# MS-GFDB Modification File Example

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# 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