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Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry

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Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1550))

Abstract

Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein–protein interactions, but the requirement to maintain protein–protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.

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Acknowledgment

We thank Wade H Dunham and Zhen-Yuan Lin for optimization of the FLAG protocol, all members of the Gingras and Raught laboratories for help in optimizing the BioID protocol and for helpful discussions, and Boris Dyakov and Cassandra Wong for comments on the manuscript. This work is funded by the Canadian Institutes of Health Research (Foundation grant FDN143301 to A.-C.G.; salary support to PST), the Natural Sciences and Engineering Research Council of Canada (Discovery grant to A.-C.G; salary support to JYY), and a Genome Canada Genome Innovation (GIN) network (through the Ontario Genomics Institute OGI-069 to A.-C.G.). Salary awards are from the Canada Research Chairs Program (ACG and BR) and a Basic Research Fellowship from Parkinson Canada (GGH).

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Authors and Affiliations

  1. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada

    Geoffrey G. Hesketh, Ji-Young Youn, Payman Samavarchi-Tehrani & Anne-Claude Gingras

  2. Princess Margaret Cancer Centre, Princess Margaret Research Institute, University Health Network, Toronto, Canada

    Brian Raught

  3. Department of Medical Biophysics, University of Toronto, Toronto, Canada

    Brian Raught

  4. Department of Molecular Genetics, University of Toronto, Toronto, Canada

    Anne-Claude Gingras

  5. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave., Rm 992A (9th floor), Toronto, ON, Canada, M5G 1X5

    Anne-Claude Gingras

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  1. Geoffrey G. Hesketh
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  2. Ji-Young Youn
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  3. Payman Samavarchi-Tehrani
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  4. Brian Raught
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  5. Anne-Claude Gingras
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Correspondence to Anne-Claude Gingras .

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Editors and Affiliations

  1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Lucio Comai

  2. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Jonathan E. Katz

  3. Stanford University, Palo Alto, California, USA

    Parag Mallick

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Hesketh, G.G., Youn, JY., Samavarchi-Tehrani, P., Raught, B., Gingras, AC. (2017). Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry. In: Comai, L., Katz, J., Mallick, P. (eds) Proteomics. Methods in Molecular Biology, vol 1550. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6747-6_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6747-6_10

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