Advances in degradomics technologies to assess proteolytic cleavage events

Proteases contribute to essential cellular processes through catalyzing proteolysis, resulting in peptide bond hydrolysis and the generation of novel polypeptide species. Identification of proteolytic cleavage events is crucial for discerning proteolytic networks in biological systems, including the contribution of individual proteases to specific disease states. As such, various mass spectrometry-based workflows have been exploited for the sensitive identification of cleavage sites. To date, a range of enrichment strategies have been developed, focusing on increasing sensitivity, ease, and throughput for protease substrate discovery. Recent advances in mass spectrometry instrumentation have also permitted enrichment-free workflows for degradomics analysis, providing simultaneous and systematic assessment of the proteome and degradome. In this review, we discuss current technologies for the enrichment and identification of both N- and C-termini, as well as their application to profile protease specificity and decipher individual substrate repertoires in diverse biological conditions.