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Shotgun Proteomics pp 265–278Cite as

Application of Shotgun Proteomics for Discovery-Driven Protein–Protein Interaction

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1156))

Abstract

Affinity purification of protein complexes and identification of co-purified proteins by mass spectrometry is a powerful method to discover novel protein–protein interactions. Application of this method to the study of biological systems often requires the ability to process a large number of samples. Hence, there is great need to generate proteomic workflows compatible with large-scale studies. The major goal of this protocol is to present a fast, reliable, and scalable method to characterize protein complexes by mass spectrometry to overcome the limitations of conventional geLC-MS/MS or MudPIT protocols. This method was successfully employed for the discovery and characterization of novel protein complexes in cultured yeast, mammalian cells, and mice.

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Acknowledgements

Z.M. was supported by the Sixth Framework Programme Integrated Project Mitocheck (LSHG-CT-2004-503464) and the Max Planck Society. M.J. was financially supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant no. 483642/2012-6 MCT/CNPq—Universal. The authors acknowledge Frank Buchholz, Andrej Shevchenko, Anthony Hyman, Mirko Theis, and Yusuke Toyoda for previous collaborations and fruitful discussion.

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Authors and Affiliations

  1. Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-909, Brazil

    Livia Goto-Silva, Jimmy Rodriguez Murillo & Magno Junqueira

  2. Department of Translational Oncology, National Center for Tumor Diseases, Heidelberg, Germany

    Mikolaj Slabicki

  3. Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    Zoltan Maliga

Authors
  1. Livia Goto-Silva
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  2. Zoltan Maliga
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  3. Mikolaj Slabicki
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  4. Jimmy Rodriguez Murillo
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  5. Magno Junqueira
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Corresponding author

Correspondence to Magno Junqueira .

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Editors and Affiliations

  1. Ludwig-Maximilians-University, Munich, Germany

    Daniel Martins-de-Souza

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Goto-Silva, L., Maliga, Z., Slabicki, M., Murillo, J.R., Junqueira, M. (2014). Application of Shotgun Proteomics for Discovery-Driven Protein–Protein Interaction. In: Martins-de-Souza, D. (eds) Shotgun Proteomics. Methods in Molecular Biology, vol 1156. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0685-7_18

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  • DOI: https://doi.org/10.1007/978-1-4939-0685-7_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0684-0

  • Online ISBN: 978-1-4939-0685-7

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