Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry

Nat Protoc. 2011 Jan;6(1):111-20. doi: 10.1038/nprot.2010.178. Epub 2011 Jan 6.


To link cleaved substrates in complex systems with a specific protease, the protease active site specificity is required. Proteomic identification of cleavage sites (PICS) simultaneously determines both the prime- and non-prime-side specificities of individual proteases through identification of hundreds of individual cleavage sequences from biologically relevant, proteome-derived peptide libraries. PICS also identifies subsite cooperativity. To generate PICS peptide libraries, cellular proteomes are digested with a specific protease such as trypsin. Following protease inactivation, primary amines are protected. After incubation with a test protease, each prime-side cleavage fragment has a free newly formed N-terminus, which is biotinylated for affinity isolation and identification by liquid chromatography-tandem mass spectrometry. The corresponding non-prime sequences are derived bioinformatically. The step-by-step protocol also presents a web service for PICS data analysis, as well as introducing and validating PICS peptide libraries made from Escherichia coli.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Chromatography, Liquid / methods
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Internet
  • Peptide Hydrolases / chemistry*
  • Peptide Library*
  • Proteome*
  • Sequence Analysis, Protein
  • Software
  • Substrate Specificity
  • Tandem Mass Spectrometry / methods*


  • Peptide Library
  • Proteome
  • Peptide Hydrolases