Proteomics and Synaptome Mapping to Uncover Diversity in Excitatory Synapses

Synapses are the fundamental computational units of the brain. Although synapses are classically classified according to the neurotransmitter they use, glutamatergic excitatory synapses also exhibit marked heterogeneity in their molecular composition and structure. Understanding this diversity requires comprehensive approaches that go beyond small-scale, candidate-based analyses of synapses. Proteomic analyses of biochemically enriched synaptic fractions have provided unbiased, quantitative measurements of synaptic protein composition, revealing differences across brain regions, cell types, developmental stages, and physiological and pathological states. Proteomics has also revealed the composition and remodeling of synaptic protein complexes and post-translational modifications. In parallel, synaptome mapping, an imaging-based approach for the large-scale in situ analysis of synapses across the brain, has emerged as a form of spatial omics. In this approach, synapses labeled with a small set of synaptic proteins are systematically imaged across the brain. Synaptome mapping reveals whole-brain variation in synapse molecular identity and structural features, including differences in synapse size, shape, and spatial distribution in vivo. Together, these approaches show that excitatory synapses are diversified across anatomical, cellular, developmental, activity-dependent, and disease-related contexts. These complementary perspectives will advance our understanding of the synaptic mechanisms underlying neural computation, behavior, and brain disorders.