Comet

Comet parameter: variable_mod2

• This parameter specifies the 2nd of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • The first entry is a decimal value specifying the modification mass difference.
  • The second entry is the residue(s) that the modifications are possibly applied to. If more than a single residue is modified by the same mass difference, list them all as a string.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '#' in the peptide string.

Example:
variable_mod2 = 15.9949 M 0 3
variable_mod2 = 79.966331 STY 0 3