Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data.
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.
Legend:
required parameter
advanced parameter
+LuciphorAdapterModification site localisation using LuciPHOr2.
version3.3.0-pre-nightly-2024-11-20
Version of the tool that generated this parameters file.
++1Instance '1' section for 'LuciphorAdapter'
in
Input spectrum fileinput file*.mzML
id
Protein/peptide identifications fileinput file*.idXML
out
Output fileoutput file*.idXML
executableluciphor2.jar
LuciPHOr2 .jar file. Provide a full or relative path, or make sure it can be found in your PATH environment.input file, is_executable
fragment_methodCID
Fragmentation methodCID, HCD
fragment_mass_tolerance0.5
Tolerance of the peaks in the fragment spectrum
fragment_error_unitsDa
Unit of fragment mass toleranceDa, ppm
min_mz150.0
Do not consider peaks below this value for matching fragment ions
target_modifications[Phospho (S), Phospho (T), Phospho (Y)]
List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'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 (D), Dehydrated (N-term C), Dehydrated (Protein C-term N), Dehydrated (Protein C-term Q), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(-1)N(-1)18O(1) (N), Delta:H(-4)O(2) (W), Delta:H(-4)O(3) (W), Delta:H(10)C(8)O(1) (K), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(2) (N-term), Delta:H(2)C(2) (Protein 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) (Protein N-term), 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(3)O(1) (R), Delta:H(4)C(3)O(2) (K), Delta:H(4)C(5)O(1) (R), 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(3)O(1) (Protein N-term), Delta:H(6)C(6)O(1) (K), Delta:H(6)C(7)O(4) (R), Delta:H(8)C(6)O(1) (K), Delta:H(8)C(6)O(1) (Protein N-term), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:O(4) (W), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Deoxyhypusine (K), Deoxyhypusine (Q), DeStreak (C), Dethiomethyl (M), dHex (N), dHex (S), dHex (T), dHex(1)Hex(1) (S), dHex(1)Hex(1) (T), dHex(1)Hex(1)HexA(1)HexNAc(3) (S), dHex(1)Hex(1)HexA(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(1)Kdn(1) (S), dHex(1)Hex(1)HexNAc(1)Kdn(1) (T), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(2)Kdn(1) (S), dHex(1)Hex(1)HexNAc(2)Kdn(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(1)HexNAc(2)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3) (S), dHex(1)Hex(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(3)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)Sulf(1) (T), dHex(1)Hex(1)HexNAc(4) (S), dHex(1)Hex(1)HexNAc(4) (T), dHex(1)Hex(2) (S), dHex(1)Hex(2) (T), dHex(1)Hex(2)HexA(1) (S), dHex(1)Hex(2)HexA(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(2) (S), dHex(1)Hex(2)HexA(1)HexNAc(2) (T), dHex(1)Hex(2)HexNAc(1) (S), dHex(1)Hex(2)HexNAc(1) (T), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T), dHex(1)Hex(2)HexNAc(2)Pent(1) (N), dHex(1)Hex(2)HexNAc(2)Sulf(1) (S), 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dHex(2)Hex(4)HexNAc(2) (N), dHex(2)Hex(4)HexNAc(2) (S), dHex(2)Hex(4)HexNAc(2) (T), dHex(2)Hex(4)HexNAc(3) (N), dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N), dHex(2)Hex(4)HexNAc(3)Pent(1) (N), dHex(2)Hex(4)HexNAc(4) (N), dHex(2)Hex(4)HexNAc(4) (S), dHex(2)Hex(4)HexNAc(4) (T), dHex(2)Hex(4)HexNAc(4)Pent(1) (N), dHex(2)Hex(4)HexNAc(4)Sulf(1) (N), dHex(2)Hex(4)HexNAc(5) (N), dHex(2)Hex(4)HexNAc(5) (S), dHex(2)Hex(4)HexNAc(5) (T), dHex(2)Hex(5)HexNAc(2)Me(1) (S), dHex(2)Hex(5)HexNAc(2)Me(1) (T), dHex(2)Hex(5)HexNAc(3)Pent(1) (N), dHex(2)Hex(5)HexNAc(4) (N), dHex(2)HexNAc(2)Kdn(1) (S), dHex(2)HexNAc(2)Kdn(1) (T), dHex(2)HexNAc(5) (S), dHex(2)HexNAc(5) (T), dHex(2)HexNAc(7) (S), dHex(2)HexNAc(7) (T), dHex(3)Hex(1)HexNAc(2)Kdn(1) (S), dHex(3)Hex(1)HexNAc(2)Kdn(1) (T), dHex(3)Hex(1)HexNAc(3)Kdn(1) (S), dHex(3)Hex(1)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T), dHex(3)Hex(2)HexNAc(2) (S), dHex(3)Hex(2)HexNAc(2) (T), dHex(3)Hex(2)HexNAc(2)Kdn(1) (S), dHex(3)Hex(2)HexNAc(2)Kdn(1) (T), dHex(3)Hex(2)HexNAc(3) (S), dHex(3)Hex(2)HexNAc(3) (T), dHex(3)Hex(2)HexNAc(3)Kdn(1) (S), dHex(3)Hex(2)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexNAc(4) (S), dHex(3)Hex(2)HexNAc(4) (T), dHex(3)Hex(2)HexNAc(4)Sulf(2) (S), dHex(3)Hex(2)HexNAc(4)Sulf(2) (T), dHex(3)Hex(3)HexNAc(1) (S), dHex(3)Hex(3)HexNAc(1) (T), dHex(3)Hex(3)HexNAc(2) (S), dHex(3)Hex(3)HexNAc(2) (T), dHex(3)Hex(3)HexNAc(3) (S), dHex(3)Hex(3)HexNAc(3) (T), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T), dHex(3)Hex(3)HexNAc(3)Pent(1) (N), dHex(3)Hex(3)HexNAc(4) (N), dHex(3)Hex(3)HexNAc(4)Pent(1) (N), dHex(3)Hex(4)HexNAc(4) (N), 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 N-term), Dimethyl:2H(4) (R), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(4)13C(2) (Protein N-term), Dimethyl:2H(4)13C(2) (R), Dimethyl:2H(6) (K), Dimethyl:2H(6) (N-term), Dimethyl:2H(6) (R), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (Protein N-term), Dimethyl:2H(6)13C(2) (R), DimethylamineGMBS (C), Dimethylaminoethyl (C), DimethylArsino (C), Dimethylphosphothione (C), Dimethylphosphothione (H), Dimethylphosphothione (K), Dimethylphosphothione (S), Dimethylphosphothione (T), Dimethylphosphothione (Y), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (E), Dioxidation (F), Dioxidation (I), Dioxidation (K), Dioxidation (L), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (U), Dioxidation (V), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyridyl (C), Dipyrrolylmethanemethyl (C), DMPO (C), DMPO (H), DMPO (Y), DNCB_hapten (C), DNCB_hapten (H), DNCB_hapten (K), DNCB_hapten (Y), dNIC (K), dNIC (N-term), DNPS (C), DNPS (W), DPIA (C), DTT (C), DVFQQQTGG (K), DyLight-maleimide (C), DYn-2 (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), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), Ethyl (Protein N-term), Ethyl+Deamidated (N), Ethyl+Deamidated (Q), ethylamino (S), ethylamino (T), Ethylphosphate (K), Ethylphosphate (N-term), 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 (Protein C-term), GluGluGluGlu (E), GluGluGluGlu (Protein C-term), Gluratylation (K), Glutathione (C), Gly (K), Gly (S), Gly (T), Gly+O(2) (H), 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), Glyceroyl (K), Glyceroyl (Protein N-term), GlycerylPE (E), glycidamide (K), glycidamide (N-term), Glycosyl (P), glyoxalAGE (R), Glyoxylyl (K), GNLLFLACYCIGG (K), GPIanchor (Protein C-term), Guanidinyl (K), Guanidinyl (N-term), Haloxon (C), Haloxon (H), Haloxon (K), Haloxon (S), Haloxon (T), Haloxon (Y), HCysteinyl (C), HCysThiolactone (K), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (S), Hex (T), Hex (W), Hex (Y), Hex(1)HexA(1) (S), Hex(1)HexA(1) (T), Hex(1)HexA(1)HexNAc(1) (S), Hex(1)HexA(1)HexNAc(1) (T), Hex(1)HexA(1)HexNAc(2) (S), Hex(1)HexA(1)HexNAc(2) (T), Hex(1)HexNAc(1) (N), Hex(1)HexNAc(1) (S), Hex(1)HexNAc(1) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(1)dHex(1) (S), Hex(1)HexNAc(1)dHex(1) (T), Hex(1)HexNAc(1)dHex(1)Me(1) (S), Hex(1)HexNAc(1)dHex(1)Me(1) (T), Hex(1)HexNAc(1)dHex(1)Me(2) (S), Hex(1)HexNAc(1)dHex(1)Me(2) (T), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T), Hex(1)HexNAc(1)NeuAc(3) (S), Hex(1)HexNAc(1)NeuAc(3) (T), Hex(1)HexNAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuGc(2) (S), Hex(1)HexNAc(1)NeuGc(2) (T), Hex(1)HexNAc(1)NeuGc(3) (S), Hex(1)HexNAc(1)NeuGc(3) (T), Hex(1)HexNAc(1)NeuGc(4) (S), Hex(1)HexNAc(1)NeuGc(4) (T), Hex(1)HexNAc(1)NeuGc(5) (S), Hex(1)HexNAc(1)NeuGc(5) (T), Hex(1)HexNAc(1)Phos(1) (S), Hex(1)HexNAc(1)Phos(1) (T), Hex(1)HexNAc(1)Sulf(1) (S), Hex(1)HexNAc(1)Sulf(1) (T), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2) (S), Hex(1)HexNAc(2) (T), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1) (S), Hex(1)HexNAc(2)dHex(1) (T), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(1)HexNAc(2)dHex(2) (S), Hex(1)HexNAc(2)dHex(2) (T), Hex(1)HexNAc(2)dHex(2)Sulf(1) (S), Hex(1)HexNAc(2)dHex(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(1) (S), Hex(1)HexNAc(2)NeuAc(1) (T), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(2) (S), Hex(1)HexNAc(2)NeuAc(2) (T), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuGc(1) (S), Hex(1)HexNAc(2)NeuGc(1) (T), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)Sulf(1) (S), Hex(1)HexNAc(2)Sulf(1) (T), Hex(1)HexNAc(3) (S), Hex(1)HexNAc(3) (T), Hex(1)HexNAc(3)NeuAc(1) (S), Hex(1)HexNAc(3)NeuAc(1) (T), Hex(1)HexNAc(3)NeuAc(2) (S), Hex(1)HexNAc(3)NeuAc(2) (T), Hex(1)HexNAc(3)NeuGc(1) (S), Hex(1)HexNAc(3)NeuGc(1) (T), Hex(1)HexNAc(3)Sulf(1) (S), Hex(1)HexNAc(3)Sulf(1) (T), Hex(1)HexNAc(4)dHex(1)Sulf(1) (S), Hex(1)HexNAc(4)dHex(1)Sulf(1) (T), Hex(1)NeuAc(1) (S), Hex(1)NeuAc(1) (T), Hex(1)NeuAc(1)Pent(1) (S), Hex(1)NeuAc(1)Pent(1) (T), Hex(1)NeuGc(1) (S), Hex(1)NeuGc(1) (T), Hex(1)Pent(1) (S), Hex(1)Pent(1) (T), Hex(1)Pent(2) (S), Hex(1)Pent(2) (T), Hex(1)Pent(2)Me(1) (S), Hex(1)Pent(2)Me(1) (T), Hex(1)Pent(3) (S), Hex(1)Pent(3) (T), Hex(1)Pent(3)Me(1) (S), Hex(1)Pent(3)Me(1) (T), Hex(10)HexNAc(1) (N), Hex(10)Phos(3) (S), Hex(10)Phos(3) (T), Hex(2) (K), Hex(2) (R), Hex(2) (S), Hex(2) (T), Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T), Hex(2)HexA(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)Pent(1)Sulf(1) (T), Hex(2)HexNAc(1) (N), Hex(2)HexNAc(1) (S), Hex(2)HexNAc(1) (T), Hex(2)HexNAc(1)Me(1) (S), Hex(2)HexNAc(1)Me(1) (T), Hex(2)HexNAc(1)NeuGc(1) (S), Hex(2)HexNAc(1)NeuGc(1) (T), Hex(2)HexNAc(1)NeuGc(2) (S), Hex(2)HexNAc(1)NeuGc(2) (T), Hex(2)HexNAc(1)NeuGc(3) (S), Hex(2)HexNAc(1)NeuGc(3) (T), Hex(2)HexNAc(1)NeuGc(4) (S), Hex(2)HexNAc(1)NeuGc(4) (T), Hex(2)HexNAc(1)Pent(1)HexA(1) (S), Hex(2)HexNAc(1)Pent(1)HexA(1) (T), Hex(2)HexNAc(1)Sulf(1) (S), Hex(2)HexNAc(1)Sulf(1) (T), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2) (S), Hex(2)HexNAc(2) (T), Hex(2)HexNAc(2)dHex(1) (N), Hex(2)HexNAc(2)dHex(1) (S), Hex(2)HexNAc(2)dHex(1) (T), Hex(2)HexNAc(2)NeuAc(1) (N), Hex(2)HexNAc(2)NeuAc(1) (S), Hex(2)HexNAc(2)NeuAc(1) (T), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(2)NeuAc(2) (S), Hex(2)HexNAc(2)NeuAc(2) (T), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(2)HexNAc(2)NeuGc(1) (S), Hex(2)HexNAc(2)NeuGc(1) (T), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)Sulf(1) (S), Hex(2)HexNAc(2)Sulf(1) (T), Hex(2)HexNAc(3) (N), Hex(2)HexNAc(3) (S), Hex(2)HexNAc(3) (T), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(3)NeuAc(2) (S), Hex(2)HexNAc(3)NeuAc(2) (T), Hex(2)HexNAc(3)NeuAc(3) (S), Hex(2)HexNAc(3)NeuAc(3) (T), Hex(2)HexNAc(3)NeuGc(1) (S), Hex(2)HexNAc(3)NeuGc(1) (T), Hex(2)HexNAc(3)NeuGc(2) (S), Hex(2)HexNAc(3)NeuGc(2) (T), Hex(2)HexNAc(3)NeuGc(3) (S), Hex(2)HexNAc(3)NeuGc(3) (T), Hex(2)HexNAc(3)Sulf(1) (S), Hex(2)HexNAc(3)Sulf(1) (T), Hex(2)HexNAc(4) (N), Hex(2)HexNAc(4) (S), Hex(2)HexNAc(4) (T), Hex(2)HexNAc(4)NeuAc(1) (S), Hex(2)HexNAc(4)NeuAc(1) (T), Hex(2)HexNAc(5) (S), Hex(2)HexNAc(5) (T), Hex(2)NeuAc(1) (S), Hex(2)NeuAc(1) (T), Hex(2)Pent(2) (S), Hex(2)Pent(2) (T), Hex(2)Pent(2)Me(1) (S), Hex(2)Pent(2)Me(1) (T), Hex(2)Sulf(1) (S), Hex(2)Sulf(1) (T), Hex(3) (N), Hex(3) (S), Hex(3) (T), Hex(3)HexNAc(1) (N), Hex(3)HexNAc(1) (S), Hex(3)HexNAc(1) (T), Hex(3)HexNAc(1)HexA(1) (S), Hex(3)HexNAc(1)HexA(1) (T), Hex(3)HexNAc(1)Me(1) (S), Hex(3)HexNAc(1)Me(1) (T), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2) (S), Hex(3)HexNAc(2) (T), Hex(3)HexNAc(2)NeuAc(1) (N), Hex(3)HexNAc(2)NeuAc(2) (S), Hex(3)HexNAc(2)NeuAc(2) (T), Hex(3)HexNAc(2)Pent(1) (N), Hex(3)HexNAc(2)Phos(1) (N), Hex(3)HexNAc(3) (N), Hex(3)HexNAc(3) (S), Hex(3)HexNAc(3) (T), Hex(3)HexNAc(3)NeuAc(1) (S), Hex(3)HexNAc(3)NeuAc(1) (T), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(2) (S), Hex(3)HexNAc(3)NeuAc(2) (T), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(3) (S), Hex(3)HexNAc(3)NeuAc(3) (T), Hex(3)HexNAc(3)NeuGc(1) (S), Hex(3)HexNAc(3)NeuGc(1) (T), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T), Hex(3)HexNAc(3)Pent(1) (N), Hex(3)HexNAc(3)Sulf(1) (N), Hex(3)HexNAc(3)Sulf(1) (S), Hex(3)HexNAc(3)Sulf(1) (T), Hex(3)HexNAc(4) (N), Hex(3)HexNAc(4) (S), Hex(3)HexNAc(4) (T), Hex(3)HexNAc(4)NeuAc(1) (N), Hex(3)HexNAc(4)NeuAc(2) (N), Hex(3)HexNAc(4)Pent(1) (N), Hex(3)HexNAc(4)Sulf(1) (N), Hex(3)HexNAc(5) (N), Hex(3)HexNAc(5) (S), Hex(3)HexNAc(5) (T), Hex(3)HexNAc(5)NeuAc(1) (N), Hex(3)HexNAc(5)Sulf(1) (N), Hex(3)HexNAc(6) (N), Hex(3)HexNAc(6) (S), Hex(3)HexNAc(6) (T), Hex(3)HexNAc(6)NeuAc(1) (N), Hex(3)HexNAc(6)Sulf(1) (N), Hex(3)HexNAc(6)Sulf(2) (N), Hex(3)HexNAc(7) (N), Hex(3)HexNAc(7)Sulf(1) (N), Hex(4) (S), Hex(4) (T), Hex(4)HexA(1) (S), Hex(4)HexA(1) (T), Hex(4)HexA(1)HexNAc(1) (S), Hex(4)HexA(1)HexNAc(1) (T), Hex(4)HexNAc(1) (N), Hex(4)HexNAc(1) (S), Hex(4)HexNAc(1) (T), Hex(4)HexNAc(2) (N), Hex(4)HexNAc(2)NeuAc(1) (N), Hex(4)HexNAc(2)NeuAc(1) (S), Hex(4)HexNAc(2)NeuAc(1) (T), Hex(4)HexNAc(2)Pent(1) (N), Hex(4)HexNAc(3) (N), Hex(4)HexNAc(3) (S), Hex(4)HexNAc(3) (T), Hex(4)HexNAc(3)NeuAc(1) (N), Hex(4)HexNAc(3)NeuAc(1) (S), Hex(4)HexNAc(3)NeuAc(1) (T), Hex(4)HexNAc(3)NeuAc(2) (N), Hex(4)HexNAc(3)NeuGc(1) (N), Hex(4)HexNAc(3)Pent(1) (N), Hex(4)HexNAc(4) (N), Hex(4)HexNAc(4) (S), Hex(4)HexNAc(4) (T), Hex(4)HexNAc(4)Me(2)Pent(1) (N), Hex(4)HexNAc(4)NeuAc(1) (N), Hex(4)HexNAc(4)NeuAc(1) (S), Hex(4)HexNAc(4)NeuAc(1) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T), Hex(4)HexNAc(4)NeuGc(1) (N), Hex(4)HexNAc(4)NeuGc(1) (S), Hex(4)HexNAc(4)NeuGc(1) (T), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T), Hex(4)HexNAc(4)Pent(1) (N), Hex(4)HexNAc(4)Sulf(1) (N), Hex(4)HexNAc(4)Sulf(2) (S), Hex(4)HexNAc(4)Sulf(2) (T), Hex(4)HexNAc(5) (N), Hex(4)HexNAc(5)NeuAc(1) (N), Hex(4)HexNAc(5)Sulf(1) (N), Hex(4)HexNAc(6) (N), Hex(4)Phos(1) (S), Hex(4)Phos(1) (T), Hex(5) (S), Hex(5) (T), Hex(5)HexA(1) (S), Hex(5)HexA(1) (T), Hex(5)HexNAc(1) (N), Hex(5)HexNAc(1) (S), Hex(5)HexNAc(1) (T), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(2)Phos(1) (N), Hex(5)HexNAc(3) (N), Hex(5)HexNAc(3)Pent(1) (N), Hex(5)HexNAc(4) (N), Hex(5)HexNAc(4) (S), Hex(5)HexNAc(4) (T), Hex(5)HexNAc(4)Me(2)Pent(1) (N), Hex(5)HexNAc(4)NeuAc(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N), Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N), Hex(5)HexNAc(4)NeuAc(2) (N), Hex(5)HexNAc(4)NeuGc(1) (N), Hex(5)HexNAc(4)Sulf(1) (N), Hex(5)HexNAc(5) (N), Hex(5)HexNAc(5) (S), Hex(5)HexNAc(5) (T), Hex(5)Phos(1) (S), Hex(5)Phos(1) (T), Hex(5)Phos(3) (S), Hex(5)Phos(3) (T), Hex(6)HexNAc(1) (N), Hex(6)HexNAc(2) (N), Hex(6)HexNAc(2)Phos(1) (N), Hex(6)HexNAc(3) (N), Hex(6)HexNAc(3)Phos(1) (N), Hex(6)HexNAc(4) (N), Hex(6)HexNAc(4) (S), Hex(6)HexNAc(4) (T), Hex(6)HexNAc(4)Me(3) (N), Hex(6)HexNAc(4)Me(3)Pent(1) (N), Hex(6)HexNAc(5) (N), Hex(6)HexNAc(5)NeuAc(3) (N), Hex(6)Phos(1) (S), Hex(6)Phos(1) (T), Hex(6)Phos(3) (S), Hex(6)Phos(3) (T), Hex(7)HexNAc(1) (N), Hex(7)HexNAc(2) (N), Hex(7)HexNAc(2)Phos(1) (N), Hex(7)HexNAc(2)Phos(2) (N), Hex(7)HexNAc(3) (N), Hex(7)HexNAc(3)Phos(1) (N), Hex(7)HexNAc(4) (N), Hex(7)HexNAc(6) (N), Hex(7)HexNAc(6) (S), Hex(7)HexNAc(6) (T), Hex(7)Phos(3) (S), Hex(7)Phos(3) (T), Hex(8)HexNAc(1) (N), Hex(8)HexNAc(2) (N), Hex(8)Phos(3) (S), Hex(8)Phos(3) (T), Hex(9) (N), Hex(9)HexNAc(1) (N), Hex(9)HexNAc(2) (N), Hex(9)Phos(3) (S), Hex(9)Phos(3) (T), HexA(2)HexNAc(3) (S), HexA(2)HexNAc(3) (T), Hexanoyl (K), HexN (K), HexN (N), HexN (S), HexN (T), HexN (W), HexNAc (C), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(1) (S), HexNAc(1)dHex(1) (T), HexNAc(1)dHex(2) (N), HexNAc(1)Kdn(2) (S), HexNAc(1)Kdn(2) (T), HexNAc(1)NeuAc(1) (S), HexNAc(1)NeuAc(1) (T), HexNAc(1)NeuGc(1) (S), HexNAc(1)NeuGc(1) (T), HexNAc(1)NeuGc(2) (S), HexNAc(1)NeuGc(2) (T), HexNAc(2) (N), HexNAc(2) (S), HexNAc(2) (T), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), HexNAc(2)NeuAc(1) (S), HexNAc(2)NeuAc(1) (T), HexNAc(2)NeuAc(1)Sulf(1) (S), HexNAc(2)NeuAc(1)Sulf(1) (T), HexNAc(2)NeuGc(1) (S), HexNAc(2)NeuGc(1) (T), HexNAc(2)Sulf(1) (S), HexNAc(2)Sulf(1) (T), HexNAc(3) (S), HexNAc(3) (T), HexNAc(3)Sulf(1) (S), HexNAc(3)Sulf(1) (T), HexNAc(4) (S), HexNAc(4) (T), HexNAc(5) (S), HexNAc(5) (T), His+O(2) (H), 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), 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 (R), 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), Homocysteic_acid (M), HPG (R), Hydroxamic_acid (D), Hydroxamic_acid (E), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), hydroxyisobutyryl (K), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IASD (C), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICDID (C), ICDID:2H(6) (C), ICPL (K), ICPL (N-term), ICPL (Protein N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6) (Protein N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:13C(6)2H(4) (Protein N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), ICPL:2H(4) (Protein N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMEHex(2)NeuAc(1) (K), IMID (K), IMID:2H(4) (K), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), Iodoacetanilide (C), Iodoacetanilide (K), 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[sty -H3PO4 -97.97690]
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 = -
decoy_mass79.966330999999997
How much to add to an amino acid to make it a decoy1.0:∞
decoy_neutral_losses[X -H3PO4 -97.97690]
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 -
max_charge_state5
Do not consider PSMs with a charge state above this value1:∞
max_peptide_length40
Restrict scoring to peptides with a length shorter than this value1:∞
max_num_perm16384
Maximum number of permutations a sequence can have1:∞
modeling_score_threshold0.95
Minimum score a PSM needs to be considered for modeling0.0:∞
scoring_threshold0.0
PSMs below this value will be discarded0.0:∞
min_num_psms_model50
The minimum number of PSMs you need for any charge state in order to build a model for it1:∞
num_threads6
For multi-threading, 0 = use all CPU found by JAVA0:∞
run_mode0
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 reported0, 1
rt_tolerance0.01
Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)0.0:∞
java_executablejava
The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Javainput file, is_executable
java_memory3500
Maximum Java heap size (in MB)
java_permgen0
Maximum Java permanent generation space (in MB); only for Java 7 and below
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
Overrides tool-specific checkstrue, false
testfalse
Enables the test mode (needed for internal use only)true, false
1.9.1