Parameter: aa_mass
Overview
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 Acid | Mass | Amino Acid | Mass | |
|---|---|---|---|---|
| A | 71.0371103 | N | 114.0429222 | |
| C | 103.0091803 | P | 97.0527595 | |
| D | 115.0269385 | Q | 128.0585714 | |
| E | 129.0425877 | R | 156.1011021 | |
| F | 147.0684087 | S | 87.0320244 | |
| G | 57.0214611 | T | 101.0476736 | |
| H | 137.0589059 | U | 150.9536303 | |
| I | 113.0840579 | V | 99.0684087 | |
| K | 128.0949557 | W | 186.0793065 | |
| L | 113.0840579 | Y | 163.0633228 | |
| M | 131.0404787 |
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.
Syntax
[Amino Acid] [Mass]
Version
2.0 - present
Example
To incorporate a synthetic amino acid with special character ‘B’ into the search space:
aa_mass = B 160.03064