Predicting where a peptidase will cleave in a native protein is difficult. Where cleavage does occur in a protein is due to a combination of the preference of the peptidase and the availability of bonds in the substrate. Although the preference of the peptidase can be quite simple, for example trypsin (MEROPS identifier S01.151) cleaves lysyl and arginyl bonds (15) and caspase-3 (C14.003) cleaves only aspartyl bonds (16) , very often peptidase preference is cryptic. It is relatively easy to predict trypsin cleavages in a denatured protein, but few lysyl and arginyl bonds will be cleaved in a native protein. This has proved useful for researchers wishing to separate structural domains in a multidomain protein using limited proteolysis (17) . It is not possible to predict where in a peptide cathepsin B (C01.060) will cleave, for example, despite its known preferences for a hydrophobic residue in the S2 pocket and arginine in S1 (18) .