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

Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins

Susanne K Pedersen  1 , Jenny L Harry, Lucille Sebastian, Jasmine Baker, Mathew D Traini, John T McCarthy, Abi Manoharan, Marc R Wilkins, Andrew A Gooley, Pier Giorgio Righetti, Nicolle H Packer, Keith L Williams, Ben R Herbert
Affiliations

Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins

Susanne K Pedersen et al. J Proteome Res. 2003 May-Jun.

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.

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