Effects of modified digestion schemes on the identification of proteins from complex mixtures

J Proteome Res. 2006 Mar;5(3):695-700. doi: 10.1021/pr050315j.

Abstract

In shotgun proteomics, a complex protein mixture is digested to peptides, separated, and identified by microcapillary liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this technology, complete protein digestion is often assumed. We show that, to the contrary, modifications to a standard digestion protocol demonstrate large, reproducible improvements in protein identification, a result consistent with digestion being a limiting factor in the efficiency of protein identification.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Complex Mixtures / analysis*
  • Complex Mixtures / chemistry
  • Escherichia coli Proteins / analysis
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Mass Spectrometry
  • Peptide Hydrolases*
  • Proteins / analysis*
  • Proteins / chemistry
  • Proteins / metabolism*
  • Proteomics

Substances

  • Complex Mixtures
  • Escherichia coli Proteins
  • Proteins
  • Peptide Hydrolases