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MyriMatchAdapter

Identifies peptides in MS/MS spectra via MyriMatch.

pot. predecessor tools $ \longrightarrow $ MyriMatchAdapter $ \longrightarrow $ pot. successor tools
any signal-/preprocessing tool
(in mzML format)
IDFilter or
any protein/peptide processing tool

MyriMatch must be installed on the system to be able to use the MyriMatchAdapter. See http://fenchurch.mc.vanderbilt.edu/bumbershoot/myrimatch/ for further information on how to download and install MyriMatch on your system.

This wrapper has been tested successfully with MyriMatch, version 2.1.x.

Use debug level >=1 to keep intermediate pepXML and configuration files for manual inspection.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

MyriMatchAdapter -- Annotates MS/MS spectra using MyriMatch.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

Usage:
  MyriMatchAdapter <options>

Options (mandatory options marked with '*'):
                                         
  -in <file>*                            Input file  (valid formats: 'mzML')
  -out <file>*                           Output file  (valid formats: 'idXML')
  -precursor_mass_tolerance <tolerance>  Precursor mono mass tolerance. (default: '1.5')
  -precursor_mass_tolerance_unit <unit>  Unit to be used for precursor mass tolerance. (default: 'Da' valid: 
                                         'Da', 'ppm')
  -precursor_mass_tolerance_avg          If this flag is set, the average mass is used in the precursor mass 
                                         tolerance.
  -fragment_mass_tolerance <tolerance>   Fragment mass error in Dalton (default: '0.3')
  -fragment_mass_tolerance_unit <unit>   Unit to be used for fragment mass tolerance. (default: 'Da' valid: 
                                         'Da', 'ppm')
  -database <fasta-file>*                FASTA protein database. (valid formats: 'FASTA')
  -min_precursor_charge <charge>         Minimum precursor ion charge (default: '1')
  -max_precursor_charge <charge>         Maximum precursor ion charge (default: '3')
  -fixed_modifications <mods>            Fixed modifications, specified using UniMod (www.unimod.org) terms, 
                                         e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)' (valid: '2-dimethylsuc
                                         cinyl (C)', '2-monomethylsuccinyl (C)', '2-nitrobenzyl (Y)', '2-succ
                                         inyl (C)', '2HPG (R)', '3-deoxyglucosone (R)', '3-phosphoglyceryl
                                         (K)', '3sulfo (N-term)', '4-ONE (C)', '4-ONE (H)', '4-ONE (K)', '4-O
                                         NE+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
                                         ...
                                         uoro (L)')
  -variable_modifications <mods>         Variable modifications, specified using UniMod (www.unimod.org) term
                                         s, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'. (valid: '2-dimethy
                                         lsuccinyl (C)', '2-monomethylsuccinyl (C)', '2-nitrobenzyl (Y)',
                                         '2-succinyl (C)', '2HPG (R)', '3-deoxyglucosone (R)', '3-phosphoglyc
                                         eryl (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-Ri
                                         bosyl (D)', 'ADP-Ribosyl (E)', 'ADP-Ribosyl (K)', 'ADP-Ribosyl (N)',
                                         ...
                                         uoro (L)')
                                         
  -myrimatch_executable <executable>*    The 'myrimatch' executable of the MyriMatch installation
  -NumChargeStates <num>                 The number of charge states that MyriMatch will handle during all 
                                         stages of the program. (default: '3')
  -TicCutoffPercentage <percentage>      Noise peaks are filtered out by sorting the original peaks in descen
                                         ding order of intensity, and then picking peaks from that list until
                                         the cumulative ion current of the picked peaks divided by the total
                                         ion current (TIC) is greater than or equal to this parameter. (defa
                                         ult: '0.98')
  -MaxDynamicMods <num>                  This parameter sets the maximum number of modified residues that 
                                         may be in any candidate sequence. (default: '2')
  -MaxResultRank <rank>                  This parameter sets the maximum rank of peptide-spectrum-matches to 
                                         report for each spectrum. (default: '5')
  -CleavageRules <rule>                  This parameter allows the user to control the way peptides are gener
                                         ated from the protein database. For more details, see http://www.ebi
                                         .ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001045&termNa
                                         me=cleavage%20agent%20name . (valid: 'Trypsin', 'Trypsin/P', 'Arg-C'
                                         , 'Asp-N', 'Asp-N_ambic', 'CNBr', 'Chymotrypsin', 'Formic_acid',
                                         'Lys-C', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'V8-DE', 'V8-E', 'glutam
                                         yl endopeptidase', 'leukocyte elastase', 'no cleavage', 'proline
                                         endopeptidase', 'unspecific cleavage')
  -MinTerminiCleavages <num>             By default, when generating peptides from the protein database, a 
                                         peptide must start and end at a valid cleavage site. Setting this
                                         parameter to 0 or 1 will reduce that requirement, so that neither
                                         terminus or only one terminus of the peptide must match one of the
                                         cleavage rules specified in the CleavageRules parameter. This parame
                                         ter is useful to turn a tryptic digest into a semi-tryptic digest.
                                         (default: '2')
  -MaxMissedCleavages <num>              By default, when generating peptides from the protein database, a 
                                         peptide may contain any number of missed cleavages. A missed cleavag
                                         e is a site within the peptide that matches one of the cleavage rule
                                         s (refer to CleavageRules). Settings this parameter to some other
                                         number will stop generating peptides from a sequence if it contains
                                         more than the specified number of missed cleavages. (default: '-1')
                                         
Common TOPP options:
  -ini <file>                            Use the given TOPP INI file
  -threads <n>                           Sets the number of threads allowed to be used by the TOPP tool (defa
                                         ult: '1')
  -write_ini <file>                      Writes the default configuration file
  --help                                 Shows options
  --helphelp                             Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MyriMatchAdapterAnnotates MS/MS spectra using MyriMatch.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MyriMatchAdapter'
in Input file input file*.mzML
out Output file output file*.idXML
precursor_mass_tolerance1.5 Precursor mono mass tolerance.
precursor_mass_tolerance_unitDa Unit to be used for precursor mass tolerance.Da,ppm
precursor_mass_tolerance_avgfalse If this flag is set, the average mass is used in the precursor mass tolerance.true,false
fragment_mass_tolerance0.3 Fragment mass error in Dalton
fragment_mass_tolerance_unitDa Unit to be used for fragment mass tolerance.Da,ppm
database FASTA protein database.input file*.FASTA
min_precursor_charge1 Minimum precursor ion charge
max_precursor_charge3 Maximum precursor ion charge
fixed_modifications[] Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)
variable_modifications[] Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'.2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)
myrimatch_executablemyrimatch The 'myrimatch' executable of the MyriMatch installationinput file
NumChargeStates3 The number of charge states that MyriMatch will handle during all stages of the program.
TicCutoffPercentage0.98 Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter.
MaxDynamicMods2 This parameter sets the maximum number of modified residues that may be in any candidate sequence.
MaxResultRank5 This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum.
CleavageRules This parameter allows the user to control the way peptides are generated from the protein database. For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001045&termName=cleavage%20agent%20name .Trypsin,Trypsin/P,Arg-C,Asp-N,Asp-N_ambic,CNBr,Chymotrypsin,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,V8-DE,V8-E,glutamyl endopeptidase,leukocyte elastase,no cleavage,proline endopeptidase,unspecific cleavage
MinTerminiCleavages2 By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.
MaxMissedCleavages-1 By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages. A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages.
MinPeptideMass0 When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified.
MaxPeptideMass10000 When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified.
MinPeptideLength5 When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified.
MaxPeptideLength75 When digesting proteins, any peptide which exceeds this specified length will be disqualified.
UseSmartPlusThreeModelfalse When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons..true,false
NumIntensityClasses3 Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter.
ClassSizeMultiplier2 When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense).
MonoisotopeAdjustmentSet0 This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z. To disable this technique, set the value to '0'.
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:42 using doxygen 1.8.9.1