Proteome-Driven Phenotyping of Identified Single Neurons in Intact Brain Tissue by Aspiration Patch Proteomics

. The workflow identified more than 1,000 proteins from single-neuron samples under optimized conditions while consuming only about 0.25% of the processed digest per analysis. These proteomes were sufficient to separate biological replicates by neuronal phenotype, distinguish neuronal subtypes on the basis of protein expression alone, and define a conserved somal proteome shared across neuronal classes. Our results establish that controlled aspiration of partial somal material can support proteome-driven phenotyping without whole-soma retrieval, cell dissociation, or loss of native tissue context. Aspiration patch proteomics therefore provides an accessible route for subtype-level proteome phenotyping in intact brain tissue.