Patent ID: 8097425

Claim:
A method for characterizing protein in a sample that comprises a mixture of proteins, said method comprising: (a) contacting protein in said sample with a protein cleaving agent, wherein said protein cleaving agent cleaves at a cleavage site to produce a set of polypeptide fragments comprising a C-terminal amino acid at said cleavage site; and wherein said polypeptide fragments comprise internal small epitopes; (b) fractionating said polypeptide fragments into fractions with a plurality of first protein-binding molecules wherein said first protein-binding molecules bind to small epitopes comprising said C-terminal amino acid; (c) contacting polypeptide fragments in at least one of said fractions with a plurality of second protein-binding molecules wherein said second protein-binding molecules bind to said internal epitopes; and (d) detecting protein bound to said second protein-binding molecules.