Proximity labeling: spatially resolved proteomic mapping for neurobiology

•Proximity labeling enables proteomic interrogation of the molecular components of subcellular regions as well as protein interaction networks.•Proximity labeling has been used to uncover novel components of the synaptic cleft and inhibitory post-synaptic density.•Different strategies have been developed to delivery small molecule probes for proximity labeling in vivo.•Proximity labeling, in combination with high-resolution imaging and genetic analysis, will advance our understanding key molecules and pathways in neurobiology. Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.