Parameter: fixed_modification


Specifies a mass adjustment to be applied to all indicated amino acids prior to spectral analysis. Amino acids are identified by their single letter designation. N-terminal and C-terminal fixed modifications are designated by n and c, respectively. The relative mass difference, positive or negative, is listed after the amino acid, separated by a space. If multiple fixed modification masses are desired, use multiple fixed_modification declarations.

NOTE: When the mass value of fixed_modification is zero, the parameter is ignored. Some configuration files may have the value set to zero, simply to have a fixed_modification placeholder in the file.


[Amino Acid] [Mass]


1.0 - present


To indicate alkylation of cysteine using iodoacetamide:

fixed_modification = C 57.02146