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Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA)

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Kinase Signaling Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1636))

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Abstract

A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92–105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.

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Acknowledgment

This work was supported by Cancer Research UK grant numbers C107/A12057, C107/A10433, and C107/A16512. Faraz Mardakheh is supported by a Medical Research Council Career Development Award (grant number MR/P009417/1).

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Authors and Affiliations

  1. Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK

    Faraz K. Mardakheh

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  1. Faraz K. Mardakheh
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Correspondence to Faraz K. Mardakheh .

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Editors and Affiliations

  1. Division of Medical Oncology, University of Colorado, Aurora, Colorado, USA

    Aik-Choon Tan

  2. Protein Networks Laboratory, Institute of Cancer Research, London, United Kingdom

    Paul H. Huang

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Mardakheh, F.K. (2017). Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA). In: Tan, AC., Huang, P. (eds) Kinase Signaling Networks. Methods in Molecular Biology, vol 1636. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7154-1_22

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  • DOI: https://doi.org/10.1007/978-1-4939-7154-1_22

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7152-7

  • Online ISBN: 978-1-4939-7154-1

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