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Mapping Protein–Protein Interactions by Quantitative Proteomics

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LC-MS/MS in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 658))

Abstract

Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein–protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.

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Acknowledgments

We thank all CEBI group members for helpful discussions and support. The research leading to these results has received funding from the European Commission’s 7th Framework Programme (grant agreement HEALTH-F4-2008-201648/PROSPECTS), the Danish Natural Science Research Council, the Danish Medical Research Council, and the Lundbeck Foundation. JD was supported by the European Molecular Biology Organization and by the Excellence Initiative of the German Federal and State Governments.

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Authors and Affiliations

  1. Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

    Joern Dengjel, Irina Kratchmarova & Blagoy Blagoev

  2. Freiburg Institute for Advanced Studies and Zentrum für Biosystemanalyse, University of Freiburg, Freiburg, Germany

    Joern Dengjel

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  1. Joern Dengjel
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  2. Irina Kratchmarova
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  3. Blagoy Blagoev
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Editors and Affiliations

  1. Bart’s and the London School of Medicine, Institute of Cancer, Queen Mary, Universtiy of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom

    Pedro R. Cutillas

  2. , EGA Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, United Kingdom

    John F. Timms

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Dengjel, J., Kratchmarova, I., Blagoev, B. (2010). Mapping Protein–Protein Interactions by Quantitative Proteomics. In: Cutillas, P., Timms, J. (eds) LC-MS/MS in Proteomics. Methods in Molecular Biology, vol 658. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-780-8_16

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  • DOI: https://doi.org/10.1007/978-1-60761-780-8_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-779-2

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