Parameter: enzyme

Overview

An enzyme string code is used to define amino acid cut sites when parsing protein sequences. Following the code, a separate label can be used to name the enzyme used.

Rules

The rules for peptide parsing are similar to other database search engines such as X!Tandem.

  1. Cleavage amino acids are specified in square braces: []
  2. A vertical line, |, indicates N- or C-terminal to the residue.
  3. Exception amino acids are specified in french braces: {}

After specifying the enzyme cleavage rules, the enzyme can be labeled.

Syntax

[Text] [Text]

Version

1.0 - present

Examples

Trypsin rule with cleavage after K or R, except when followed by P:

enzyme = [KR]|{P} Trypsin

Trypsin rule with cleavage after K or R, ignoring any restrictions:

enzyme = [KR]| TrypsinP

GluC rule with cleavage after D or E, except when followed by P:

enzyme = [DE]|{P} GluC

LysN rule with cleavage before K:

enzyme = |[K] LysN