Unseen Proteome: Mining Below the Tip of the Iceberg to Find Low Abundance and Membrane Proteins

J Proteome Res. May-Jun 2003;2(3):303-11. doi: 10.1021/pr025588i.

Abstract

Abundant and hydrophilic nonmembrane proteins with isoelectric points below pH 8 are the predominant proteins identified in most proteomics projects. In yeast, however, low-abundance proteins make up 80% of the predicted proteome, approximately 50% have pl's above pH 8 and 30% of the yeast ORFs are predicted to encode membrane proteins with at least 1 trans-membrane span. By applying highly solubilizing reagents and isoelectric fractionation to a membrane fraction of yeast we have a purified and identified 780 protein isoforms, representing 323 gene products, including 28% low abundance proteins and 49% membrane or membrane associated proteins. More importantly, considering the frequency and importance of co- and post-translational modifications, the separation of protein isoforms is essential and two-dimensional electrophoresis remains the only technique which offers sufficient resolution to address this at a proteomic level.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cytochrome-B(5) Reductase / genetics
  • Electrophoresis, Gel, Two-Dimensional / methods
  • Hydrophobic and Hydrophilic Interactions
  • Membrane Proteins / genetics*
  • Membrane Proteins / physiology
  • Molecular Sequence Data
  • Proteomics / methods*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / physiology

Substances

  • Membrane Proteins
  • Cytochrome-B(5) Reductase