I),CUSTOM6 (K),CUSTOM6 (L),CUSTOM6 (M),CUSTOM6 (N),CUSTOM6 (N-term),CUSTOM6 (P),CUSTOM6 (Q),CUSTOM6 (R),CUSTOM6 (S),CUSTOM6 (T),CUSTOM6 (V),CUSTOM6 (W),CUSTOM6 (Y),CUSTOM7 (A),CUSTOM7 (C),CUSTOM7 (C-term),CUSTOM7 (D),CUSTOM7 (E),CUSTOM7 (F),CUSTOM7 (G),CUSTOM7 (H),CUSTOM7 (I),CUSTOM7 (K),CUSTOM7 (L),CUSTOM7 (M),CUSTOM7 (N),CUSTOM7 (N-term),CUSTOM7 (P),CUSTOM7 (Q),CUSTOM7 (R),CUSTOM7 (S),CUSTOM7 (T),CUSTOM7 (V),CUSTOM7 (W),CUSTOM7 (Y),CUSTOM8 (A),CUSTOM8 (C),CUSTOM8 (C-term),CUSTOM8 (D),CUSTOM8 (E),CUSTOM8 (F),CUSTOM8 (G),CUSTOM8 (H),CUSTOM8 (I),CUSTOM8 (K),CUSTOM8 (L),CUSTOM8 (M),CUSTOM8 (N),CUSTOM8 (N-term),CUSTOM8 (P),CUSTOM8 (Q),CUSTOM8 (R),CUSTOM8 (S),CUSTOM8 (T),CUSTOM8 (V),CUSTOM8 (W),CUSTOM8 (Y),CUSTOM9 (A),CUSTOM9 (C),CUSTOM9 (C-term),CUSTOM9 (D),CUSTOM9 (E),CUSTOM9 (F),CUSTOM9 (G),CUSTOM9 (H),CUSTOM9 (I),CUSTOM9 (K),CUSTOM9 (L),CUSTOM9 (M),CUSTOM9 (N),CUSTOM9 (N-term),CUSTOM9 (P),CUSTOM9 (Q),CUSTOM9 (R),CUSTOM9 (S),CUSTOM9 (T),CUSTOM9 (V),CUSTOM9 (W),CUSTOM9 (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 (U),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),Carboxyethylpyrrole (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (U),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:Cu[I] (H),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),Cation:Zn[II] (H),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->CamSec (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->SecNEM (C),Cys->SecNEM:2H(5) (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) (K),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),Deoxyhypusine (Q),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(2)13C (K),Dimethyl:2H(2)13C (N),Dimethyl:2H(2)13C (N-term),Dimethyl:2H(2)13C (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4) (R),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(4)13C(2) (R),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 (U),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),Fluorescein-tyramine (Y),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GEE (Q),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),Galactosyl (N-term),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),Glu->pyro-Glu+Methyl (N-term E),Glu->pyro-Glu+Methyl (N-term E),Glu->pyro-Glu+Methyl:2H(2)13C (N-term E),Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Glucosylgalactosyl (K),Glucuronyl (S),Glucuronyl (T),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)HexA(1) (S),Hex(1)HexA(1) (T),Hex(1)HexA(1)HexNAc(1) (S),Hex(1)HexA(1)HexNAc(1) (T),Hex(1)HexA(1)HexNAc(2) (S),Hex(1)HexA(1)HexNAc(2) (T),Hex(1)HexNAc(1) (N),Hex(1)HexNAc(1) (S),Hex(1)HexNAc(1) (T),Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S),Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T),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(1)Ac(1) (S),Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T),Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S),Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T),Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S),Hex(1)HexNAc(1)NeuAc(1)Sulf(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)NeuAc(2)Ac(1) (S),Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T),Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S),Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T),Hex(1)HexNAc(1)NeuAc(3) (S),Hex(1)HexNAc(1)NeuAc(3) (T),Hex(1)HexNAc(1)NeuGc(1) (S),Hex(1)HexNAc(1)NeuGc(1) (T),Hex(1)HexNAc(1)NeuGc(2) (S),Hex(1)HexNAc(1)NeuGc(2) (T),Hex(1)HexNAc(1)NeuGc(3) (S),Hex(1)HexNAc(1)NeuGc(3) (T),Hex(1)HexNAc(1)NeuGc(4) (S),Hex(1)HexNAc(1)NeuGc(4) (T),Hex(1)HexNAc(1)NeuGc(5) (S),Hex(1)HexNAc(1)NeuGc(5) (T),Hex(1)HexNAc(1)Phos(1) (S),Hex(1)HexNAc(1)Phos(1) (T),Hex(1)HexNAc(1)Sulf(1) (S),Hex(1)HexNAc(1)Sulf(1) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(1)dHex(1) (S),Hex(1)HexNAc(1)dHex(1) (T),Hex(1)HexNAc(1)dHex(1)Me(1) (S),Hex(1)HexNAc(1)dHex(1)Me(1) (T),Hex(1)HexNAc(1)dHex(1)Me(2) (S),Hex(1)HexNAc(1)dHex(1)Me(2) (T),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2) (S),Hex(1)HexNAc(2) (T),Hex(1)HexNAc(2)NeuAc(1) (S),Hex(1)HexNAc(2)NeuAc(1) (T),Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S),Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T),Hex(1)HexNAc(2)NeuAc(2) (S),Hex(1)HexNAc(2)NeuAc(2) (T),Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S),Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T),Hex(1)HexNAc(2)NeuGc(1) (S),Hex(1)HexNAc(2)NeuGc(1) (T),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)Sulf(1) (S),Hex(1)HexNAc(2)Sulf(1) (T),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1) (S),Hex(1)HexNAc(2)dHex(1) (T),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(1)HexNAc(2)dHex(2) (S),Hex(1)HexNAc(2)dHex(2) (T),Hex(1)HexNAc(3) (S),Hex(1)HexNAc(3) (T),Hex(1)HexNAc(3)NeuAc(1) (S),Hex(1)HexNAc(3)NeuAc(1) (T),Hex(1)HexNAc(3)NeuAc(2) (S),Hex(1)HexNAc(3)NeuAc(2) (T),Hex(1)HexNAc(3)NeuGc(1) (S),Hex(1)HexNAc(3)NeuGc(1) (T),Hex(1)HexNAc(3)Sulf(1) (S),Hex(1)HexNAc(3)Sulf(1) (T),Hex(1)NeuAc(1) (S),Hex(1)NeuAc(1) (T),Hex(1)NeuAc(1)Pent(1) (S),Hex(1)NeuAc(1)Pent(1) (T),Hex(1)NeuGc(1) (S),Hex(1)NeuGc(1) (T),Hex(1)Pent(1) (S),Hex(1)Pent(1) (T),Hex(1)Pent(2) (S),Hex(1)Pent(2) (T),Hex(10)Phos(3) (S),Hex(10)Phos(3) (T),Hex(2) (K),Hex(2) (R),Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T),Hex(2)HexA(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)Pent(1)Sulf(1) (T),Hex(2)HexNAc(1) (S),Hex(2)HexNAc(1) (T),Hex(2)HexNAc(1)Me(1) (S),Hex(2)HexNAc(1)Me(1) (T),Hex(2)HexNAc(1)NeuGc(1) (S),Hex(2)HexNAc(1)NeuGc(1) (T),Hex(2)HexNAc(1)NeuGc(2) (S),Hex(2)HexNAc(1)NeuGc(2) (T),Hex(2)HexNAc(1)NeuGc(3) (S),Hex(2)HexNAc(1)NeuGc(3) (T),Hex(2)HexNAc(1)NeuGc(4) (S),Hex(2)HexNAc(1)NeuGc(4) (T),Hex(2)HexNAc(1)Sulf(1) (S),Hex(2)HexNAc(1)Sulf(1) (T),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2) (S),Hex(2)HexNAc(2) (T),Hex(2)HexNAc(2)NeuAc(1) (N),Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S),Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T),Hex(2)HexNAc(2)NeuAc(2) (S),Hex(2)HexNAc(2)NeuAc(2) (T),Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S),Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T),Hex(2)HexNAc(2)NeuGc(1) (S),Hex(2)HexNAc(2)NeuGc(1) (T),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)Sulf(1) (S),Hex(2)HexNAc(2)Sulf(1) (T),Hex(2)HexNAc(2)dHex(1) (N),Hex(2)HexNAc(2)dHex(1) (S),Hex(2)HexNAc(2)dHex(1) (T),Hex(2)HexNAc(3) (S),Hex(2)HexNAc(3) (T),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(2)HexNAc(3)NeuAc(2) (S),Hex(2)HexNAc(3)NeuAc(2) (T),Hex(2)HexNAc(3)NeuAc(3) (S),Hex(2)HexNAc(3)NeuAc(3) (T),Hex(2)HexNAc(3)NeuGc(1) (S),Hex(2)HexNAc(3)NeuGc(1) (T),Hex(2)HexNAc(3)NeuGc(2) (S),Hex(2)HexNAc(3)NeuGc(2) (T),Hex(2)HexNAc(3)NeuGc(3) (S),Hex(2)HexNAc(3)NeuGc(3) (T),Hex(2)HexNAc(3)Sulf(1) (S),Hex(2)HexNAc(3)Sulf(1) (T),Hex(2)HexNAc(4) (S),Hex(2)HexNAc(4) (T),Hex(2)HexNAc(4)NeuAc(1) (S),Hex(2)HexNAc(4)NeuAc(1) (T),Hex(2)HexNAc(5) (S),Hex(2)HexNAc(5) (T),Hex(2)NeuAc(1) (S),Hex(2)NeuAc(1) (T),Hex(3) (N),Hex(3) (S),Hex(3) (T),Hex(3)HexNAc(1) (S),Hex(3)HexNAc(1) (T),Hex(3)HexNAc(1)Me(1) (S),Hex(3)HexNAc(1)Me(1) (T),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2) (S),Hex(3)HexNAc(2) (T),Hex(3)HexNAc(2)NeuAc(1) (N),Hex(3)HexNAc(2)NeuAc(2) (S),Hex(3)HexNAc(2)NeuAc(2) (T),Hex(3)HexNAc(2)Pent(1) (N),Hex(3)HexNAc(2)Phos(1) (N),Hex(3)HexNAc(3) (N),Hex(3)HexNAc(3) (S),Hex(3)HexNAc(3) (T),Hex(3)HexNAc(3)NeuAc(1) (S),Hex(3)HexNAc(3)NeuAc(1) (T),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(3)HexNAc(3)NeuAc(2) (S),Hex(3)HexNAc(3)NeuAc(2) (T),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T),Hex(3)HexNAc(3)NeuGc(1) (S),Hex(3)HexNAc(3)NeuGc(1) (T),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T),Hex(3)HexNAc(3)Pent(1) (N),Hex(3)HexNAc(3)Sulf(1) (S),Hex(3)HexNAc(3)Sulf(1) (T),Hex(3)HexNAc(4) (N),Hex(3)HexNAc(4) (S),Hex(3)HexNAc(4) (T),Hex(3)HexNAc(4)NeuAc(1) (N),Hex(3)HexNAc(4)Pent(1) (N),Hex(3)HexNAc(4)Sulf(1) (N),Hex(3)HexNAc(5) (N),Hex(3)HexNAc(5) (S),Hex(3)HexNAc(5) (T),Hex(3)HexNAc(5)Sulf(1) (N),Hex(3)HexNAc(6) (N),Hex(3)HexNAc(6) (S),Hex(3)HexNAc(6) (T),Hex(3)HexNAc(6)NeuAc(1) (N),Hex(3)HexNAc(6)Sulf(1) (N),Hex(3)HexNAc(6)Sulf(2) (N),Hex(3)HexNAc(7) (N),Hex(3)HexNAc(7)Sulf(1) (N),Hex(3)Phos(1) (S),Hex(3)Phos(1) (T),Hex(4) (S),Hex(4) (T),Hex(4)HexNAc(1) (S),Hex(4)HexNAc(1) (T),Hex(4)HexNAc(2) (N),Hex(4)HexNAc(2)NeuAc(1) (N),Hex(4)HexNAc(2)Pent(1) (N),Hex(4)HexNAc(3) (N),Hex(4)HexNAc(3) (S),Hex(4)HexNAc(3) (T),Hex(4)HexNAc(3)NeuAc(1) (N),Hex(4)HexNAc(3)NeuAc(1) (S),Hex(4)HexNAc(3)NeuAc(1) (T),Hex(4)HexNAc(3)NeuAc(2) (N),Hex(4)HexNAc(3)NeuGc(1) (N),Hex(4)HexNAc(3)Pent(1) (N),Hex(4)HexNAc(4) (N),Hex(4)HexNAc(4) (S),Hex(4)HexNAc(4) (T),Hex(4)HexNAc(4)Me(2)Pent(1) (N),Hex(4)HexNAc(4)NeuAc(1) (N),Hex(4)HexNAc(4)NeuAc(1) (S),Hex(4)HexNAc(4)NeuAc(1) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T),Hex(4)HexNAc(4)Pent(1) (N),Hex(4)HexNAc(4)Sulf(1) (N),Hex(4)HexNAc(4)Sulf(2) (S),Hex(4)HexNAc(4)Sulf(2) (T),Hex(4)HexNAc(5) (N),Hex(4)HexNAc(5)NeuAc(1) (N),Hex(4)HexNAc(5)Sulf(1) (N),Hex(4)HexNAc(6) (N),Hex(4)Phos(1) (S),Hex(4)Phos(1) (T),Hex(5) (S),Hex(5) (T),Hex(5)HexNAc(1) (S),Hex(5)HexNAc(1) (T),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(2)Phos(1) (N),Hex(5)HexNAc(3) (N),Hex(5)HexNAc(3)Pent(1) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4) (S),Hex(5)HexNAc(4) (T),Hex(5)HexNAc(4)Me(2)Pent(1) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex(5)HexNAc(4)NeuGc(1) (N),Hex(5)HexNAc(4)Sulf(1) (N),Hex(5)HexNAc(5) (N),Hex(5)HexNAc(5) (S),Hex(5)HexNAc(5) (T),Hex(5)Phos(1) (S),Hex(5)Phos(1) (T),Hex(5)Phos(3) (S),Hex(5)Phos(3) (T),Hex(6)HexNAc(2) (N),Hex(6)HexNAc(2)Phos(1) (N),Hex(6)HexNAc(3) (N),Hex(6)HexNAc(3)Phos(1) (N),Hex(6)HexNAc(4) (N),Hex(6)HexNAc(4) (S),Hex(6)HexNAc(4) (T),Hex(6)HexNAc(4)Me(3) (N),Hex(6)HexNAc(4)Me(3)Pent(1) (N),Hex(6)HexNAc(5) (N),Hex(6)Phos(1) (S),Hex(6)Phos(1) (T),Hex(6)Phos(3) (S),Hex(6)Phos(3) (T),Hex(7)HexNAc(1) (N),Hex(7)HexNAc(2) (N),Hex(7)HexNAc(2)Phos(1) (N),Hex(7)HexNAc(2)Phos(2) (N),Hex(7)HexNAc(3) (N),Hex(7)HexNAc(3)Phos(1) (N),Hex(7)HexNAc(4) (N),Hex(7)Phos(3) (S),Hex(7)Phos(3) (T),Hex(8)HexNAc(1) (N),Hex(8)HexNAc(2) (N),Hex(8)Phos(3) (S),Hex(8)Phos(3) (T),Hex(9)HexNAc(2) (N),Hex(9)Phos(3) (S),Hex(9)Phos(3) (T),HexN (K),HexN (N),HexN (S),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)Kdn(2) (S),HexNAc(1)Kdn(2) (T),HexNAc(1)NeuAc(1) (S),HexNAc(1)NeuAc(1) (T),HexNAc(1)NeuGc(1) (S),HexNAc(1)NeuGc(1) (T),HexNAc(1)NeuGc(2) (S),HexNAc(1)NeuGc(2) (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(1) (S),HexNAc(1)dHex(1) (T),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2) (S),HexNAc(2) (T),HexNAc(2)NeuAc(1) (S),HexNAc(2)NeuAc(1) (T),HexNAc(2)NeuAc(1)Sulf(1) (S),HexNAc(2)NeuAc(1)Sulf(1) (T),HexNAc(2)NeuGc(1) (S),HexNAc(2)NeuGc(1) (T),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),HexNAc(3) (S),HexNAc(3) (T),HexNAc(3)Sulf(1) (S),HexNAc(3)Sulf(1) (T),HexNAc(4) (S),HexNAc(4) (T),HexNAc(5) (S),HexNAc(5) (T),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),IASD (C),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),LRGG+dimethyl (K),LRGG+methyl (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(2)15N(2) (K),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(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(2) (N-term),Methyl:2H(2)13C (C),Methyl:2H(2)13C (C-term),Methyl:2H(2)13C (D),Methyl:2H(2)13C (E),Methyl:2H(2)13C (H),Methyl:2H(2)13C (I),Methyl:2H(2)13C (K),Methyl:2H(2)13C (L),Methyl:2H(2)13C (N),Methyl:2H(2)13C (N-term),Methyl:2H(2)13C (Q),Methyl:2H(2)13C (R),Methyl:2H(2)13C (S),Methyl:2H(2)13C (T),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3) (X),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (N-term),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 (U),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),NP40 (N-term),NQIGG (K),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 (U),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),Pentose (S),Pentose (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),PhosphoHex (T),PhosphoHex(2) (N),PhosphoHex(2) (S),PhosphoHex(2) (T),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 (C-term),Propyl (D),Propyl (E),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),RNPXL (N-term K),RNPXL (N-term R),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),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 (X),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),Tris (N),Triton (C-term),Triton (N-term),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),Tween20 (N-term),Tween80 (C-term),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:DSS-NH2 (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),beta FNA (C),beta FNA (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(1)HexA(1)HexNAc(3) (S),dHex(1)Hex(1)HexA(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(1)Kdn(1) (S),dHex(1)Hex(1)HexNAc(1)Kdn(1) (T),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Kdn(1) (S),dHex(1)Hex(1)HexNAc(2)Kdn(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3) (S),dHex(1)Hex(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(3)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)Sulf(1) (T),dHex(1)Hex(1)HexNAc(4) (S),dHex(1)Hex(1)HexNAc(4) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(2)HexA(1) (S),dHex(1)Hex(2)HexA(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(2) (S),dHex(1)Hex(2)HexA(1)HexNAc(2) (T),dHex(1)Hex(2)HexNAc(1) (S),dHex(1)Hex(2)HexNAc(1) (T),dHex(1)Hex(2)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T),dHex(1)Hex(2)HexNAc(2)Pent(1) (N),dHex(1)Hex(2)HexNAc(2)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)Sulf(1) (T),dHex(1)Hex(2)HexNAc(3) (N),dHex(1)Hex(2)HexNAc(3) (S),dHex(1)Hex(2)HexNAc(3) (T),dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S),dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T),dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(3)Sulf(1) (S),dHex(1)Hex(2)HexNAc(3)Sulf(1) (T),dHex(1)Hex(2)HexNAc(4) (S),dHex(1)Hex(2)HexNAc(4) (T),dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S),dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T),dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S),dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexA(1)HexNAc(1) (S),dHex(1)Hex(3)HexA(1)HexNAc(1) (T),dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S),dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T),dHex(1)Hex(3)HexA(1)HexNAc(2) (S),dHex(1)Hex(3)HexA(1)HexNAc(2) (T),dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S),dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T),dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S),dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T),dHex(1)Hex(3)HexA(2)HexNAc(2) (S),dHex(1)Hex(3)HexA(2)HexNAc(2) (T),dHex(1)Hex(3)HexNAc(1) (S),dHex(1)Hex(3)HexNAc(1) (T),dHex(1)Hex(3)HexNAc(1)Sulf(1) (S),dHex(1)Hex(3)HexNAc(1)Sulf(1) (T),dHex(1)Hex(3)HexNAc(2) (N),dHex(1)Hex(3)HexNAc(2) (S),dHex(1)Hex(3)HexNAc(2) (T),dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(3)HexNAc(2)Pent(1) (N),dHex(1)Hex(3)HexNAc(2)Sulf(1) (N),dHex(1)Hex(3)HexNAc(2)Sulf(1) (S),dHex(1)Hex(3)HexNAc(2)Sulf(1) (T),dHex(1)Hex(3)HexNAc(3) (N),dHex(1)Hex(3)HexNAc(3) (S),dHex(1)Hex(3)HexNAc(3) (T),dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S),dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T),dHex(1)Hex(3)HexNAc(3)Pent(1) (N),dHex(1)Hex(3)HexNAc(3)Pent(2) (N),dHex(1)Hex(3)HexNAc(3)Pent(3) (N),dHex(1)Hex(3)HexNAc(3)Sulf(1) (S),dHex(1)Hex(3)HexNAc(3)Sulf(1) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(3)HexNAc(4) (S),dHex(1)Hex(3)HexNAc(4) (T),dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(3)HexNAc(4)Pent(1) (N),dHex(1)Hex(3)HexNAc(4)Pent(2) (N),dHex(1)Hex(3)HexNAc(4)Pent(3) (N),dHex(1)Hex(3)HexNAc(4)Sulf(1) (N),dHex(1)Hex(3)HexNAc(5) (N),dHex(1)Hex(3)HexNAc(5) (S),dHex(1)Hex(3)HexNAc(5) (T),dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N),dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S),dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T),dHex(1)Hex(3)HexNAc(5)Sulf(1) (N),dHex(1)Hex(3)HexNAc(6) (N),dHex(1)Hex(3)HexNAc(6) (S),dHex(1)Hex(3)HexNAc(6) (T),dHex(1)Hex(3)HexNAc(6)Sulf(1) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexA(1)HexNAc(2) (S),dHex(1)Hex(4)HexA(1)HexNAc(2) (T),dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S),dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T),dHex(1)Hex(4)HexNAc(1)Pent(1) (N),dHex(1)Hex(4)HexNAc(2) (N),dHex(1)Hex(4)HexNAc(2) (S),dHex(1)Hex(4)HexNAc(2) (T),dHex(1)Hex(4)HexNAc(2)Pent(1) (N),dHex(1)Hex(4)HexNAc(3) (N),dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N),dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N),dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N),dHex(1)Hex(4)HexNAc(3)Pent(1) (N),dHex(1)Hex(4)HexNAc(3)Sulf(1) (N),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(4)HexNAc(4) (S),dHex(1)Hex(4)HexNAc(4) (T),dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S),dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T),dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N),dHex(1)Hex(4)HexNAc(4)Pent(1) (N),dHex(1)Hex(4)HexNAc(4)Sulf(1) (N),dHex(1)Hex(4)HexNAc(5) (N),dHex(1)Hex(4)HexNAc(5)Sulf(1) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N),dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N),dHex(1)Hex(5)HexNAc(2) (N),dHex(1)Hex(5)HexNAc(2)Pent(1) (N),dHex(1)Hex(5)HexNAc(3) (N),dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N),dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N),dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N),dHex(1)Hex(5)HexNAc(3)Sulf(1) (N),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(5)HexNAc(4)Pent(1) (N),dHex(1)Hex(5)HexNAc(4)Sulf(1) (N),dHex(1)Hex(5)HexNAc(4)Sulf(2) (N),dHex(1)Hex(5)HexNAc(5) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dHex(1)Hex(6)HexNAc(2) (N),dHex(1)Hex(6)HexNAc(3) (N),dHex(1)Hex(6)HexNAc(3)Sulf(1) (N),dHex(1)Hex(6)HexNAc(4) (N),dHex(1)Hex(7)HexNAc(2) (N),dHex(1)Hex(7)HexNAc(3) (N),dHex(1)Hex(7)HexNAc(3)Phos(1) (N),dHex(1)Hex(7)HexNAc(3)Sulf(1) (N),dHex(1)Hex(7)HexNAc(4) (N),dHex(1)HexNAc(3) (S),dHex(1)HexNAc(3) (T),dHex(1)HexNAc(4) (S),dHex(1)HexNAc(4) (T),dHex(1)HexNAc(5) (S),dHex(1)HexNAc(5) (T),dHex(2)Hex(1)HexNAc(1)Kdn(1) (S),dHex(2)Hex(1)HexNAc(1)Kdn(1) (T),dHex(2)Hex(1)HexNAc(2)Kdn(1) 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| <LISTITEM value="Carbamidomethyl (C)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications given as UniMod definitions." required="false" advanced="false" restrictions="15N-oxobutanoic (N-term C),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),ADP-Ribosyl (T),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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(Q),Biotin:Thermo-21360 (X),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (X),Biotin:Thermo-33033-H (X),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Brij35 (N-term),Brij58 (N-term),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),CUSTOM0 (A),CUSTOM0 (C),CUSTOM0 (C-term),CUSTOM0 (D),CUSTOM0 (E),CUSTOM0 (F),CUSTOM0 (G),CUSTOM0 (H),CUSTOM0 (I),CUSTOM0 (K),CUSTOM0 (L),CUSTOM0 (M),CUSTOM0 (N),CUSTOM0 (N-term),CUSTOM0 (P),CUSTOM0 (Q),CUSTOM0 (R),CUSTOM0 (S),CUSTOM0 (T),CUSTOM0 (V),CUSTOM0 (W),CUSTOM0 (Y),CUSTOM1 (A),CUSTOM1 (C),CUSTOM1 (C-term),CUSTOM1 (D),CUSTOM1 (E),CUSTOM1 (F),CUSTOM1 (G),CUSTOM1 (H),CUSTOM1 (I),CUSTOM1 (K),CUSTOM1 (L),CUSTOM1 (M),CUSTOM1 (N),CUSTOM1 (N-term),CUSTOM1 (P),CUSTOM1 (Q),CUSTOM1 (R),CUSTOM1 (S),CUSTOM1 (T),CUSTOM1 (V),CUSTOM1 (W),CUSTOM1 (Y),CUSTOM2 (A),CUSTOM2 (C),CUSTOM2 (C-term),CUSTOM2 (D),CUSTOM2 (E),CUSTOM2 (F),CUSTOM2 (G),CUSTOM2 (H),CUSTOM2 (I),CUSTOM2 (K),CUSTOM2 (L),CUSTOM2 (M),CUSTOM2 (N),CUSTOM2 (N-term),CUSTOM2 (P),CUSTOM2 (Q),CUSTOM2 (R),CUSTOM2 (S),CUSTOM2 (T),CUSTOM2 (V),CUSTOM2 (W),CUSTOM2 (Y),CUSTOM3 (A),CUSTOM3 (C),CUSTOM3 (C-term),CUSTOM3 (D),CUSTOM3 (E),CUSTOM3 (F),CUSTOM3 (G),CUSTOM3 (H),CUSTOM3 (I),CUSTOM3 (K),CUSTOM3 (L),CUSTOM3 (M),CUSTOM3 (N),CUSTOM3 (N-term),CUSTOM3 (P),CUSTOM3 (Q),CUSTOM3 (R),CUSTOM3 (S),CUSTOM3 (T),CUSTOM3 (V),CUSTOM3 (W),CUSTOM3 (Y),CUSTOM4 (A),CUSTOM4 (C),CUSTOM4 (C-term),CUSTOM4 (D),CUSTOM4 (E),CUSTOM4 (F),CUSTOM4 (G),CUSTOM4 (H),CUSTOM4 (I),CUSTOM4 (K),CUSTOM4 (L),CUSTOM4 (M),CUSTOM4 (N),CUSTOM4 (N-term),CUSTOM4 (P),CUSTOM4 (Q),CUSTOM4 (R),CUSTOM4 (S),CUSTOM4 (T),CUSTOM4 (V),CUSTOM4 (W),CUSTOM4 (Y),CUSTOM5 (A),CUSTOM5 (C),CUSTOM5 (C-term),CUSTOM5 (D),CUSTOM5 (E),CUSTOM5 (F),CUSTOM5 (G),CUSTOM5 (H),CUSTOM5 (I),CUSTOM5 (K),CUSTOM5 (L),CUSTOM5 (M),CUSTOM5 (N),CUSTOM5 (N-term),CUSTOM5 (P),CUSTOM5 (Q),CUSTOM5 (R),CUSTOM5 (S),CUSTOM5 (T),CUSTOM5 (V),CUSTOM5 (W),CUSTOM5 (Y),CUSTOM6 (A),CUSTOM6 (C),CUSTOM6 (C-term),CUSTOM6 (D),CUSTOM6 (E),CUSTOM6 (F),CUSTOM6 (G),CUSTOM6 (H),CUSTOM6 (I),CUSTOM6 (K),CUSTOM6 (L),CUSTOM6 (M),CUSTOM6 (N),CUSTOM6 (N-term),CUSTOM6 (P),CUSTOM6 (Q),CUSTOM6 (R),CUSTOM6 (S),CUSTOM6 (T),CUSTOM6 (V),CUSTOM6 (W),CUSTOM6 (Y),CUSTOM7 (A),CUSTOM7 (C),CUSTOM7 (C-term),CUSTOM7 (D),CUSTOM7 (E),CUSTOM7 (F),CUSTOM7 (G),CUSTOM7 (H),CUSTOM7 (I),CUSTOM7 (K),CUSTOM7 (L),CUSTOM7 (M),CUSTOM7 (N),CUSTOM7 (N-term),CUSTOM7 (P),CUSTOM7 (Q),CUSTOM7 (R),CUSTOM7 (S),CUSTOM7 (T),CUSTOM7 (V),CUSTOM7 (W),CUSTOM7 (Y),CUSTOM8 (A),CUSTOM8 (C),CUSTOM8 (C-term),CUSTOM8 (D),CUSTOM8 (E),CUSTOM8 (F),CUSTOM8 (G),CUSTOM8 (H),CUSTOM8 (I),CUSTOM8 (K),CUSTOM8 (L),CUSTOM8 (M),CUSTOM8 (N),CUSTOM8 (N-term),CUSTOM8 (P),CUSTOM8 (Q),CUSTOM8 (R),CUSTOM8 (S),CUSTOM8 (T),CUSTOM8 (V),CUSTOM8 (W),CUSTOM8 (Y),CUSTOM9 (A),CUSTOM9 (C),CUSTOM9 (C-term),CUSTOM9 (D),CUSTOM9 (E),CUSTOM9 (F),CUSTOM9 (G),CUSTOM9 (H),CUSTOM9 (I),CUSTOM9 (K),CUSTOM9 (L),CUSTOM9 (M),CUSTOM9 (N),CUSTOM9 (N-term),CUSTOM9 (P),CUSTOM9 (Q),CUSTOM9 (R),CUSTOM9 (S),CUSTOM9 (T),CUSTOM9 (V),CUSTOM9 (W),CUSTOM9 (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 (U),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),Carboxyethylpyrrole (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (U),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:Cu[I] (H),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),Cation:Zn[II] (H),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->CamSec (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->SecNEM (C),Cys->SecNEM:2H(5) (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) (K),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),Deoxyhypusine (Q),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(2)13C (K),Dimethyl:2H(2)13C (N),Dimethyl:2H(2)13C (N-term),Dimethyl:2H(2)13C (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4) (R),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(4)13C(2) (R),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 (U),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),Fluorescein-tyramine (Y),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GEE (Q),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),Galactosyl (N-term),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),Glu->pyro-Glu+Methyl (N-term E),Glu->pyro-Glu+Methyl (N-term E),Glu->pyro-Glu+Methyl:2H(2)13C (N-term E),Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Glucosylgalactosyl (K),Glucuronyl (S),Glucuronyl (T),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)HexA(1) (S),Hex(1)HexA(1) (T),Hex(1)HexA(1)HexNAc(1) (S),Hex(1)HexA(1)HexNAc(1) (T),Hex(1)HexA(1)HexNAc(2) (S),Hex(1)HexA(1)HexNAc(2) (T),Hex(1)HexNAc(1) (N),Hex(1)HexNAc(1) (S),Hex(1)HexNAc(1) (T),Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S),Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T),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(1)Ac(1) (S),Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T),Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S),Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T),Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S),Hex(1)HexNAc(1)NeuAc(1)Sulf(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)NeuAc(2)Ac(1) (S),Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T),Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S),Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T),Hex(1)HexNAc(1)NeuAc(3) (S),Hex(1)HexNAc(1)NeuAc(3) (T),Hex(1)HexNAc(1)NeuGc(1) (S),Hex(1)HexNAc(1)NeuGc(1) (T),Hex(1)HexNAc(1)NeuGc(2) (S),Hex(1)HexNAc(1)NeuGc(2) (T),Hex(1)HexNAc(1)NeuGc(3) (S),Hex(1)HexNAc(1)NeuGc(3) (T),Hex(1)HexNAc(1)NeuGc(4) (S),Hex(1)HexNAc(1)NeuGc(4) (T),Hex(1)HexNAc(1)NeuGc(5) (S),Hex(1)HexNAc(1)NeuGc(5) (T),Hex(1)HexNAc(1)Phos(1) (S),Hex(1)HexNAc(1)Phos(1) (T),Hex(1)HexNAc(1)Sulf(1) (S),Hex(1)HexNAc(1)Sulf(1) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(1)dHex(1) (S),Hex(1)HexNAc(1)dHex(1) (T),Hex(1)HexNAc(1)dHex(1)Me(1) (S),Hex(1)HexNAc(1)dHex(1)Me(1) (T),Hex(1)HexNAc(1)dHex(1)Me(2) (S),Hex(1)HexNAc(1)dHex(1)Me(2) (T),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2) (S),Hex(1)HexNAc(2) (T),Hex(1)HexNAc(2)NeuAc(1) (S),Hex(1)HexNAc(2)NeuAc(1) (T),Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S),Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T),Hex(1)HexNAc(2)NeuAc(2) (S),Hex(1)HexNAc(2)NeuAc(2) (T),Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S),Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T),Hex(1)HexNAc(2)NeuGc(1) (S),Hex(1)HexNAc(2)NeuGc(1) (T),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)Sulf(1) (S),Hex(1)HexNAc(2)Sulf(1) (T),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1) (S),Hex(1)HexNAc(2)dHex(1) (T),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(1)HexNAc(2)dHex(2) (S),Hex(1)HexNAc(2)dHex(2) (T),Hex(1)HexNAc(3) (S),Hex(1)HexNAc(3) (T),Hex(1)HexNAc(3)NeuAc(1) (S),Hex(1)HexNAc(3)NeuAc(1) (T),Hex(1)HexNAc(3)NeuAc(2) (S),Hex(1)HexNAc(3)NeuAc(2) (T),Hex(1)HexNAc(3)NeuGc(1) (S),Hex(1)HexNAc(3)NeuGc(1) (T),Hex(1)HexNAc(3)Sulf(1) (S),Hex(1)HexNAc(3)Sulf(1) (T),Hex(1)NeuAc(1) (S),Hex(1)NeuAc(1) (T),Hex(1)NeuAc(1)Pent(1) (S),Hex(1)NeuAc(1)Pent(1) (T),Hex(1)NeuGc(1) (S),Hex(1)NeuGc(1) (T),Hex(1)Pent(1) (S),Hex(1)Pent(1) (T),Hex(1)Pent(2) (S),Hex(1)Pent(2) (T),Hex(10)Phos(3) (S),Hex(10)Phos(3) (T),Hex(2) (K),Hex(2) (R),Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T),Hex(2)HexA(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)Pent(1)Sulf(1) (T),Hex(2)HexNAc(1) (S),Hex(2)HexNAc(1) (T),Hex(2)HexNAc(1)Me(1) (S),Hex(2)HexNAc(1)Me(1) (T),Hex(2)HexNAc(1)NeuGc(1) (S),Hex(2)HexNAc(1)NeuGc(1) (T),Hex(2)HexNAc(1)NeuGc(2) (S),Hex(2)HexNAc(1)NeuGc(2) (T),Hex(2)HexNAc(1)NeuGc(3) (S),Hex(2)HexNAc(1)NeuGc(3) (T),Hex(2)HexNAc(1)NeuGc(4) (S),Hex(2)HexNAc(1)NeuGc(4) (T),Hex(2)HexNAc(1)Sulf(1) (S),Hex(2)HexNAc(1)Sulf(1) (T),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2) (S),Hex(2)HexNAc(2) (T),Hex(2)HexNAc(2)NeuAc(1) (N),Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S),Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T),Hex(2)HexNAc(2)NeuAc(2) (S),Hex(2)HexNAc(2)NeuAc(2) (T),Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S),Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T),Hex(2)HexNAc(2)NeuGc(1) (S),Hex(2)HexNAc(2)NeuGc(1) (T),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)Sulf(1) (S),Hex(2)HexNAc(2)Sulf(1) (T),Hex(2)HexNAc(2)dHex(1) (N),Hex(2)HexNAc(2)dHex(1) (S),Hex(2)HexNAc(2)dHex(1) (T),Hex(2)HexNAc(3) (S),Hex(2)HexNAc(3) (T),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(2)HexNAc(3)NeuAc(2) (S),Hex(2)HexNAc(3)NeuAc(2) (T),Hex(2)HexNAc(3)NeuAc(3) (S),Hex(2)HexNAc(3)NeuAc(3) (T),Hex(2)HexNAc(3)NeuGc(1) (S),Hex(2)HexNAc(3)NeuGc(1) (T),Hex(2)HexNAc(3)NeuGc(2) (S),Hex(2)HexNAc(3)NeuGc(2) (T),Hex(2)HexNAc(3)NeuGc(3) (S),Hex(2)HexNAc(3)NeuGc(3) (T),Hex(2)HexNAc(3)Sulf(1) (S),Hex(2)HexNAc(3)Sulf(1) (T),Hex(2)HexNAc(4) (S),Hex(2)HexNAc(4) (T),Hex(2)HexNAc(4)NeuAc(1) (S),Hex(2)HexNAc(4)NeuAc(1) (T),Hex(2)HexNAc(5) (S),Hex(2)HexNAc(5) (T),Hex(2)NeuAc(1) (S),Hex(2)NeuAc(1) (T),Hex(3) (N),Hex(3) (S),Hex(3) (T),Hex(3)HexNAc(1) (S),Hex(3)HexNAc(1) (T),Hex(3)HexNAc(1)Me(1) (S),Hex(3)HexNAc(1)Me(1) (T),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2) (S),Hex(3)HexNAc(2) (T),Hex(3)HexNAc(2)NeuAc(1) (N),Hex(3)HexNAc(2)NeuAc(2) (S),Hex(3)HexNAc(2)NeuAc(2) (T),Hex(3)HexNAc(2)Pent(1) (N),Hex(3)HexNAc(2)Phos(1) (N),Hex(3)HexNAc(3) (N),Hex(3)HexNAc(3) (S),Hex(3)HexNAc(3) (T),Hex(3)HexNAc(3)NeuAc(1) (S),Hex(3)HexNAc(3)NeuAc(1) (T),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(3)HexNAc(3)NeuAc(2) (S),Hex(3)HexNAc(3)NeuAc(2) (T),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T),Hex(3)HexNAc(3)NeuGc(1) (S),Hex(3)HexNAc(3)NeuGc(1) (T),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T),Hex(3)HexNAc(3)Pent(1) (N),Hex(3)HexNAc(3)Sulf(1) (S),Hex(3)HexNAc(3)Sulf(1) (T),Hex(3)HexNAc(4) (N),Hex(3)HexNAc(4) (S),Hex(3)HexNAc(4) (T),Hex(3)HexNAc(4)NeuAc(1) (N),Hex(3)HexNAc(4)Pent(1) (N),Hex(3)HexNAc(4)Sulf(1) (N),Hex(3)HexNAc(5) (N),Hex(3)HexNAc(5) (S),Hex(3)HexNAc(5) (T),Hex(3)HexNAc(5)Sulf(1) (N),Hex(3)HexNAc(6) (N),Hex(3)HexNAc(6) (S),Hex(3)HexNAc(6) (T),Hex(3)HexNAc(6)NeuAc(1) (N),Hex(3)HexNAc(6)Sulf(1) (N),Hex(3)HexNAc(6)Sulf(2) (N),Hex(3)HexNAc(7) (N),Hex(3)HexNAc(7)Sulf(1) (N),Hex(3)Phos(1) (S),Hex(3)Phos(1) (T),Hex(4) (S),Hex(4) (T),Hex(4)HexNAc(1) (S),Hex(4)HexNAc(1) (T),Hex(4)HexNAc(2) (N),Hex(4)HexNAc(2)NeuAc(1) (N),Hex(4)HexNAc(2)Pent(1) (N),Hex(4)HexNAc(3) (N),Hex(4)HexNAc(3) (S),Hex(4)HexNAc(3) (T),Hex(4)HexNAc(3)NeuAc(1) (N),Hex(4)HexNAc(3)NeuAc(1) (S),Hex(4)HexNAc(3)NeuAc(1) (T),Hex(4)HexNAc(3)NeuAc(2) (N),Hex(4)HexNAc(3)NeuGc(1) (N),Hex(4)HexNAc(3)Pent(1) (N),Hex(4)HexNAc(4) (N),Hex(4)HexNAc(4) (S),Hex(4)HexNAc(4) (T),Hex(4)HexNAc(4)Me(2)Pent(1) (N),Hex(4)HexNAc(4)NeuAc(1) (N),Hex(4)HexNAc(4)NeuAc(1) (S),Hex(4)HexNAc(4)NeuAc(1) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T),Hex(4)HexNAc(4)Pent(1) (N),Hex(4)HexNAc(4)Sulf(1) (N),Hex(4)HexNAc(4)Sulf(2) (S),Hex(4)HexNAc(4)Sulf(2) (T),Hex(4)HexNAc(5) (N),Hex(4)HexNAc(5)NeuAc(1) (N),Hex(4)HexNAc(5)Sulf(1) (N),Hex(4)HexNAc(6) (N),Hex(4)Phos(1) (S),Hex(4)Phos(1) (T),Hex(5) (S),Hex(5) (T),Hex(5)HexNAc(1) (S),Hex(5)HexNAc(1) (T),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(2)Phos(1) (N),Hex(5)HexNAc(3) (N),Hex(5)HexNAc(3)Pent(1) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4) (S),Hex(5)HexNAc(4) (T),Hex(5)HexNAc(4)Me(2)Pent(1) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex(5)HexNAc(4)NeuGc(1) (N),Hex(5)HexNAc(4)Sulf(1) (N),Hex(5)HexNAc(5) (N),Hex(5)HexNAc(5) (S),Hex(5)HexNAc(5) (T),Hex(5)Phos(1) (S),Hex(5)Phos(1) (T),Hex(5)Phos(3) (S),Hex(5)Phos(3) (T),Hex(6)HexNAc(2) (N),Hex(6)HexNAc(2)Phos(1) (N),Hex(6)HexNAc(3) (N),Hex(6)HexNAc(3)Phos(1) (N),Hex(6)HexNAc(4) (N),Hex(6)HexNAc(4) (S),Hex(6)HexNAc(4) (T),Hex(6)HexNAc(4)Me(3) (N),Hex(6)HexNAc(4)Me(3)Pent(1) (N),Hex(6)HexNAc(5) (N),Hex(6)Phos(1) (S),Hex(6)Phos(1) (T),Hex(6)Phos(3) (S),Hex(6)Phos(3) (T),Hex(7)HexNAc(1) (N),Hex(7)HexNAc(2) (N),Hex(7)HexNAc(2)Phos(1) (N),Hex(7)HexNAc(2)Phos(2) (N),Hex(7)HexNAc(3) (N),Hex(7)HexNAc(3)Phos(1) (N),Hex(7)HexNAc(4) (N),Hex(7)Phos(3) (S),Hex(7)Phos(3) (T),Hex(8)HexNAc(1) (N),Hex(8)HexNAc(2) (N),Hex(8)Phos(3) (S),Hex(8)Phos(3) (T),Hex(9)HexNAc(2) (N),Hex(9)Phos(3) (S),Hex(9)Phos(3) (T),HexN (K),HexN (N),HexN (S),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)Kdn(2) (S),HexNAc(1)Kdn(2) (T),HexNAc(1)NeuAc(1) (S),HexNAc(1)NeuAc(1) (T),HexNAc(1)NeuGc(1) (S),HexNAc(1)NeuGc(1) (T),HexNAc(1)NeuGc(2) (S),HexNAc(1)NeuGc(2) (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(1) (S),HexNAc(1)dHex(1) (T),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2) (S),HexNAc(2) (T),HexNAc(2)NeuAc(1) (S),HexNAc(2)NeuAc(1) (T),HexNAc(2)NeuAc(1)Sulf(1) (S),HexNAc(2)NeuAc(1)Sulf(1) (T),HexNAc(2)NeuGc(1) (S),HexNAc(2)NeuGc(1) (T),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),HexNAc(3) (S),HexNAc(3) (T),HexNAc(3)Sulf(1) (S),HexNAc(3)Sulf(1) (T),HexNAc(4) (S),HexNAc(4) (T),HexNAc(5) (S),HexNAc(5) (T),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),IASD (C),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),LRGG+dimethyl (K),LRGG+methyl (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(2)15N(2) (K),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(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(2) (N-term),Methyl:2H(2)13C (C),Methyl:2H(2)13C (C-term),Methyl:2H(2)13C (D),Methyl:2H(2)13C (E),Methyl:2H(2)13C (H),Methyl:2H(2)13C (I),Methyl:2H(2)13C (K),Methyl:2H(2)13C (L),Methyl:2H(2)13C (N),Methyl:2H(2)13C (N-term),Methyl:2H(2)13C (Q),Methyl:2H(2)13C (R),Methyl:2H(2)13C (S),Methyl:2H(2)13C (T),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3) (X),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (N-term),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 (U),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),NP40 (N-term),NQIGG (K),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 (U),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),Pentose (S),Pentose (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),PhosphoHex (T),PhosphoHex(2) (N),PhosphoHex(2) (S),PhosphoHex(2) (T),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 (C-term),Propyl (D),Propyl (E),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),RNPXL (N-term K),RNPXL (N-term R),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),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 (X),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),Tris (N),Triton (C-term),Triton (N-term),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),Tween20 (N-term),Tween80 (C-term),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:DSS-NH2 (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),beta FNA (C),beta FNA (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(1)HexA(1)HexNAc(3) (S),dHex(1)Hex(1)HexA(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(1)Kdn(1) (S),dHex(1)Hex(1)HexNAc(1)Kdn(1) (T),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Kdn(1) (S),dHex(1)Hex(1)HexNAc(2)Kdn(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3) (S),dHex(1)Hex(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(3)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)Sulf(1) (T),dHex(1)Hex(1)HexNAc(4) (S),dHex(1)Hex(1)HexNAc(4) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(2)HexA(1) (S),dHex(1)Hex(2)HexA(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(2) (S),dHex(1)Hex(2)HexA(1)HexNAc(2) (T),dHex(1)Hex(2)HexNAc(1) (S),dHex(1)Hex(2)HexNAc(1) (T),dHex(1)Hex(2)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T),dHex(1)Hex(2)HexNAc(2)Pent(1) (N),dHex(1)Hex(2)HexNAc(2)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)Sulf(1) (T),dHex(1)Hex(2)HexNAc(3) (N),dHex(1)Hex(2)HexNAc(3) (S),dHex(1)Hex(2)HexNAc(3) (T),dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S),dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T),dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(3)Sulf(1) (S),dHex(1)Hex(2)HexNAc(3)Sulf(1) (T),dHex(1)Hex(2)HexNAc(4) (S),dHex(1)Hex(2)HexNAc(4) (T),dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S),dHex(1)Hex(2)HexNAc(4)NeuAc(1) 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(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),s-GlcNAc (S),s-GlcNAc (T),spermidine (Q),spermine (Q),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEM name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)" type="string" description="Modifications with specificity groups that are used by Mascot and have to be treated specially" required="false" advanced="true" /> | |
| <ITEM name="mass_type" value="monoisotopic" type="string" description="Defines the mass type, either monoisotopic or average" required="false" advanced="false" restrictions="monoisotopic,average" /> | |
| <ITEM name="number_of_hits" value="0" type="int" description="Number of hits which should be returned, if 0 AUTO mode is enabled." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="skip_spectrum_charges" value="false" type="string" description="Sometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="search_title" value="OpenMS_search" type="string" description="Sets the title of the search." required="false" advanced="true" /> | |
| <ITEM name="username" value="OpenMS" type="string" description="Sets the username which is mentioned in the results file." required="false" advanced="true" /> | |
| <ITEM name="email" value="" type="string" description="Sets the email which is mentioned in the results file. Note: Some server require that a proper email is provided." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="Mascot_server" description="Mascot server details"> | |
| <ITEM name="hostname" value="" type="string" description="Address of the host where Mascot listens, e.g. 'mascot-server' or '127.0.0.1'" required="false" advanced="false" /> | |
| <ITEM name="host_port" value="80" type="int" description="Port where the Mascot server listens, 80 should be a good guess" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="server_path" value="mascot" type="string" description="Path on the server where Mascot server listens, 'mascot' should be a good guess" required="false" advanced="false" /> | |
| <ITEM name="timeout" value="1500" type="int" description="Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps. Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq" type="string" description="Boundary for the MIME section" required="false" advanced="true" /> | |
| <ITEM name="use_proxy" value="false" type="string" description="Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="proxy_host" value="" type="string" description="Host where the proxy server runs on" required="false" advanced="true" /> | |
| <ITEM name="proxy_port" value="0" type="int" description="Port where the proxy server listens" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="proxy_username" value="" type="string" description="Login name for the proxy server, if needed" required="false" advanced="true" /> | |
| <ITEM name="proxy_password" value="" type="string" description="Login password for the proxy server, if needed" required="false" advanced="true" /> | |
| <ITEM name="login" value="false" type="string" description="Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="username" value="" type="string" description="Name of the user if login is used (Mascot security must be enabled!)" required="false" advanced="false" /> | |
| <ITEM name="password" value="" type="string" description="Password of the user if login is used (Mascot security must be enabled!)" required="false" advanced="false" /> | |
| <ITEM name="use_ssl" value="false" type="string" description="Flag indicating wether the server uses HTTPS or not." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0" type="string" description="Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script). Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides." required="false" advanced="true" /> | |
| <ITEM name="skip_export" value="false" type="string" description="For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results. The output file produced by MascotAdapterOnline will contain only the Mascot search number." required="false" advanced="true" restrictions="true,false" /> | |
| </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="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="500" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-160" 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="1/4" 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="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="6/7" 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="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/8" 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="3" 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="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/10" 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="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="10/11" 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="6" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="11/12" 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="7" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="8/13" 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="id" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" 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="9" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="23/24" 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="10" 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="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="15/19" 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="12" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="13/16" 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="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="19/21" 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="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="14" 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="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="12/17" 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="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="16" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="18/23" 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="protein_groups" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="17" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/2" 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="18" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/4" 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="19" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/13" 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="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="20" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="20/22" 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="21" 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="22" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/5" 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="23" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/6" 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" /> | |
| </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="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="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="25" 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="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="reference:file" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="26" 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="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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