Mass spectrometry-based proteomics strategies for protease cleavage site identification

Proteomics. 2012 Feb;12(4-5):516-29. doi: 10.1002/pmic.201100379. Epub 2012 Jan 19.


Protease-catalyzed hydrolysis of peptide bonds is one of the most pivotal post-translational modifications fulfilling manifold functions in the regulation of cellular processes. Therefore, dysregulation of proteolytic reactions plays a central role in many pathophysiological events. For this reason, understanding the molecular mechanisms in proteolytic reactions, in particular the knowledge of proteases involved in complex processes, expression levels and activity of protease and knowledge of the targeted substrates are an indispensable prerequisite for targeted drug development. The present review focuses on mass spectrometry-based proteomic methods for the analysis of protease cleavage sites, including the identification of the hydrolyzed bonds as well as of the surrounding sequence. Peptide- and protein-centric approaches and bioinformatic tools for experimental data interpretation will be presented and the major advantages and drawbacks of the different approaches will be addressed. The recent applications of these approaches for the analysis of biological function of different protease classes and potential future directions will be discussed.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Databases, Protein
  • Mass Spectrometry / methods
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism*
  • Proteins / metabolism*
  • Proteomics / methods*


  • Proteins
  • Peptide Hydrolases