Unseen proteome: Mining below the tip of the Iceberg to find low abundance and membrane proteins

Susanne K. Pedersen, 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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

126 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)303-311
Number of pages9
JournalJournal of Proteome Research
Issue number3
Publication statusPublished - May 2003
Externally publishedYes


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