Identification of Protease Substrates by Mass Spectrometry Approaches-1

Abstract

The identification of protease substrates is a challenging task, especially in vivo. Bioinformatics-based prediction of cleavage sites and determination of protease preferences on synthetic substrates are important techniques in predicting natural protease substrates. These techniques tell us what a protease can do, but to enable a clear understanding of what a protease actually does in vivo, different approaches are required. The introduction of diverse proteomics-based methods is now leading toward the identification of natural protease substrates. These methods can provide a picture of the general protein cleavage pattern at a given time, that is, the proteolytic signature, in a complex biological sample. While gel-based (two-dimensional polyacrylamide gel electrophoresis and two-dimensional differential gel electrophoresis) methods have been used for a long time, there are some disadvantages with these methods. The introduction of protein- and peptide-labeling strategies, such as isotope-coded affinity tags, isobaric tag for relative and absolute quantification, and NHS-SS-biotin, together with enrichment procedures, such as combined fractional diagonal chromatography, have opened up new possibilities for the identification and relative quantification of protease cleavage in vivo, and thus have set the scene for a new direction in the study of proteolytic pathways. We give an overview of the different gel-based and solution-based strategies, provide examples of substrate identification, and also discuss the benefits and the pitfalls of the existing strategies.