## Comet parameter: variable_mod01

- This parameter specifies the 1st of 9 variable modifications.
- There are 6 entries/settings 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. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
  - 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.
  - The fifth entry specifies the distance the modification is applied to from the respective protein terminus:
    - -1 = no distance contraint
    - 0 = only applies to terminal residue
    - 1 = only applies to terminal residue and next residue
    - 2 = only applies to terminal residue through next 2 residues
    - N = only applies to terminal residue through next N residues where N is a positive integer
  - The sixth entry specifies whichprotein terminus the distance constraint is applied to:
    - 0 = protein N-terminus
    - 1 = protein C-terminus
    - 2 = peptide N-terminus
    - 3 = peptide C-terminus
  - The seventh entry specifies whether peptides are must contain this modification
    - 0 = not forced to be present
    - 1 = modification is required
- In the output, this first modification is encoded with the character '*' in the peptide string.
- The default value is "0.0 null 0 4 -1 0" if this parameter is missing.

Example:
`variable_mod01 = 15.9949 M 0 3 -1 0 0`
`variable_mod01 = 79.966331 STY 0 3 -1 0 0` ... possible phosphorylation on any S, T, Y residue
`variable_mod01 = 79.966331 STY 0 3 -1 0 1` ... force peptide IDs to contain at least one phosphorylation mod
`variable_mod01 = 42.010565 nK 0 3 -1 0 0` ... acetylation mod to lysine and N-terminus of all peptides
`variable_mod01 = 15.994915 n 0 3 0 0 0` ... oxidation of protein's N-terminus
`variable_mod01 = 28.0 c 0 3 8 1 0` ... modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein
`variable_mod01 = -17.026549 Q 0 1 0 2` ... cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)
`variable_mod01 = -18.010565 E 0 1 0 2` ... cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)