Parameter: aa_mass


Changes the default mass of the specified amino acid. Any other modification masses specified by fixed_modification and modification are subsequently applied to the mass value specified by this parameter.

NOTE: This parameter can be specified any number of times as necessary to change multiple amino acid mass designations.

By default, Kojak uses the following amino acid mass values:

Amino AcidMass   Amino AcidMass
A71.0371103   N114.0429222
C103.0091803   P97.0527595
D115.0269385   Q128.0585714
E129.0425877   R156.1011021
F147.0684087   S87.0320244
G57.0214611   T101.0476736
H137.0589059   U150.9536303
I113.0840579   V99.0684087
K128.0949557   W186.0793065
L113.0840579   Y163.0633228
SPECIAL AMINO ACIDS: Letters not assigned to an amino acid (e.g. 'O' or 'J') can be assigned a user-defined amino acid mass specific to the experiment. For example, synthetic amino acids integrated into proteins can be identified in the search space by providing the novel character in the FASTA database and specifying this parameter.


[Amino Acid] [Mass]


2.0 - present


To incorporate a synthetic amino acid with special character ‘B’ into the search space:

aa_mass = B 160.03064