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Originally published In Press as doi:10.1074/mcp.T500013-MCP200 on November 4, 2005.
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Molecular & Cellular Proteomics 5:53-56, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)*

Emily I. Chen{ddagger},§, Johannes Hewel{ddagger},¶, Brunhilde Felding-Habermann|| and John R. Yates, III{ddagger}

From the Departments of {ddagger} Cell Biology and || Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037

In the past decade, shotgun proteomic analysis has been utilized extensively to answer complex biological questions. New challenges arise in large scale proteomic profiling when dealing with complex biological mixtures such as the mammalian cell lysate. In this study, we explored the approach of protein separation prior to the shotgun multidimensional protein identification technology (MudPIT) analysis. We fractionated the mammalian cancer cell lysate using the PF 2D ProteomeLab system and analyzed the distribution of molecular weight, isoelectric point, and cellular localization of the eluted proteins. As a result, we were able to reduce sample complexity by protein fractionation and increase the possibility of detecting proteins with lower abundance in the complex protein mixture.

To whom correspondence should be addressed: Dept. of Cell Biology, The Scripps Research Inst., 10550 N. Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-8876; Fax: 858-784-8883; E-mail: emilyc{at}scripps.edu


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