Described herein are methods and techniques to study the “degradome”. The degradome of a specific
protease is the complete product of the natural substrate
repertoire of that
enzyme in a
cell, tissue or
organism. The complete set of
proteases that are expressed at a particular moment or circumstance by a
cell, tissue or
organism produces the collective degradome. Included in the methods described herein are approaches that allow the direct identification and characterization of degradome peptides from approx. 400 to approx. 12,000 Da. The methods of the invention avoid the inherent problems of studying the peptidome by focusing on specific or unique proteolytic cleavages that occur as a result of endogenous
protease activity induced by specific diseases. Once characterized, the presence of, or change in level of, specific peptides of the degradome can be used, e.g., to identify specific peptides having elevated levels compared to a reference normal / or to correlate identified peptides with specific proteins and / or to identify
protein fragmentation patterns (e.g.,
peptide ladders) and the specific
protease(s) that brought them about and then correlate this information with the presence or absense of a specific
disease or condition. Thus, the methods of the invention can be used, for example, to identify new diagnostic markers and / or therapeutic targets, as specific clinical
diagnostic methods for individual patients and as methods of monitoring the progress of a therapeutic
regimen for the treatment of a patient.