Identification of protease substrates by mass spectrometry approaches-2

Proteolysis is a major posttranslational modification of proteins with critical functional consequences to the protein, cell, and organism. The most effective way to monitor proteolytic events is to analyze the proteins directly. This chapter summarizes advantages and limitations of different mass spectrometry-based approaches for detection of proteolysis products. In general, liquid chromatography separation-based proteomics approaches are superior to 2D gel-based techniques and, in turn, quantitative proteomics have a significant advantage over label-free methods. Isotopic labeling of samples helps to identify substrates but fails to detect the exact cleavage site. Techniques that enrich for peptides containing the N-terminus of each protein provide a more relevant context for protease substrate discovery -they focus on the analysis of the neo-N-termini resulting from proteolysis. These techniques identify not only the substrates but also the prime side of the cleavage sites with a potential to extract further information of the protease sequence site specificity, thus setting the gold standard for the future of the degradomics field.