In vivo-compatible proximity labeling technologies

Proximity labeling (PL) has emerged as a powerful technology for mapping subcellular compositions and molecular interactions. This approach employs promiscuous enzymes that generate reactive species to tag endogenous biomolecules, which are then identified by mass spectrometry or sequencing. However, conventional PL methods-such as peroxidases, biotin ligases, and photocatalytic systems-face significant limitations for in vivo applications, hindering their use in native biological contexts. In this review, we first summarize the application of peroxidases and biotin ligases in living animals, highlighting how they have provided insights into cell surface proteomes and cell type-specific secretion, despite their constraints. We then explore recent advances in in vivo-compatible PL technologies, including novel enzymes like tyrosinase, laccase, and lipoic acid ligase, as well as innovative photocatalytic strategies activated by near-infrared light, ultrasound, or bioluminescence. These emerging tools hold great potential to expand spatial multi-omics from cellular systems to living organisms.