protein, cleavage semi

# protein, cleavage semi ## Syntax This parameter is a text string that may be yes or no. ## Notes Introduced in version 2005.12.01. Default value is no 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. see also: protein, cleavage site | refine, cleavage semi X! TANDEM API description project