Proteomic discovery of protease substrates

Curr Opin Chem Biol. 2007 Feb;11(1):36-45. doi: 10.1016/j.cbpa.2006.11.037. Epub 2006 Dec 27.


Elucidation of in vivo substrate degradomes of a protease is a daunting endeavor because of the large number of proteins in a proteome and often minute and transient amounts of key substrates. Proteomic substrate screens for proteases are currently experiencing impressive progress. Mass spectrometry-based global proteome analysis, interfaced with liquid-chromatography and together with stable isotope labeling strategies, has provided increased coverage and sensitivity for quantitative proteomics. ICAT and iTRAQ labeling have been used to identify a plethora of new matrix metalloproteinase substrates. Emerging techniques focus on the quantitative analysis of proteolytically generated neo amino-termini, which we call terminopes, on a system-wide basis. In vivo SILAC pulse-chase experiments have also enabled the study of individual protein turnover and global proteome dynamics in cells and whole organisms. Together with activity-based probes for the profiling of functional proteases, there is now in place an array of complementary technologies to dissect the 'protease web' and its distortion in pathology.

Publication types

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

MeSH terms

  • Chromatography, Liquid / methods
  • Indicators and Reagents
  • Isotope Labeling*
  • Models, Biological
  • Peptide Hydrolases / chemistry
  • Peptide Hydrolases / genetics
  • Peptide Hydrolases / metabolism*
  • Proteomics / methods*
  • Proteomics / trends
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
  • Substrate Specificity


  • Indicators and Reagents
  • Peptide Hydrolases