This tab offers the analysis of cleavage preferences, comparison how different digestion conditions affect them, or to compare different proteases. It is especially useful for non- or semi-specific proteases but those using specific enzymes might find surprising features when they run their search in a non-specific mode and then parse through a DigDig.
The cleavage preferences are calculated based on the identified peptides and the data are normalized according to Keil using the following equation:
CSnorm = (Σ(P1AA)/Σ(P1tot))/(Σ(seqAA)/Σ(seqtot))
CSnorm - normalized cleavage specificity P1AA - number of occurrences of an individual amino acid in P1 position P1tot - total number of identified cleavage sites seqAA - number of occurrences of an individual amino acid in all protein substrate sequences seqtot - is the total number of residues in all protein substrate sequences For details see e.g. Specificity of Proteolysis or Kadek et al. 2014.
Cleavage after (P-site) and before (P'-site) are shown. Position can be adjusted but primarily the P1-P1' pairs (the cleavage site) are shown.
In contrast to Cleavage map and Redundancy plot the preferences can be extracted for one protein, selected proteins or all identified proteins.