# Known modification file.
#
# Each line has format:
#    ID, short name, long name, modified groups, affected residues, molecule change, mass change  (optional)
#
# ID          : the name a user used to turn on/off the PTM in the program parameter file.
# short name  : X (short name) will be used to represent the modified residue.
# long name   : Both short name and long name will be used to parse a string to a modified residue.
# modified groups : must be one of n--, -r-, --c, nr-, -rc
#     where n and c can be upper case letters too, indicating protein n term and c term
#     nr- and -rc indicate that the modification will occupy both the terminus and the R group.
# affected residues : the affected residues, * means every residue
# molecule change   : when the molecule change is non empty, delta mass will be calculated from the molecule change and
#                     the mass change is optional and used for error checking purpose only.
# mass change : to override the calculation of the mass from molecule change, set molecule change column empty.

Acetyl (K), Acetyl, Acetyl, -r-, K, +C2H2O,
Acetyl (N-term), Acetyl, Acetyl, n--, *, +C2H2O,
Amidated (C-term), Amidated, Amidation, --c, *, -O+NH, -1
Ammonia-loss (N-term C), Ammonia-loss, Ammonia-loss, nr-, C, -NH3, -17.026548
Biotin (K), Biotin, Biotinylation, -r-, K, +H14C10N2O2S, 226.07759
Biotin (N-term), Biotin, Biotinylation, n--, *, +H14C10N2O2S, 226.07759
Carbamidomethyl (C), Cam, Carbamidomethyl, -r-, C, +H3C2NO,
Carbamyl (K), Carbamyl, Carbamylation, -r-, K, +HCNO, 43.005814
Carbamyl (N-term), Carbamyl, Carbamylation, n--, *, +HCNO, 43.005814
Carboxymethyl (C), Carboxymethyl, Carboxymethyl, -r-, C, +C2H2O2, +58
Deamidated (NQ), Deamidated, Deamindation, -r-, NQ, -HN+O, 0.984016
Dehydrated (N-term C), Dehydrated, Dehydration, nr-, C, -H2O, -18.010565
Dioxidation (M), Dioxidation, Dioxidation, -r-, M, +O2, +31.989828
Methyl (C-term), Methyl, Methylation, --c, *, +H2C, 14.01565
Methyl (DE), Methyl, Methylation, -r-, DE, +H2C, 14.01565
Oxidation (M), O, Oxidation, -r-, M, +O,
Oxidation (HW), O, Oxidation, -r-, HW, +O, +16
Phospho (ST), Phospho, Phosphorylation, -r-, ST, +HO3P, 79.96633
Phospho (Y), Phospho, Phosphorylation, -r-, Y, +HO3P, 79.96633
Pyro-carbamidomethyl (N-term C), PyroCam, Pyro-carbamidomethyl, nr-, C, +C2O,
Pyro-Glu (E), Pyro-Glu, Glu->pyro-Glu, nr-, E, -H2O,
Pyro-Glu (Q), Pyro-Glu, Gln->pyro-Glu, nr-, Q, -NH3,
Sodium (C-term), Sodium, Sodium, --c, *, +Na-H, +21.981943
Sodium (DE), Sodium, Sodium, -r-, DE, +Na-H, +21.981943
Sulfo (STY), Sulfo, O-Sulfonation, -r-, STY, +O3S, 79.95682
Trimethyl (RK), Trimethyl, tri-Methylation, -r-, RK, +H6C3, 42.04695

# Acetyl (Protein N-term), Acetyl, Acetyl, N--, *, +C2H2O, +42
# Amidated (Protein C-term), Amidated, Amidation, --C, *, -O+NH, -1
