Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared

The characterization of protein-protein interactions (PPIs) is of high value for understanding protein function. Two stra-tegies are popular for identification of PPIs direct from the cellular environment: affinity capture (pulldown) isolates the protein of interest with an immobilized matrix that specifically captures the target and potential partners, whereas in BioID, genetic fusion of biotin ligase facilitates proximity bio-tinylation, and labeled proteins are isolated with streptavidin. Whilst both methods provide valuable insights, they can reveal distinct PPIs, but the basis for these differences is less obvious. Here, we compare both methods using four different trypanosome proteins as baits: poly(A)-binding proteins PABP1 and PABP2, mRNA export receptor MEX67, and the nucleoporin NUP158. With BioID, we found that the popula-tion of candidate interacting proteins decreases with more confined bait protein localization, but the candidate population is less variable with affinity capture. BioID returned more likely false positives, in particular for proteins with less confined localization, and identified low molecular weight proteins less efficiently. Surprisingly, BioID for MEX67 identified exclu-sively proteins lining the inner channel of the nuclear pore complex (NPC), consistent with the function of MEX67, whereas the entire NPC was isolated by pulldown. Similarly, for NUP158, BioID returned surprisingly few PPIs within NPC outer rings that were by contrast detected with pulldown but instead returned a larger cohort of nuclear proteins. These rather significant differences highlight a clear issue with reli-ance on a single method to identify PPIs and suggest that BioID and affinity capture are complementary rather than alternative approaches.

Automated summary

The characterization of protein-protein interactions (PPIs) is important for understanding protein function. Two popular strategies, affinity capture and BioID, are used to identify PPIs in the cellular environment. A comparison of these methods using different trypanosome proteins as baits showed that BioID had fewer candidate interacting proteins with more confined bait protein localization, produced more false positives, and was less efficient in identifying low molecular weight proteins. These differences indicate the importance of using multiple methods to identify PPIs and suggest that BioID and affinity capture are complementary approaches.