MS-GFDB Modification File Example

# This file is used to specify modifications
# # for comments
#
# Max Number of Modifications per peptide (default 2). If this value is large, the search takes long.
NumMods=2

# To input a modification, use the following command:
# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
#     - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
#     - Atom can be omitted. The sequence of atoms must be followed.
#     - Negative numbers are allowed.
#     - E.g. C2H2O1 (valid), H2C1O1 (invalid)
# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
#     - E.g. 15.994915
# Residues: affected amino acids (must be upper letters)
#     - Must be upper letters or *
#     - Use * if this modification is applicable to any residue.
#     - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.)
#     - E.g. NQ, *
# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
# Position: position in the peptide where the modification can be attached.
#     - One of the following five values should be used:
#     - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term)
#     - Case insensitive
#     - "-" can be omitted
#     - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
# Name: name of the modification
#     - E.g. Oxidation

C2H3N1O1,C,fix,any,Carbamidomethylation     # Fixed Carbamidomethyl C

# Variable Modifications (default: none)
O1,M,opt,any,Oxidation                # Oxidation M
#15.994915,M,opt,any,Oxidation            # Oxidation M (mass is used instead of CompositionStr)
#H-1N-1O1,NQ,opt,any,Deamidation        # Negative numbers are allowed.
#C2H3NO,*,opt,N-term,Carbamidomethylation    # Variable Carbamidomethyl N-term
#H-2O-1,E,opt,N-term,Pyro-glu            # Pyro-glu from E
#H-3N-1,Q,opt,N-term,Pyro-glu            # Pyro-glu from Q
#C2H2O,*,opt,Prot-N-term,Acetylation        # Acetylation Protein N-term
#C2H2O1,K,opt,any,Acetylation            # Acetylation K
#CH2,K,opt,any,Methylation            # Methylation K
#H3O4P,STY,opt,any,Phosphorylation        # Phosphorylation STY