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Comet parameter: variable_mod01 through variable_mod15

There are 8 fields/settings that are associated with these parameters:

Example:

variable_mod01 = 15.9949 M 0 3 -1 0 0 0.0
variable_mod02 = 79.966331 STY 0 3 -1 0 0 97.976896  ... possible phosphorylation on any S, T, Y residue with a neutral loss of 98
variable_mod02 = 79.966331 STY 0 3 -1 0 1 0.0        ... force peptide IDs to contain at least one phosphorylation mod
variable_mod01 = 42.010565 nK 0 3 -1 0 0 0.0         ... acetylation mod to lysine and N-terminus of all peptides
variable_mod01 = 15.994915 n 0 3 0 0 0 0.0           ... oxidation of protein N-terminus
variable_mod01 = 28.0 c 0 3 8 1 0 0.0                ... modification applied to C-terminus as long as the C-term residue is one of last 9 residues in protein
variable_mod03 = -17.026549 Q 0 1 0 2 0 0.0          ... cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)
variable_mod04 = -18.010565 E 0 1 0 2 0 0.0          ... cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)

Here is a binary modification search example of triple SILAC plus acetylation of lysine. The SILAC modifications are “R +6 and K +4” (medium) and “R +10 and K +8” (heavy). In conjunction with K +42 acetylation, the binary modification sets would be “R +6, K +4, K +4+42” for SILAC medium (binary group 1)> and “R +10, K +8, K +8+42” for SILAC heavy (binary group 2). Mass values are listed with no precision for clarity; definitely use precise modification masses in practice.

variable_mod01 = 42.0 K 0 3 -1 0 0 0.0
variable_mod02 =  6.0 R 1 3 -1 0 0 0.0
variable_mod03 =  4.0 K 1 3 -1 0 0 0.0
variable_mod04 = 46.0 K 1 3 -1 0 0 0.0
variable_mod05 = 10.0 R 2 3 -1 0 0 0.0
variable_mod06 =  8.0 K 2 3 -1 0 0 0.0
variable_mod07 = 50.0 K 2 3 -1 0 0 0.0
variable_mod08 =  0.0 X 0 3 -1 0 0 0.0
variable_mod09 =  0.0 X 0 3 -1 0 0 0.0
variable_mod10 =  0.0 X 0 3 -1 0 0 0.0
variable_mod11 =  0.0 X 0 3 -1 0 0 0.0
variable_mod12 =  0.0 X 0 3 -1 0 0 0.0
variable_mod13 =  0.0 X 0 3 -1 0 0 0.0
variable_mod14 =  0.0 X 0 3 -1 0 0 0.0
variable_mod15 =  0.0 X 0 3 -1 0 0 0.0