Comet parameter: variable_mod01

  • This parameter specifies the 1st of 9 variable modifications.
  • There are 7 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).
      • 0 = variable modification analyzes all permutations of modified and unmodified residues.
      • 1 = 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 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 which 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 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 long as the C-term residue is one of last 9 residues in protein
variable_mod01 = -17.026549 Q 0 1 0 2 0     ... cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)
variable_mod01 = -18.010565 E 0 1 0 2 0     ... cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)