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.
version2.5.0-nightly-2020-03-06
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
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-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),a-type-ion (C-term),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (Protein N-term),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),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),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),Atto495Maleimide (C),azole (C),azole (S),Bacillosamine (N),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (Protein N-term),BDMAPP (W),BDMAPP (Y),Benzoyl (K),Benzoyl (N-term),benzylguanidine (K),beta FNA (C),beta FNA (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 (Y),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21330 (K),Biotin:Thermo-21330 (N-term),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (X),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (X),Biotin:Thermo-33033-H (X),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),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),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bodipy (C),Brij35 (N-term),Brij58 (N-term),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),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 (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),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:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Cu[I] (H),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Cation:Zn[II] (H),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),CHDH (D),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),Cholesterol (Protein C-term),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),DAET (S),DAET (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),Deamidated (N),Deamidated (Protein N-term F),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),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(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(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(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: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),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(1)HexA(1)HexNAc(3) (S),dHex(1)Hex(1)HexA(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(1)Kdn(1) (S),dHex(1)Hex(1)HexNAc(1)Kdn(1) (T),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Kdn(1) (S),dHex(1)Hex(1)HexNAc(2)Kdn(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(2)Sulf(1) (S),dHex(1)Hex(1)HexNAc(2)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3) (S),dHex(1)Hex(1)HexNAc(3) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S),dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T),dHex(1)Hex(1)HexNAc(3)Sulf(1) (S),dHex(1)Hex(1)HexNAc(3)Sulf(1) (T),dHex(1)Hex(1)HexNAc(4) (S),dHex(1)Hex(1)HexNAc(4) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(2)HexA(1) (S),dHex(1)Hex(2)HexA(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexA(1)HexNAc(2) (S),dHex(1)Hex(2)HexA(1)HexNAc(2) (T),dHex(1)Hex(2)HexNAc(1) (S),dHex(1)Hex(2)HexNAc(1) (T),dHex(1)Hex(2)HexNAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S),dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S),dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T),dHex(1)Hex(2)HexNAc(2)Pent(1) 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(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(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(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),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),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),DimethylArsino (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (U),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),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),DTBP (K),DTBP (N),DTBP (Protein N-term),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl (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),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),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 (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->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 (N-term E),Glu->pyro-Glu+Methyl:2H(2)13C (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),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),glycidamide (K),glycidamide (N-term),Glycosyl (P),GPIanchor (Protein C-term),Guanidinyl (K),Guanidinyl (N-term),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)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)NeuAc(1) (S),Hex(1)NeuAc(1) (T),Hex(1)NeuAc(1)Pent(1) (S),Hex(1)NeuAc(1)Pent(1) (T),Hex(1)NeuGc(1) (S),Hex(1)NeuGc(1) (T),Hex(1)Pent(1) (S),Hex(1)Pent(1) (T),Hex(1)Pent(2) (S),Hex(1)Pent(2) (T),Hex(10)Phos(3) (S),Hex(10)Phos(3) (T),Hex(2) (K),Hex(2) (R),Hex(2)HexA(1)HexNAc(1)Sulf(1) (S),Hex(2)HexA(1)HexNAc(1)Sulf(1) (T),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T),Hex(2)HexA(1)Pent(1)Sulf(1) (S),Hex(2)HexA(1)Pent(1)Sulf(1) (T),Hex(2)HexNAc(1) (S),Hex(2)HexNAc(1) (T),Hex(2)HexNAc(1)Me(1) (S),Hex(2)HexNAc(1)Me(1) (T),Hex(2)HexNAc(1)NeuGc(1) (S),Hex(2)HexNAc(1)NeuGc(1) (T),Hex(2)HexNAc(1)NeuGc(2) (S),Hex(2)HexNAc(1)NeuGc(2) (T),Hex(2)HexNAc(1)NeuGc(3) (S),Hex(2)HexNAc(1)NeuGc(3) (T),Hex(2)HexNAc(1)NeuGc(4) (S),Hex(2)HexNAc(1)NeuGc(4) (T),Hex(2)HexNAc(1)Sulf(1) (S),Hex(2)HexNAc(1)Sulf(1) (T),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2) (S),Hex(2)HexNAc(2) (T),Hex(2)HexNAc(2)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)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) (S),Hex(2)HexNAc(3) (T),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S),Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(2)HexNAc(3)NeuAc(2) (S),Hex(2)HexNAc(3)NeuAc(2) (T),Hex(2)HexNAc(3)NeuAc(3) (S),Hex(2)HexNAc(3)NeuAc(3) (T),Hex(2)HexNAc(3)NeuGc(1) (S),Hex(2)HexNAc(3)NeuGc(1) (T),Hex(2)HexNAc(3)NeuGc(2) (S),Hex(2)HexNAc(3)NeuGc(2) (T),Hex(2)HexNAc(3)NeuGc(3) (S),Hex(2)HexNAc(3)NeuGc(3) (T),Hex(2)HexNAc(3)Sulf(1) (S),Hex(2)HexNAc(3)Sulf(1) (T),Hex(2)HexNAc(4) (S),Hex(2)HexNAc(4) (T),Hex(2)HexNAc(4)NeuAc(1) (S),Hex(2)HexNAc(4)NeuAc(1) (T),Hex(2)HexNAc(5) (S),Hex(2)HexNAc(5) (T),Hex(2)NeuAc(1) (S),Hex(2)NeuAc(1) (T),Hex(3) (N),Hex(3) (S),Hex(3) (T),Hex(3)HexNAc(1) (S),Hex(3)HexNAc(1) (T),Hex(3)HexNAc(1)Me(1) (S),Hex(3)HexNAc(1)Me(1) (T),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2) (S),Hex(3)HexNAc(2) (T),Hex(3)HexNAc(2)NeuAc(1) (N),Hex(3)HexNAc(2)NeuAc(2) (S),Hex(3)HexNAc(2)NeuAc(2) (T),Hex(3)HexNAc(2)Pent(1) (N),Hex(3)HexNAc(2)Phos(1) (N),Hex(3)HexNAc(3) (N),Hex(3)HexNAc(3) (S),Hex(3)HexNAc(3) (T),Hex(3)HexNAc(3)NeuAc(1) (S),Hex(3)HexNAc(3)NeuAc(1) (T),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T),Hex(3)HexNAc(3)NeuAc(2) (S),Hex(3)HexNAc(3)NeuAc(2) (T),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S),Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T),Hex(3)HexNAc(3)NeuGc(1) (S),Hex(3)HexNAc(3)NeuGc(1) (T),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S),Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T),Hex(3)HexNAc(3)Pent(1) (N),Hex(3)HexNAc(3)Sulf(1) (S),Hex(3)HexNAc(3)Sulf(1) (T),Hex(3)HexNAc(4) (N),Hex(3)HexNAc(4) (S),Hex(3)HexNAc(4) (T),Hex(3)HexNAc(4)NeuAc(1) (N),Hex(3)HexNAc(4)Pent(1) (N),Hex(3)HexNAc(4)Sulf(1) (N),Hex(3)HexNAc(5) (N),Hex(3)HexNAc(5) (S),Hex(3)HexNAc(5) (T),Hex(3)HexNAc(5)Sulf(1) (N),Hex(3)HexNAc(6) (N),Hex(3)HexNAc(6) (S),Hex(3)HexNAc(6) (T),Hex(3)HexNAc(6)NeuAc(1) (N),Hex(3)HexNAc(6)Sulf(1) (N),Hex(3)HexNAc(6)Sulf(2) (N),Hex(3)HexNAc(7) (N),Hex(3)HexNAc(7)Sulf(1) (N),Hex(3)Phos(1) (S),Hex(3)Phos(1) (T),Hex(4) (S),Hex(4) (T),Hex(4)HexNAc(1) (S),Hex(4)HexNAc(1) (T),Hex(4)HexNAc(2) (N),Hex(4)HexNAc(2)NeuAc(1) (N),Hex(4)HexNAc(2)Pent(1) (N),Hex(4)HexNAc(3) (N),Hex(4)HexNAc(3) (S),Hex(4)HexNAc(3) (T),Hex(4)HexNAc(3)NeuAc(1) (N),Hex(4)HexNAc(3)NeuAc(1) (S),Hex(4)HexNAc(3)NeuAc(1) (T),Hex(4)HexNAc(3)NeuAc(2) (N),Hex(4)HexNAc(3)NeuGc(1) (N),Hex(4)HexNAc(3)Pent(1) (N),Hex(4)HexNAc(4) (N),Hex(4)HexNAc(4) (S),Hex(4)HexNAc(4) (T),Hex(4)HexNAc(4)Me(2)Pent(1) (N),Hex(4)HexNAc(4)NeuAc(1) (N),Hex(4)HexNAc(4)NeuAc(1) (S),Hex(4)HexNAc(4)NeuAc(1) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S),Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S),Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T),Hex(4)HexNAc(4)Pent(1) (N),Hex(4)HexNAc(4)Sulf(1) (N),Hex(4)HexNAc(4)Sulf(2) (S),Hex(4)HexNAc(4)Sulf(2) (T),Hex(4)HexNAc(5) (N),Hex(4)HexNAc(5)NeuAc(1) (N),Hex(4)HexNAc(5)Sulf(1) (N),Hex(4)HexNAc(6) (N),Hex(4)Phos(1) (S),Hex(4)Phos(1) (T),Hex(5) (S),Hex(5) (T),Hex(5)HexNAc(1) (S),Hex(5)HexNAc(1) (T),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(2)Phos(1) (N),Hex(5)HexNAc(3) (N),Hex(5)HexNAc(3)Pent(1) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4) (S),Hex(5)HexNAc(4) (T),Hex(5)HexNAc(4)Me(2)Pent(1) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex(5)HexNAc(4)NeuGc(1) (N),Hex(5)HexNAc(4)Sulf(1) (N),Hex(5)HexNAc(5) (N),Hex(5)HexNAc(5) (S),Hex(5)HexNAc(5) (T),Hex(5)Phos(1) (S),Hex(5)Phos(1) (T),Hex(5)Phos(3) (S),Hex(5)Phos(3) (T),Hex(6)HexNAc(2) (N),Hex(6)HexNAc(2)Phos(1) (N),Hex(6)HexNAc(3) (N),Hex(6)HexNAc(3)Phos(1) (N),Hex(6)HexNAc(4) (N),Hex(6)HexNAc(4) (S),Hex(6)HexNAc(4) (T),Hex(6)HexNAc(4)Me(3) (N),Hex(6)HexNAc(4)Me(3)Pent(1) (N),Hex(6)HexNAc(5) (N),Hex(6)Phos(1) (S),Hex(6)Phos(1) (T),Hex(6)Phos(3) (S),Hex(6)Phos(3) (T),Hex(7)HexNAc(1) (N),Hex(7)HexNAc(2) (N),Hex(7)HexNAc(2)Phos(1) (N),Hex(7)HexNAc(2)Phos(2) (N),Hex(7)HexNAc(3) (N),Hex(7)HexNAc(3)Phos(1) (N),Hex(7)HexNAc(4) (N),Hex(7)Phos(3) (S),Hex(7)Phos(3) (T),Hex(8)HexNAc(1) (N),Hex(8)HexNAc(2) (N),Hex(8)Phos(3) (S),Hex(8)Phos(3) (T),Hex(9)HexNAc(2) (N),Hex(9)Phos(3) (S),Hex(9)Phos(3) (T),HexN (K),HexN (N),HexN (S),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)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(3) (S),HexNAc(3) (T),HexNAc(3)Sulf(1) (S),HexNAc(3)Sulf(1) (T),HexNAc(4) (S),HexNAc(4) (T),HexNAc(5) (S),HexNAc(5) (T),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),Homocysteic_acid (M),HPG (R),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IASD (C),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL (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),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (Protein N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (Protein N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(2)15N(2) (K),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),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 (K),LG-pyrrole (N-term),Lipoyl (K),LRGG (K),LRGG+dimethyl (K),LRGG+methyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),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 (S),MDCC (C),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Met-loss (Protein N-term M),Met-loss+Acetyl (Protein N-term M),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),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),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),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),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),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),NP40 (N-term),NQIGG (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 (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (U),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),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),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),phenylsulfonylethyl (C),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),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),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->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),pyrophospho (S),pyrophospho (T),PyruvicAcidIminyl (K),PyruvicAcidIminyl (Protein N-term C),PyruvicAcidIminyl (Protein N-term V),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),Retinylidene (K),RNPXL (N-term K),RNPXL (N-term R),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),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),SMA (K),SMA (N-term),SMCC-maleimide (C),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 (N-term C),Thioacyl (K),Thioacyl (X),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),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (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),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 (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-amide (C),Ub-Br2 (C),Ub-fluorescein (C),Ub-VME (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),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),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:DMP (K),Xlink:DMP (Protein N-term),Xlink:DMP-de (K),Xlink:DMP-de (Protein N-term),Xlink:DMP-s (K),Xlink:DMP-s (Protein N-term),Xlink:DSS (K),Xlink:DSS (Protein N-term),Xlink:DSS-NH2 (K),Xlink:DSS-NH2 (Protein N-term),Xlink:DST (K),Xlink:DST (Protein N-term),Xlink:DTSSP (K),Xlink:DTSSP (Protein N-term),Xlink:EGS (K),Xlink:EGS (Protein N-term),Xlink:EGScleaved (K),Xlink:EGScleaved (Protein N-term),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term)
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
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
Overwrite tool specific checks.true,false
testfalse
Enables the test mode (needed for internal use only)true,false
LuciphorAdapter 
1.8.16