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Molecular & Cellular Proteomics 1:3-10, 2002.
© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

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Perspective

Charting the Protein Complexome in Yeast by Mass Spectrometry^*

Raymond J. Deshaies^,,¶, Jae Hong Seol, W. Hayes McDonald^||, Greg Cope, Svetlana Lyapina, Andrej Shevchenko^**, Anna Shevchenko^**, Rati Verma^, and John R. Yates, III^||

Divison of Biology, California Institute of Technology, Pasadena, California 91125
Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125
^|| Department of Cell Biology, Scripps Research Institute, La Jolla, California 93037
^** Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany

It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin-dependent proteolysis, are carried out by sophisticated multisubunit protein machines that are dynamic in abundance, post-translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin-dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks.

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