Locating peptides generated by limited proteolysis in known protein sequences by means of computer search

A computational method is presented for locating peptides on known protein sequences using their molecular weights (estimated by SDS polyacrylamide gel electrophoresis) and their composition (obtained by amino acid analysis from eluted gel bands). The technique is easy and rapid, and appears particularly valuable if recoveries of peptides are low, or if they are heterogeneous due to secondary proteolytic degradation. An analysis of limited proteolysis of maltoporin (Schenkman, S. et al. [1984] J. Biol. Chem. 259, 7570-7576) is used to illustrate applicability and reliability of the method, which can also be applied to confirm gene-derived sequences.