Bead-based assays for protein analysis

A method for characterizing a proteolytic cleavage status of a naturally occurring protein in a biological material, the method comprising the steps of:

• obtaining a sample produced by digesting a biological material using an external protease, the sample containing a first peptide and a second peptide, the first and the second peptides being distinct fragments of a naturally occurring protein, the first peptide containing both an N-terminus and a C-terminus cleaved by an endogenous protease, the second peptide containing both an N-terminus and a C-terminus cleaved by the external protease,
• providing a reactive site, the reactive site comprising a bead and a capture agent associated with the bead,
• causing the first and the second peptides to specifically bind to the same reactive site,
• individually analyzing the reactive site to obtain a mass spectrum that contains a signal from the first peptide and a signal from the second peptide,
• detecting relative abundances of the first peptide and the second peptide by analyzing the signal from the first peptide and the signal from the second peptide, and
• correlating the relative abundances of the first peptide and the second peptide with a proteolytic cleavage status of the naturally occurring protein in the biological material.