The invention provides a method of determining activity of a protease. The method can include the steps of (a) providing a protease substrate including a protein moiety attached to a nucleic acid moiety and a ligand moiety; (b) contacting the protease substrate with a protease under conditions wherein the protease catalyzes cleavage of the protein moiety, thereby producing a proteolytic product wherein the nucleic acid moiety is separated from at least a portion of the protein moiety and the ligand moiety; (c) contacting the proteolytic product with a receptor under conditions wherein the ligand moiety binds to the receptor to form a complex; (d) separating the complex from the nucleic acid moiety, thereby forming a separation product including the nucleic acid moiety; (e) contacting the separation product with a probe nucleic acid under conditions wherein the nucleic acid moiety hybridizes to a complementary sequence of the probe; and (f) detecting hybridization of the separation product to the probe, thereby determining activity of the protease.