protein, cleavage semi

Syntax

This parameter is a text string that may be yes or no.

Notes

1. Introduced in version 2005.12.01.
2. Default value is no
3. The value of this parameter is only used in the first round of identification: to apply this semi cleavage to refinement rounds, use the refine, cleavage semi parameter.

Description

In real experiments, there are often contaminating proteolytic enzymes which will act on proteins in a difficult to predict manner. Therefore, the idea of a "semi-tryptic" digest was developed to attempt to compensate for this additional cleavage activity. This cleavage type assumes that one of the cleavage sites is tryptic ([KR]|{P}), but the other site may be at any residue. For example, if an expected tryptic peptide has a sequence of TFGQVVAR, then the semi-tryptic peptides associated with this sequence would be:

TFGQVVAR
 FGQVVAR
  GQVVAR
   QVVAR
    VVAR
     VAR
      AR
TFGQVVA
TFGQVV
TFGQV
TFGQ
TFG
TF

Tandem has broadened this concept to include any cleavage site specification, except for cleavage at any site ([X]|[X]), which doesn't require any additional type of cleavage.