Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

Nat Biotechnol. 2007 Jan;25(1):117-24. doi: 10.1038/nbt1270. Epub 2006 Dec 24.


We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about approximately 5,600 ( approximately 540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.

Publication types

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

MeSH terms

  • Algorithms*
  • Escherichia coli Proteins / analysis
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Bacterial / physiology
  • Mass Spectrometry / methods
  • Peptide Mapping / methods
  • Peptides / analysis
  • Peptides / chemistry
  • Protein Biosynthesis / physiology*
  • Proteome / analysis
  • Proteome / chemistry
  • Proteome / metabolism*
  • Sequence Analysis, Protein / methods*
  • Transcription, Genetic / physiology*


  • Escherichia coli Proteins
  • Peptides
  • Proteome