title: Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins.
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.
authors.affiliation: Proteome Systems, 35 Waterloo Rd, North Ryde, Sydney, NSW 2113, Australia.
authors.forename: Susanne K
authors.initials: SK
authors.lastname: Pedersen
authors.forename: Jenny L
authors.initials: JL
authors.lastname: Harry
authors.forename: Lucille
authors.initials: L
authors.lastname: Sebastian
authors.forename: Jasmine
authors.initials: J
authors.lastname: Baker
authors.forename: Mathew D
authors.initials: MD
authors.lastname: Traini
authors.forename: John T
authors.initials: JT
authors.lastname: McCarthy
authors.forename: Abi
authors.initials: A
authors.lastname: Manoharan
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Gooley
authors.forename: Pier Giorgio
authors.initials: PG
authors.lastname: Righetti
authors.forename: Nicolle H
authors.initials: NH
authors.lastname: Packer
authors.forename: Keith L
authors.initials: KL
authors.lastname: Williams
authors.forename: Ben R
authors.initials: BR
authors.lastname: Herbert
mesh_terms: D000595:Amino Acid Sequence; D042966:Cytochrome-B(5) Reductase / Q000235:genetics; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000235:genetics* / Q000502:physiology; D008969:Molecular Sequence Data; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000502:physiology
chemical_list: D008565:Membrane Proteins; D042966:Cytochrome-B(5) Reductase