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Originally published In Press as doi:10.1074/mcp.M200005-MCP200 on February 1, 2002.
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Molecular & Cellular Proteomics 1:204-212, 2002.
© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Deciphering Protein Complexes and Protein Interaction Networks by Tandem Affinity Purification and Mass Spectrometry

Analytical Perspective*

Anna Shevchenko{ddagger}, Daniel Schaft§, Assen Roguev§, W. W. M. Pim Pijnappel§, A. Francis Stewart§,¶ and Andrej Shevchenko{ddagger},||

{ddagger} Max Planck Institute of Molecular Cell Biology and Genetics (MPI CBG)
§ Genomics, Technische Universität Dresden, c/o MPI CBG, Pfotenhauerstrasse 108, 01307 Dresden, Germany

We employed a combination of tandem affinity purification and mass spectrometry for deciphering protein complexes and the protein interaction network in budding yeast. 53 genes were epitope-tagged, and their interaction partners were isolated by two-step immunoaffinity chromatography from whole cell lysates. 38 baits pulled down a total of 220 interaction partners, which are members of 19 functionally distinct protein complexes. We identified four proteins shared between complexes of different functionality thus charting segments of a protein interaction network. Concordance with the results of genome-wide two-hybrid screening was poor (14% of identified interactors overlapped) suggesting that the two approaches may provide complementary views on physical interactions within the proteome.

To whom correspondence may be addressed. E-mail: stewart{at}mpi-cbg.de.

|| To whom correspondence may be addressed. Tel.: 49-351-210-2615; Fax: 49-351-210-2000; E-mail: shevchenko{at}mpi-cbg.de.


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