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
# 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