Nature Biotechnology
19, 242 - 247 (2001)
doi:10.1038/85686
Large-scale analysis of the yeast proteome by multidimensional protein identification technologyMichael P. Washburn1, 3, Dirk Wolters1, 3
& John R. Yates III1, 21
Syngenta Agricultural Discovery Institute, 3115 Merryfield Row, Suite 100, San Diego, CA 92121. 2
Department of Cell Biology SR11, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, CA 92037. 3
These authors contributed equally to this work.
Correspondence should be addressed to John R. Yates III jyates@scripps.eduWe describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology (MudPIT). MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date. A total of 1,484 proteins were detected and identified. Categorization of these hits demonstrated the ability of this technology to detect and identify proteins rarely seen in proteome analysis, including low-abundance proteins like transcription factors and protein kinases. Furthermore, we identified 131 proteins with three or more predicted transmembrane domains, which allowed us to map the soluble domains of many of the integral membrane proteins. MudPIT is useful for proteome analysis and may be specifically applied to integral membrane proteins to obtain detailed biochemical information on this unwieldy class of proteins.
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