The quantitative and condition-dependent Escherichia coli proteome

Nat Biotechnol. 2016 Jan;34(1):104-10. doi: 10.1038/nbt.3418. Epub 2015 Dec 7.


Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2,300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / metabolism*
  • Mass Spectrometry
  • Proteome*


  • Escherichia coli Proteins
  • Proteome