# MS-GFDB Modification File Example

This mod file was used by MS-GFDB, an old application that is no longer under development.
It was supserseded by MS-GF+, which supports a modification file with additional features

- MS-GF+ Documentation home
- MS-GFDB help page

    # This file is used to specify modifications
    # Use # for comments, either at the start of a line or in the middle of line

    # Max Number of Dynamic (Variable) Modifications per peptide (default 3).
    # If this value is large, the search takes long.
    NumMods=3

    # 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 monoisotopic 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 are all valid
    # Name: name of the modification (Unimod PSI-MS name)
    # 	- E.g. Oxidation

    # Static (fixed) modifications:
    C2H3N1O1,C,fix,any,Carbamidomethylation     # Fixed Carbamidomethyl C

    # Variable Modifications (default: none)
    O1,M,opt,any,Oxidation                      # Oxidation M

    # Additional Modification Examples
    # C2H3N1O1,C,fix,any,Carbamidomethyl        # Fixed Carbamidomethyl C (alkylation)
    # 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,Deamidated            # Negative numbers are allowed.
    # CH2,K,opt,any,Methyl                      # Methylation K
    # C2H2O1,K,opt,any,Acetyl                   # Acetylation K
    # HO3P,STY,opt,any,Phospho                  # Phosphorylation STY
    # C2H3NO,*,opt,N-term,Carbamidomethyl       # Variable Carbamidomethyl N-term
    # H-2O-1,E,opt,N-term,Glu->pyro-Glu         # Pyro-glu from E
    # H-3N-1,Q,opt,N-term,Gln->pyro-Glu         # Pyro-glu from Q
    # C2H2O,*,opt,Prot-N-term,Acetyl            # Acetylation Protein N-term