Patent ID: 7618788

Claim:
A method for achieving high sensitivity detection and/or high accuracy quantitation of a plurality of target proteins in a biological sample, at least one of which comprises an expression product of an alternative splicing form of a single DNA, the method comprising the steps of: (1) fragmenting proteins in the sample using a predetermined denaturation and proteolytic protocol to generate a solution of polypeptide analytes comprising sequences comprising peptide epitope tags (PETs) unambiguously indicative of the presence in the sample of the target proteins from which they are derived, at least one PET being unambiguously indicative of the presence in the sample of the alternative splicing form protein from which it is derived and comprising an amino acid sequence encoded by an RNA spanning a splice junction; (2) contacting said solution with a plurality of capture agents specific for respective said PETs and immobilized on a solid support in an addressable array, at least one of said capture agents being specific for amino acids spanning the splice junction encoded by the RNA, to yield captured polypeptide analytes bound by interaction between respective capture agents and said PETs presented by respective said polypeptide analytes; and, (3) detecting the presence and amounts or absence of said target proteins in the sample, including at least said protein expression product of an alternative splicing form, by detecting the presence and amounts or absence of said captured polypeptide analytes, including said at least one polypeptide analyte comprising an amino acid sequence encoded by an RNA spanning a splice junction, using secondary capture agents specific for sites separate from said PETs on the captured polypeptide analytes and labeled with a detectable moiety.