Proteomics pp 115-136 | Cite as

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

  • Geoffrey G. Hesketh
  • Ji-Young Youn
  • Payman Samavarchi-Tehrani
  • Brian Raught
  • Anne-Claude GingrasEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1550)


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.

Key words

Mass spectrometry BioID Biotin Streptavidin FLAG tag Proximity labeling Affinity purification Proteomics Protein interactions Protein network Protein identification 



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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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Geoffrey G. Hesketh
    • 1
  • Ji-Young Youn
    • 1
  • Payman Samavarchi-Tehrani
    • 1
  • Brian Raught
    • 2
    • 3
  • Anne-Claude Gingras
    • 1
    • 4
    • 5
    Email author
  1. 1.Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
  2. 2.Princess Margaret Cancer Centre, Princess Margaret Research InstituteUniversity Health NetworkTorontoCanada
  3. 3.Department of Medical BiophysicsUniversity of TorontoTorontoCanada
  4. 4.Department of Molecular GeneticsUniversity of TorontoTorontoCanada
  5. 5.Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada

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