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Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry - Analytical perspective

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Shevchenko,  Anna
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Schaft,  D.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Roguev,  A.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Pijnappel,  W. W. M. P.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Stewart,  A. F.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Shevchenko,  Andrej
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Shevchenko, A., Schaft, D., Roguev, A., Pijnappel, W. W. M. P., Stewart, A. F., & Shevchenko, A. (2002). Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry - Analytical perspective. Molecular & Cellular Proteomics, 1(3), 204-212.


Cite as: https://hdl.handle.net/21.11116/0000-0001-1368-5
Abstract
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.