scoring, maximum missed cleavage sites
This value is a positive integer represented as a character string.
When a cleavage reagent (either chemical or enzymatic) is used to cleave the peptide backbone of a protein to produce peptides, different sites along the backbone will have different reaction rates and kinetics. Therefore, there may be some sites that should be cleaved by the reagent that are not completely cleaved during the course of the experiment. The value of this parameter represents the maximum number of missed cleavage sites allowed within a peptide. For a specific, aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate.
The value chosen for this parameter affects the overall speed of the calculation. The number of peptides considered for a particular protein sequence is linearly proportional to the parameter value, so the amount of time necessary for the calculation will vary roughly linearly with the value chosen. In practice, TANDEM performs somewhat better than linear when doing this type of calculation.
see also: protein, cleavage site
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