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OpenMS
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Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data.
| pot. predecessor tools | → LuciphorAdapter → | pot. successor tools |
|---|---|---|
| IDFileConverter | IDFilter or any protein/peptide processing tool |
LuciPHOr2 must be installed before this wrapper can be used. Please make sure that Java and LuciPHOr2 are working.
The following LuciPHOr2 version is required: luciphor2 (JAVA-based version of Luciphor) (1.2014Oct10). At the time of writing, it could be downloaded from http://luciphor2.sourceforge.net.
Input spectra for LuciPHOr2 have to be in pepXML file format. The input mzML file must be the same as the one used to create the pepXML input file.
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device
LuciphorAdapter -- Modification site localisation using LuciPHOr2.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_LuciphorAdapter.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
LuciphorAdapter <options>
Options (mandatory options marked with '*'):
-in <file>* Input spectrum file (valid formats: 'mzML')
-id <file>* Protein/peptide identifications file (valid formats: 'idXML')
-out <file>* Output file (valid formats: 'idXML')
-executable <file>* LuciPHOr2 .jar file. Provide a full or relative path, or make sure it can be found in your PATH environment.
-fragment_method <choice> Fragmentation method (default: 'CID') (valid: 'CID', 'HCD')
-fragment_mass_tolerance <value> Tolerance of the peaks in the fragment spectrum (default: '0.5')
-fragment_error_units <choice> Unit of fragment mass tolerance (default: 'Da') (valid: 'Da', 'ppm')
-min_mz <value> Do not consider peaks below this value for matching fragment ions (default: '150.0')
-target_modifications <mods> List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' (default: '[Phospho (S) Phospho (T) Phospho (Y)]') (valid: '15N-oxobutanoic (N-term C)', '15N-oxobutanoic (Protein N-term S)', '15N-oxobutanoic (Protein N-term T)', '2-dimethylsuccinyl (C)', '2-methylbutyryl (K)', '2-monomethylsuccinyl (C)', '2-nitrobenzyl (Y)', '2-succinyl (C)', '2HPG (R)', '2PCA-triazole-ethanethiol (N-term)', '3-deoxyglucosone (R)', '3-hydroxy-3-methylglutaryl (K)', '3-hydroxybenzyl-phosphate (K)', '3-hydroxybenzyl-phosphate (S)', '3-hydroxybenzyl-phosphate (T)', '3-hydroxybenzyl-phosphate (Y)', '3-methylglutaconyl (K)', '3-methylglutaryl (K)', '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)', '6C-CysPAT (C)', '6C-CysPAT (D)', '6C-CysPAT (E)', '6C-CysPAT (H)', '6C-CysPAT (K)', '6C-CysPAT (N-term)', '6C-CysPAT (S)', '6C-CysPAT (T)', '6C-CysPAT (Y)', 'a-type-ion (C-term)', 'AccQTag (K)', 'AccQTag (N-term)', 'Acetoacetyl (K)', 'Acetyl (C)', 'Acetyl (H)', 'Acetyl (K)', 'Acetyl (N-term)', 'Acetyl (Protein N-term)', 'Acetyl (R)', 'Acetyl (S)', 'Acetyl (T)', 'Acetyl (Y)', 'Acetyl:13C(2) (K)', 'Acetyl:13C(2) (Protein N-term)', 'Acetyl:2H(3) (H)', 'Acetyl:2H(3) (K)', 'Acetyl:2H(3) (N-term)', 'Acetyl:2H(3) (Protein N-term)', 'Acetyl:2H(3) (S)', 'Acetyl:2H(3) (T)', 'Acetyl:2H(3) (Y)', 'Acetyldeoxyhypusine (K)', 'Acetylhypusine (K)', '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 (Protein N-term)', 'AEBS (S)', 'AEBS (Y)', 'AEC-MAEC (S)', 'AEC-MAEC (T)', 'AEC-MAEC:2H(4) (S)', 'AEC-MAEC:2H(4) (T)', 'AFB1_Dialdehyde (K)', 'AHA-Alkyne (M)', 'AHA-Alkyne-KDDDD (M)', 'AHA-SS (M)', 'AHA-SS_CAM (M)', '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)', 'Amidated (Protein C-term)', 'Amidine (K)', 'Amidine (N-term)', 'Amidino (C)', 'Amino (Y)', 'Ammonia-loss (N)', 'Ammonia-loss (N-term C)', 'Ammonia-loss (Protein N-term S)', 'Ammonia-loss (Protein N-term T)', 'Ammonium (C-term)', 'Ammonium (D)', 'Ammonium (E)', 'AMTzHexNAc2 (N)', 'AMTzHexNAc2 (S)', 'AMTzHexNAc2 (T)', 'Andro-H2O (C)', '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)', 'AROD (C)', '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)', 'Aspartylurea (H)', 'Atto495Maleimide (C)', 'AzidoF (F)', 'azole (C)', 'azole (S)', 'Bacillosamine (N)', 'BADGE (C)', 'BDMAPP (H)', 'BDMAPP (K)', 'BDMAPP (Protein N-term)', 'BDMAPP (W)', 'BDMAPP (Y)', 'BEMAD_C (C)', 'BEMAD_C:2H(6) (C)', 'BEMAD_ST (S)', 'BEMAD_ST (T)', 'BEMAD_ST:2H(6) (S)', 'BEMAD_ST:2H(6) (T)', 'Benzoyl (K)', 'Benzoyl (N-term)', 'benzylguanidine (K)', 'betaFNA (C)', 'betaFNA (K)', 'BHT (C)', 'BHT (H)', 'BHT (K)', 'BHTOH (C)', 'BHTOH (H)', 'BHTOH (K)', 'Biotin (K)', 'Biotin (N-term)', 'Biotin-HPDP (C)', 'Biotin-PEG-PRA (M)', 'Biotin-PEO-Amine (D)', 'Biotin-PEO-Amine (E)', 'Biotin-PEO-Amine (Protein C-term)', 'Biotin-phenacyl (C)', 'Biotin-phenacyl (H)', 'Biotin-phenacyl (S)', 'Biotin-tyramide (C)', 'Biotin-tyramide (W)', 'Biotin-tyramide (Y)', 'Biotin:Aha-DADPS (M)', 'Biotin:Aha-PC (M)', 'Biotin:Cayman-10013 (C)', 'Biotin:Cayman-10141 (C)', 'Biotin:Invitrogen-M1602 (C)', 'Biotin:Sigma-B1267 (C)', 'Biotin:Thermo-21325 (K)', 'Biotin:Thermo-21328 (K)', 'Biotin:Thermo-21328 (N-term)', '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)', 'biotinAcrolein298 (C)', 'biotinAcrolein298 (H)', 'biotinAcrolein298 (K)', 'biotinAcrolein298 (Protein N-term)', 'BisANS (K)', 'bisANS-sulfonates (K)', 'bisANS-sulfonates (S)', 'bisANS-sulfonates (T)', 'BITC (C)', 'BITC (K)', 'BITC (N-term)', 'BMP-piperidinol (C)', 'BMP-piperidinol (M)', '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)', 'CAMthiopropanoyl (Protein N-term)', 'Can-FP-biotin (S)', 'Can-FP-biotin (T)', 'Can-FP-biotin (Y)', 'Carbamidomethyl (C)', 'Carbamidomethyl (D)', 'Carbamidomethyl (E)', 'Carbamidomethyl (H)', 'Carbamidomethyl (K)', 'Carbamidomethyl (M)', 'Carbamidomethyl (N-term)', 'Carbamidomethyl (S)', 'Carbamidomethyl (T)', 'Carbamidomethyl (U)', 'Carbamidomethyl (Y)', 'CarbamidomethylDTT (C)', 'Carbamyl (C)', 'Carbamyl (K)', 'Carbamyl (M)', 'Carbamyl (N-term)', 'Carbamyl (Protein N-term)', 'Carbamyl (R)', 'Carbamyl (S)', 'Carbamyl (T)', 'Carbamyl (Y)', 'Carbofuran (S)', 'Carbonyl (A)', 'Carbonyl (E)', 'Carbonyl (I)', 'Carbonyl (L)', 'Carbonyl (Q)', 'Carbonyl (R)', 'Carbonyl (S)', 'Carbonyl (V)', 'Carboxy (D)', 'Carboxy (E)', 'Carboxy (K)', 'Carboxy (Protein N-term M)', 'Carboxy (W)', 'Carboxy->Thiocarboxy (Protein C-term G)', '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:Al[III] (C-term)', 'Cation:Al[III] (D)', 'Cation:Al[III] (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:Fe[III] (C-term)', 'Cation:Fe[III] (D)', 'Cation:Fe[III] (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)', 'cGMP (C)', 'cGMP (S)', 'cGMP+RMP-loss (C)', 'cGMP+RMP-loss (S)', 'CHDH (D)', 'Chlorination (W)', 'Chlorination (Y)', 'Cholesterol (Protein C-term)', 'CIGG (K)', '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)', 'CoenzymeA (C)', 'Cresylphosphate (H)', 'Cresylphosphate (K)', 'Cresylphosphate (R)', 'Cresylphosphate (S)', 'Cresylphosphate (T)', 'Cresylphosphate (Y)', 'CresylSaligeninPhosphate (H)', 'CresylSaligeninPhosphate (K)', 'CresylSaligeninPhosphate (R)', 'CresylSaligeninPhosphate (S)', 'CresylSaligeninPhosphate (T)', 'CresylSaligeninPhosphate (Y)', 'Crotonaldehyde (C)', 'Crotonaldehyde (H)', 'Crotonaldehyde (K)', 'Crotonyl (K)', 'CuSMo (C)', '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)', 'Cy3-maleimide (C)', 'Cy3b-maleimide (C)', 'Cyano (C)', 'CyDye-Cy3 (C)', 'CyDye-Cy5 (C)', 'Cys->Ala (C)', 'Cys->Arg (C)', 'Cys->Asn (C)', 'Cys->Asp (C)', 'Cys->CamSec (C)', 'Cys->Dha (C)', 'Cys->ethylaminoAla (C)', 'Cys->Gln (C)', 'Cys->Glu (C)', 'Cys->Gly (C)', 'Cys->His (C)', 'Cys->Lys (C)', 'Cys->Met (C)', 'Cys->methylaminoAla (C)', 'Cys->Oxoalanine (C)', 'Cys->Phe (C)', 'Cys->Pro (C)', 'Cys->PyruvicAcid (Protein N-term 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)', 'Cysteinyl (C)', 'cysTMT (C)', 'cysTMT6plex (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)', 'DABCYL-C2-maleimide (C)', 'DABCYL-C2-maleimide (K)', 'DAET (S)', 'DAET (T)', 'Dansyl (K)', 'Dansyl (N-term)', 'Dap-DSP (A)', 'Dap-DSP (E)', 'Dap-DSP (K)', 'DBIA (C)', 'DCP (C)', 'Deamidated (N)', 'Deamidated (Protein N-term F)', 'Deamidated (Q)', 'Deamidated (R)', 'Deamidated:18O(1) (N)', 'Deamidated:18O(1) (Q)', 'Decanoyl (S)', 'Decanoyl (T)', 'Decarboxylation (D)', 'Decarboxylation (E)', 'DEDGFLYMVYASQETFG (K)', 'Dehydrated 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'dHex(3)Hex(4)HexNAc(4) (S)', 'dHex(3)Hex(4)HexNAc(4) (T)', 'dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)', 'dHex(3)HexNAc(3)Kdn(1) (S)', 'dHex(3)HexNAc(3)Kdn(1) (T)', 'dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)', 'dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)', 'dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)', 'dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)', 'dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)', 'dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)', 'dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)', 'dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)', 'dHex(4)Hex(2)HexNAc(3) (S)', 'dHex(4)Hex(2)HexNAc(3) (T)', 'dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)', 'dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)', 'dHex(4)Hex(3)HexNAc(3) (S)', 'dHex(4)Hex(3)HexNAc(3) (T)', 'dHex(4)HexNAc(3)Kdn(1) (S)', 'dHex(4)HexNAc(3)Kdn(1) (T)', 'DHP (C)', 'Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (D)', 'Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (E)', 'Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (D)', 'Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (E)', 'Diacylglycerol (C)', 'DiART6plex (K)', 'DiART6plex (N-term)', 'DiART6plex (Protein N-term)', 'DiART6plex (Y)', 'DiART6plex115 (K)', 'DiART6plex115 (N-term)', 'DiART6plex115 (Protein N-term)', 'DiART6plex115 (Y)', 'DiART6plex116/119 (K)', 'DiART6plex116/119 (N-term)', 'DiART6plex116/119 (Protein N-term)', 'DiART6plex116/119 (Y)', 'DiART6plex117 (K)', 'DiART6plex117 (N-term)', 'DiART6plex117 (Protein N-term)', 'DiART6plex117 (Y)', 'DiART6plex118 (K)', 'DiART6plex118 (N-term)', 'DiART6plex118 (Protein N-term)', 'DiART6plex118 (Y)', 'Dibromo (Y)', 'Dicarbamidomethyl (C)', 'Dicarbamidomethyl (H)', 'Dicarbamidomethyl (K)', 'Dicarbamidomethyl (N-term)', 'Dicarbamidomethyl (R)', 'dichlorination (C)', 'dichlorination (Y)', '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)', 'Diethylphosphothione (C)', 'Diethylphosphothione (H)', 'Diethylphosphothione (K)', 'Diethylphosphothione (S)', 'Diethylphosphothione (T)', 'Diethylphosphothione (Y)', 'Difuran (Y)', 'Dihydroxyimidazolidine (R)', 'Diiodo (H)', 'Diiodo (Y)', 'Diironsubcluster (C)', 'Diisopropylphosphate (K)', 'Diisopropylphosphate (N-term)', 'Diisopropylphosphate (S)', 'Diisopropylphosphate (T)', 'Diisopropylphosphate (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)', 'Dimethyl (K)', 'Dimethyl (N)', 'Dimethyl (N-term)', 'Dimethyl (Protein N-term P)', 'Dimethyl (Protein N-term)', 'Dimethyl (R)', 'Dimethyl:2H(2)13C (K)', 'Dimethyl:2H(2)13C (N)', 'Dimethyl:2H(2)13C (N-term)', 'Dimethyl:2H(2)13C (Protein N-term P)', 'Dimethyl:2H(2)13C (R)', 'Dimethyl:2H(4) (K)', 'Dimethyl:2H(4) (N-term)', 'Dimethyl:2H(4) (Protein 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'Ethylphosphate (S)', 'Ethylphosphate (T)', 'Ethylphosphate (Y)', 'ethylsulfonylethyl (C)', 'ethylsulfonylethyl (H)', 'ethylsulfonylethyl (K)', 'Ethynyl (C)', 'ExacTagAmine (K)', 'ExacTagThiol (C)', 'FAD (C)', 'FAD (H)', 'FAD (Y)', 'Farnesyl (C)', 'Fluorescein (C)', 'Fluorescein-tyramine (Y)', 'Fluoro (A)', 'Fluoro (F)', 'Fluoro (W)', 'Fluoro (Y)', 'FMN (S)', 'FMN (T)', 'FMNC (C)', 'FMNH (C)', 'FMNH (H)', 'FNEM (C)', 'Formyl (K)', 'Formyl (N-term)', 'Formyl (Protein N-term)', 'Formyl (S)', 'Formyl (T)', 'Formylasparagine (H)', 'FormylMet (Protein N-term)', 'FP-Biotin (K)', 'FP-Biotin (S)', 'FP-Biotin (T)', 'FP-Biotin (Y)', 'FTC (C)', 'FTC (K)', 'FTC (P)', 'FTC (R)', 'FTC (S)', 'Furan (Y)', 'G-H1 (R)', 'Galactosyl (K)', 'Galactosyl (N-term)', 'GEE (Q)', 'GeranylGeranyl (C)', 'GG (C)', 'GG (K)', 'GG (Protein N-term)', '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)', '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->pyro-Glu (N-term Q)', 'Gln->Ser (Q)', 'Gln->Thr (Q)', 'Gln->Trp (Q)', 'Gln->Tyr (Q)', 'Gln->Val (Q)', 'Gln->Xle (Q)', 'Glu (E)', 'Glu (Protein C-term)', 'Glu+O(2) (H)', '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->pyro-Glu (N-term E)', 'Glu->pyro-Glu+Methyl (N-term E)', 'Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)', 'Glu->Ser (E)', 'Glu->Thr (E)', 'Glu->Trp (E)', 'Glu->Tyr (E)', 'Glu->Val (E)', 'Glu->Xle (E)', 'glucosone (R)', 'Glucosylgalactosyl (K)', 'Glucuronyl (Protein N-term)', 'Glucuronyl (S)', 'Glucuronyl (T)', 'GluGlu (E)', 'GluGlu (Protein C-term)', 'GluGluGlu (E)', 'GluGluGlu 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'Iodoacetanilide (N-term)', 'Iodoacetanilide:13C(6) (C)', 'Iodoacetanilide:13C(6) (K)', 'Iodoacetanilide:13C(6) (N-term)', 'iodoTMT (C)', 'iodoTMT (D)', 'iodoTMT (E)', 'iodoTMT (H)', 'iodoTMT (K)', 'iodoTMT6plex (C)', 'iodoTMT6plex (D)', 'iodoTMT6plex (E)', 'iodoTMT6plex (H)', 'iodoTMT6plex (K)', 'IodoU-AMP (F)', 'IodoU-AMP (W)', 'IodoU-AMP (Y)', 'ISD_z+2_ion (N-term)', 'Isopropylphospho (S)', 'Isopropylphospho (T)', 'Isopropylphospho (Y)', 'Isovaleryl (K)', 'iST-NHS specific cysteine modification (C)', 'Itaconatyl (C)', 'Itaconyl (K)', 'iTRAQ4plex (C)', 'iTRAQ4plex (H)', 'iTRAQ4plex (K)', 'iTRAQ4plex (N-term)', 'iTRAQ4plex (Protein N-term)', 'iTRAQ4plex (S)', 'iTRAQ4plex (T)', 'iTRAQ4plex (Y)', 'iTRAQ4plex114 (C)', 'iTRAQ4plex114 (K)', 'iTRAQ4plex114 (N-term)', 'iTRAQ4plex114 (Y)', 'iTRAQ4plex115 (C)', 'iTRAQ4plex115 (K)', 'iTRAQ4plex115 (N-term)', 'iTRAQ4plex115 (Y)', 'iTRAQ8plex (C)', 'iTRAQ8plex (H)', 'iTRAQ8plex (K)', 'iTRAQ8plex (N-term)', 'iTRAQ8plex (Protein N-term)', 'iTRAQ8plex (S)', 'iTRAQ8plex (T)', 'iTRAQ8plex (Y)', 'iTRAQ8plex:13C(6)15N(2) (C)', 'iTRAQ8plex:13C(6)15N(2) (K)', 'iTRAQ8plex:13C(6)15N(2) (N-term)', 'iTRAQ8plex:13C(6)15N(2) (Y)', 'L-Gln (D)', 'L-Gln (E)', 'Label:13C(1)2H(3) (M)', 'Label:13C(1)2H(3)+Oxidation (M)', 'Label:13C(2)15N(1) (G)', 'Label:13C(2)15N(2) (K)', 'Label:13C(3) (A)', 'Label:13C(3)15N(1) (A)', 'Label:13C(3)15N(1) (S)', '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(2)+TMT6plex (K)', 'Label:13C(6)15N(2)+TMTpro (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) (A)', 'Label:2H(4) (F)', 'Label:2H(4) (K)', 'Label:2H(4) (U)', '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)', 'Lactylation (K)', 'lapachenole (C)', 'Leu->MetOx (L)', 'LG-anhydrolactam (K)', 'LG-anhydrolactam (N-term)', 'LG-anhyropyrrole (K)', 'LG-anhyropyrrole (N-term)', 'LG-Hlactam-K (K)', 'LG-Hlactam-K (Protein N-term)', 'LG-Hlactam-R (R)', 'LG-lactam-K (K)', 'LG-lactam-K (Protein N-term)', 'LG-lactam-R (R)', 'LG-pyrrole (C)', 'LG-pyrrole (K)', 'LG-pyrrole (N-term)', 'Lipoyl (K)', 'LRGG (K)', 'LRGG+dimethyl (K)', 'LRGG+methyl (K)', 'LTX+Lophotoxin (Y)', 'Lys (N-term)', 'Lys+O(2) (H)', '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)', 'Lys-loss (K)', 'Lys-loss (Protein C-term K)', 'Lysbiotinhydrazide (K)', 'maleimide (C)', 'maleimide (K)', 'Maleimide-PEO2-Biotin (C)', 'maleimide3 (C)', 'maleimide3 (K)', 'maleimide5 (C)', 'maleimide5 (K)', 'Malonyl (C)', 'Malonyl (K)', 'Malonyl (S)', 'MBS+peptide (C)', 'MDCC (C)', 'MeMePhosphorothioate (S)', 'Menadione (C)', 'Menadione (K)', 'Menadione-HQ (C)', 'Menadione-HQ (K)', 'MercaptoEthanol (S)', 'MercaptoEthanol (T)', 'MesitylOxide (H)', 'MesitylOxide (K)', 'MesitylOxide (Protein N-term)', 'Met+O(2) (H)', 'Met->Aha (M)', 'Met->Ala (M)', 'Met->Arg (M)', 'Met->Asn (M)', 'Met->Asp (M)', 'Met->AspSA (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)', 'Met-loss (Protein N-term M)', 'Met-loss+Acetyl (Protein N-term M)', 'Methamidophos-O (C)', 'Methamidophos-O (H)', 'Methamidophos-O (K)', 'Methamidophos-O (S)', 'Methamidophos-O (T)', 'Methamidophos-O (Y)', 'Methamidophos-S (C)', 'Methamidophos-S (H)', 'Methamidophos-S (K)', 'Methamidophos-S (S)', 'Methamidophos-S (T)', 'Methamidophos-S (Y)', 'Methyl (C)', 'Methyl (C-term)', 'Methyl (D)', 'Methyl (E)', 'Methyl (H)', 'Methyl (I)', 'Methyl (K)', 'Methyl (L)', 'Methyl (N)', 'Methyl (N-term)', 'Methyl (Protein 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 (Protein 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)', 'methylol (K)', 'methylol (W)', 'methylol (Y)', 'Methylphosphonate (S)', 'Methylphosphonate (T)', 'Methylphosphonate (Y)', 'Methylpyrroline (K)', 'methylsulfonylethyl (C)', 'methylsulfonylethyl (H)', 'methylsulfonylethyl (K)', 'Methylthio (C)', 'Methylthio (D)', 'Methylthio (K)', 'Methylthio (N)', 'Methylthio (N-term)', 'MG-H1 (R)', 'Microcin (Protein C-term)', 'MicrocinC7 (Protein C-term)', 'MM-diphenylpentanone (C)', 'Molybdopterin (C)', 'MolybdopterinGD (C)', 'MolybdopterinGD (D)', 'MolybdopterinGD (U)', 'MolybdopterinGD+Delta:S(-1)Se(1) (C)', 'Mono_Ngamma-propargyl-L-Gln_desthiobiotin (C)', 'monomethylphosphothione (C)', 'monomethylphosphothione (H)', 'monomethylphosphothione (K)', 'monomethylphosphothione (S)', 'monomethylphosphothione (T)', 'monomethylphosphothione (Y)', '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)', 'MTSL (C)', 'MurNAc (A)', 'Myristoleyl (Protein N-term G)', 'Myristoyl (C)', 'Myristoyl (K)', 'Myristoyl (N-term G)', 'Myristoyl+Delta:H(-4) (Protein N-term G)', 'N-dimethylphosphate (S)', 'N6pAMP (S)', 'N6pAMP (T)', 'N6pAMP (Y)', 'NA-LNO2 (C)', 'NA-LNO2 (H)', 'NA-OA-NO2 (C)', 'NA-OA-NO2 (H)', 'NBF (C)', 'NBF (K)', 'NBF (R)', '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)', 'Nethylmaleimide (C)', 'Nethylmaleimide+water (C)', 'Nethylmaleimide+water (K)', 'NeuAc (N)', 'NeuAc (S)', 'NeuAc (T)', 'NeuGc (N)', 'NeuGc (S)', 'NeuGc (T)', 'NHS-fluorescein (K)', 'NHS-LC-Biotin (K)', 'NHS-LC-Biotin (N-term)', 'NIC (K)', 'NIC (N-term)', 'NIPCAM (C)', 'Nitrene (Y)', 'Nitro (F)', 'Nitro (W)', 'Nitro (Y)', 'Nitrosyl (C)', 'Nitrosyl (Y)', 'Nmethylmaleimide (C)', 'Nmethylmaleimide (K)', 'Nmethylmaleimide+water (C)', 'NO_SMX_SEMD (C)', 'NO_SMX_SIMD (C)', 'NP40 (N-term)', 'NQIGG (K)', 'NQTGG (K)', '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)', 'Oxidation (C)', 'Oxidation (C-term G)', 'Oxidation (D)', 'Oxidation (E)', 'Oxidation (F)', 'Oxidation (H)', 'Oxidation (I)', 'Oxidation (K)', 'Oxidation (L)', 'Oxidation (M)', 'Oxidation (N)', 'Oxidation (P)', 'Oxidation (Q)', 'Oxidation (R)', 'Oxidation (S)', 'Oxidation (T)', 'Oxidation (U)', 'Oxidation (V)', 'Oxidation (W)', 'Oxidation (Y)', 'Oxidation+NEM (C)', 'OxLysBiotin (K)', 'OxLysBiotinRed (K)', 'OxProBiotin (P)', 'OxProBiotinRed (P)', 'Palmitoleyl (C)', 'Palmitoleyl (S)', 'Palmitoleyl (T)', 'Palmitoyl (C)', 'Palmitoyl (K)', 'Palmitoyl (Protein N-term)', 'Palmitoyl (S)', 'Palmitoyl (T)', 'PEITC (C)', 'PEITC (K)', 'PEITC (N-term)', 'Pent(1)HexNAc(1) (S)', 'Pent(1)HexNAc(1) (T)', 'Pent(2) (S)', 'Pent(2) (T)', 'Pentanoyl (K)', 'Pentose (S)', 'Pentose (T)', 'Pentylamine (Q)', 'PEO-Iodoacetyl-LC-Biotin (C)', 'PET (S)', 'PET (T)', '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)', 'phenyl-phosphate (K)', 'phenyl-phosphate (S)', 'phenyl-phosphate (T)', 'phenyl-phosphate (Y)', 'Phenylisocyanate (N-term)', 'Phenylisocyanate:2H(5) (N-term)', 'phenylsulfonylethyl (C)', 'Phospho (C)', 'Phospho (D)', 'Phospho (E)', 'Phospho (H)', 'Phospho (K)', 'Phospho (R)', 'Phospho (S)', 'Phospho (T)', 'Phospho (Y)', 'Phosphoadenosine (H)', 'Phosphoadenosine (K)', 'Phosphoadenosine (S)', 'Phosphoadenosine (T)', 'Phosphoadenosine (Y)', 'PhosphoCytidine (S)', 'PhosphoCytidine (T)', 'PhosphoCytidine (Y)', 'PhosphoDecoy (A)', 'PhosphoDecoy (G)', 'PhosphoDecoy (L)', 'Phosphogluconoylation (K)', 'Phosphogluconoylation (N-term)', 'Phosphoguanosine (H)', 'Phosphoguanosine (K)', 'PhosphoHex (S)', 'PhosphoHex (T)', 'PhosphoHex(2) (N)', 'PhosphoHex(2) (S)', 'PhosphoHex(2) (T)', 'PhosphoHexNAc (S)', 'PhosphoHexNAc (T)', 'Phosphopantetheine (S)', 'Phosphopropargyl (S)', 'Phosphopropargyl (T)', 'Phosphopropargyl (Y)', 'phosphoRibosyl (D)', 'phosphoRibosyl (E)', 'phosphoRibosyl (R)', 'PhosphoribosyldephosphoCoA (S)', 'PhosphoUridine (H)', 'PhosphoUridine (Y)', 'Phycocyanobilin (C)', 'Phycoerythrobilin (C)', 'Phytochromobilin (C)', 'Piperidine (K)', 'Piperidine (N-term)', 'pRBS-ID_4-thiouridine (F)', 'pRBS-ID_6-thioguanosine (W)', 'Pro+O(2) (H)', '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->HAVA (P)', 'Pro->His (P)', 'Pro->Lys (P)', 'Pro->Met (P)', 'Pro->Phe (P)', 'Pro->pyro-Glu (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)', 'probiotinhydrazide (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 (Protein 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 (Protein C-term)', 'Propyl:2H(6) (K)', 'Propyl:2H(6) (N-term)', 'PropylNAGthiazoline (C)', 'PS_Hapten (C)', 'PS_Hapten (H)', 'PS_Hapten (K)', 'pupylation (K)', 'Puromycin (C-term)', 'PyMIC (N-term)', 'PyridoxalPhosphate (K)', 'PyridoxalPhosphateH2 (K)', 'Pyridylacetyl (K)', 'Pyridylacetyl (N-term)', 'Pyridylethyl (C)', 'Pyro-carbamidomethyl (N-term C)', 'Pyro-QQTGG (K)', 'pyrophospho (S)', 'pyrophospho (T)', 'PyruvicAcidIminyl (K)', 'PyruvicAcidIminyl (Protein N-term C)', 'PyruvicAcidIminyl (Protein N-term V)', 'Pyruvoyl (K)', 'QAT (C)', 'QAT:2H(3) (C)', 'QEQTGG (K)', 'QQQTGG (K)', 'QQTGG (K)', 'QTGG (K)', 'Quinone (W)', 'Quinone (Y)', 'RBS-ID_Uridine (Y)', 'Retinylidene (K)', 'RNPXL (N-term K)', 'RNPXL (N-term R)', 'RNPXlink1 (C)', 's-GlcNAc (S)', 's-GlcNAc (T)', '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->LacticAcid (Protein N-term 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)', 'Ser/Thr-KDO (S)', 'Ser/Thr-KDO (T)', 'serotonylation (Q)', 'shTMT (K)', 'shTMT (N-term)', 'shTMT (Protein N-term)', 'shTMTpro (K)', 'shTMTpro (N-term)', 'shTMTpro (Protein N-term)', 'SMA (K)', 'SMA (N-term)', 'spermidine (Q)', 'spermine (Q)', 'SPITC (K)', 'SPITC (N-term)', 'SPITC:13C(6) (K)', 'SPITC:13C(6) (N-term)', 'Succinyl (K)', 'Succinyl (N-term)', 'Succinyl (Protein 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+amino (Y)', 'Sulfo-NHS-LC-LC-Biotin (K)', 'Sulfo-NHS-LC-LC-Biotin (N-term)', 'SulfoGMBS (C)', 'SulfurDioxide (C)', 'SUMO2135 (K)', 'SUMO3549 (K)', 'TAMRA-FP (S)', 'TAMRA-FP (Y)', 'Thiadiazole (C)', 'Thiazolidine (C)', 'Thiazolidine (F)', 'Thiazolidine (H)', 'Thiazolidine (K)', 'Thiazolidine (Protein N-term)', 'Thiazolidine (R)', 'Thiazolidine (W)', 'Thiazolidine (Y)', 'thioacylPA (K)', '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)', 'Tiglyl (K)', 'TMAB (K)', 'TMAB (N-term)', 'TMAB:2H(9) (K)', 'TMAB:2H(9) (N-term)', 'TMPP-Ac (K)', 'TMPP-Ac (N-term)', 'TMPP-Ac (Y)', 'TMPP-Ac:13C(9) (K)', 'TMPP-Ac:13C(9) (N-term)', 'TMPP-Ac:13C(9) (Y)', 'TMT (H)', 'TMT (K)', 'TMT (N-term)', 'TMT (Protein N-term)', 'TMT (S)', 'TMT (T)', 'TMT2plex (H)', 'TMT2plex (K)', 'TMT2plex (N-term)', 'TMT2plex (Protein N-term)', 'TMT2plex (S)', 'TMT2plex (T)', 'TMT6plex (H)', 'TMT6plex (K)', 'TMT6plex (N-term)', 'TMT6plex (Protein N-term)', 'TMT6plex (S)', 'TMT6plex (T)', 'TMTpro (H)', 'TMTpro (K)', 'TMTpro (N-term)', 'TMTpro (Protein N-term)', 'TMTpro (S)', 'TMTpro (T)', 'TMTpro_zero (H)', 'TMTpro_zero (K)', 'TMTpro_zero (N-term)', 'TMTpro_zero (Protein N-term)', 'TMTpro_zero (S)', 'TMTpro_zero (T)', 'TNBS (K)', 'TNBS (N-term)', 'trifluoro (L)', 'Triiodo (Y)', 'Triiodothyronine (Y)', 'Trimethyl (K)', 'Trimethyl (Protein N-term A)', '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 (F)', 'Trioxidation (W)', 'Trioxidation (Y)', 'Tripalmitate (Protein N-term C)', '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-fluorescein (C)', 'Ub-VME (C)', 'UgiJoullie (D)', 'UgiJoullie (E)', 'UgiJoullieProGly (D)', 'UgiJoullieProGly (E)', 'UgiJoullieProGlyProGly (D)', 'UgiJoullieProGlyProGly (E)', 'Unknown:162 (C-term)', 'Unknown:162 (D)', 'Unknown:162 (E)', 'Unknown:162 (N-term)', 'Unknown:177 (C-term)', 'Unknown:177 (D)', 'Unknown:177 (E)', 'Unknown:177 (N-term)', 'Unknown:210 (C-term)', 'Unknown:210 (D)', 'Unknown:210 (E)', 'Unknown:210 (N-term)', 'Unknown:216 (C-term)', 'Unknown:216 (D)', 'Unknown:216 (E)', 'Unknown:216 (N-term)', 'Unknown:234 (C-term)', 'Unknown:234 (D)', 'Unknown:234 (E)', 'Unknown:234 (N-term)', 'Unknown:248 (C-term)', 'Unknown:248 (D)', 'Unknown:248 (E)', 'Unknown:248 (N-term)', 'Unknown:250 (C-term)', 'Unknown:250 (D)', 'Unknown:250 (E)', 'Unknown:250 (N-term)', 'Unknown:302 (C-term)', 'Unknown:302 (D)', 'Unknown:302 (E)', 'Unknown:302 (N-term)', 'Unknown:306 (C-term)', 'Unknown:306 (D)', 'Unknown:306 (E)', 'Unknown:306 (N-term)', 'Unknown:420 (C-term)', 'Unknown:420 (N-term)', '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)', 'ValGly (K)', 'VFQQQTGG (K)', 'VIEVYQEQTGG (K)', '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:BMOE (C)', 'Xlink:BS2G[113] (K)', 'Xlink:BS2G[113] (Protein N-term)', 'Xlink:BS2G[114] (K)', 'Xlink:BS2G[114] (Protein N-term)', 'Xlink:BS2G[217] (K)', 'Xlink:BS2G[217] (Protein N-term)', 'Xlink:BS2G[96] (K)', 'Xlink:BS2G[96] (Protein N-term)', 'Xlink:BuUrBu[111] (K)', 'Xlink:BuUrBu[111] (Protein N-term)', 'Xlink:BuUrBu[111] (S)', 'Xlink:BuUrBu[111] (T)', 'Xlink:BuUrBu[111] (Y)', 'Xlink:BuUrBu[196] (K)', 'Xlink:BuUrBu[196] (Protein N-term)', 'Xlink:BuUrBu[196] (S)', 'Xlink:BuUrBu[196] (T)', 'Xlink:BuUrBu[196] (Y)', 'Xlink:BuUrBu[213] (K)', 'Xlink:BuUrBu[213] (Protein N-term)', 'Xlink:BuUrBu[213] (S)', 'Xlink:BuUrBu[213] (T)', 'Xlink:BuUrBu[213] (Y)', 'Xlink:BuUrBu[214] (K)', 'Xlink:BuUrBu[214] (Protein N-term)', 'Xlink:BuUrBu[214] (S)', 'Xlink:BuUrBu[214] (T)', 'Xlink:BuUrBu[214] (Y)', 'Xlink:BuUrBu[317] (K)', 'Xlink:BuUrBu[317] (Protein N-term)', 'Xlink:BuUrBu[317] (S)', 'Xlink:BuUrBu[317] (T)', 'Xlink:BuUrBu[317] (Y)', 'Xlink:BuUrBu[85] (K)', 'Xlink:BuUrBu[85] (Protein N-term)', 'Xlink:BuUrBu[85] (S)', 'Xlink:BuUrBu[85] (T)', 'Xlink:BuUrBu[85] (Y)', 'Xlink:DFDNB (K)', 'Xlink:DFDNB (N)', 'Xlink:DFDNB (Q)', 'Xlink:DFDNB (R)', 'Xlink:DMP[122] (K)', 'Xlink:DMP[122] (Protein N-term)', 'Xlink:DMP[139] (K)', 'Xlink:DMP[139] (Protein N-term)', 'Xlink:DMP[140] (K)', 'Xlink:DMP[140] (Protein N-term)', 'Xlink:DMP[154] (K)', 'Xlink:DMP[154] (Protein N-term)', 'Xlink:DSPP[210] (K)', 'Xlink:DSPP[210] (Protein N-term)', 'Xlink:DSPP[226] (K)', 'Xlink:DSPP[226] (Protein N-term)', 'Xlink:DSPP[228] (K)', 'Xlink:DSPP[228] (Protein N-term)', 'Xlink:DSPP[331] (K)', 'Xlink:DSPP[331] (Protein N-term)', 'Xlink:DSS[138] (K)', 'Xlink:DSS[138] (Protein N-term)', 'Xlink:DSS[155] (K)', 'Xlink:DSS[155] (Protein N-term)', 'Xlink:DSS[156] (K)', 'Xlink:DSS[156] (Protein N-term)', 'Xlink:DSS[259] (K)', 'Xlink:DSS[259] (Protein N-term)', 'Xlink:DSSO[104] (K)', 'Xlink:DSSO[104] (Protein N-term)', 'Xlink:DSSO[158] (K)', 'Xlink:DSSO[158] (Protein N-term)', 'Xlink:DSSO[175] (K)', 'Xlink:DSSO[175] (Protein N-term)', 'Xlink:DSSO[176] (K)', 'Xlink:DSSO[176] (Protein N-term)', 'Xlink:DSSO[279] (K)', 'Xlink:DSSO[279] (Protein N-term)', 'Xlink:DSSO[54] (K)', 'Xlink:DSSO[54] (Protein N-term)', 'Xlink:DSSO[86] (K)', 'Xlink:DSSO[86] (Protein N-term)', 'Xlink:DST[114] (K)', 'Xlink:DST[114] (Protein N-term)', 'Xlink:DST[132] (K)', 'Xlink:DST[132] (Protein N-term)', 'Xlink:DST[56] (K)', 'Xlink:DST[56] (Protein N-term)', 'Xlink:DTBP[172] (K)', 'Xlink:DTBP[172] (Protein N-term)', 'Xlink:DTBP[87] (K)', 'Xlink:DTBP[87] (Protein N-term)', 'Xlink:DTSSP[174] (K)', 'Xlink:DTSSP[174] (Protein N-term)', 'Xlink:DTSSP[192] (K)', 'Xlink:DTSSP[192] (Protein N-term)', 'Xlink:DTSSP[88] (K)', 'Xlink:DTSSP[88] (Protein N-term)', 'Xlink:EGS[115] (K)', 'Xlink:EGS[115] (Protein N-term)', 'Xlink:EGS[226] (K)', 'Xlink:EGS[226] (Protein N-term)', 'Xlink:EGS[244] (K)', 'Xlink:EGS[244] (Protein N-term)', 'Xlink:SMCC[219] (C)', 'Xlink:SMCC[219] (K)', 'Xlink:SMCC[219] (Protein N-term)', 'Xlink:SMCC[237] (C)', 'Xlink:SMCC[237] (K)', 'Xlink:SMCC[237] (Protein N-term)', 'Xlink:SMCC[321] (C)', 'ZGB (K)', 'ZGB (N-term)', 'ZQG (K)')
-neutral_losses <value> List the types of neutral losses that you want to consider. The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = <RESDIUES> -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (default: '[sty -H3PO4 -97.97690]')
-decoy_mass <value> How much to add to an amino acid to make it a decoy (default: '79.966330999999997') (min: '1.0')
-decoy_neutral_losses <value> For handling the neutral loss from a decoy sequence. The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (default: '[X -H3PO4 -97.97690]')
-max_charge_state <num> Do not consider PSMs with a charge state above this value (default: '5') (min: '1')
-max_peptide_length <num> Restrict scoring to peptides with a length shorter than this value (default: '40') (min: '1')
-max_num_perm <num> Maximum number of permutations a sequence can have (default: '16384') (min: '1')
-modeling_score_threshold <value> Minimum score a PSM needs to be considered for modeling (default: '0.95') (min: '0.0')
-scoring_threshold <value> PSMs below this value will be discarded (default: '0.0') (min: '0.0')
-min_num_psms_model <num> The minimum number of PSMs you need for any charge state in order to build a model for it (default: '50') (min: '1')
-num_threads <num> For multi-threading, 0 = use all CPU found by JAVA (default: '6') (min: '0')
-run_mode <choice> Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported (default: '0') (valid: '0', '1')
-rt_tolerance <num> Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used) (default: '0.01') (min: '0.0')
-java_executable <file> The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Java
-java_memory <num> Maximum Java heap size (in MB) (default: '3500')
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 (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
1.9.1