Updated project metadata. In this project, we enabled mass spectrometry based proteomics characterization of single neurons in sections of the mouse brain. We accessed cells in a whole-cell patch clamp configuration and aspirated a portion of the neuronal soma into the patch clamp probe. The collected aspirate was expelled into a microvial, where proteins were extracted and processed for shot-gun analysis. The resulting trace amounts of protein digests were analyzed on a custom-built microanalytical capillary electrophoresis platform that was connected to an electrospray ionization high-resolution mass spectrometer. This “patch proteomics” technology identified ~150 proteins from triplicate measurement of single dopaminergic neurons in the mouse substantia nigra.