Evolving advances of proximity labeling in capturing biomolecular interactions

Proximity labeling (PL), with its capability to resolve spatiotemporal dynamics of biomolecular interactions, has become a pivotal technology for interrogating protein–protein interaction networks, subcellular proteomics, and intercellular communication. This review focuses on the breakthrough developments in PL from 2023 to 2025, highlighting three major frontiers: (1) catalytic system innovation, including the development of new enzymes, cascade reactions, and environment-responsive labeling systems, which collectively lead to increased spatiotemporal resolution and enhanced in vivo applicability; (2) new strategies to address endogenous targets, facilitating interactome mapping in native tissues and live animals; and (3) determination of the labeling radius for different PL tools using super-resolution imaging or DNA nanostructures. We also briefly discuss the desired innovation in the next-generation PL research.