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Patch-Clamp Single-Cell Proteomics of Rat Prefrontal Cortex Neurons

ABSTRACT: This dataset supports a study introducing a framework for patch-clamp single-cell proteomics (patch-SCP) in acute rat brain slices. Patch-SCP combines whole-cell electrophysiology with mass spectrometry to directly link neuronal excitability with molecular composition. We systematically analyzed neurons from layer 2/3 of the medial prefrontal cortex (mPFC) using a shotgun retrieval strategy in which all patched cells were collected, regardless of electrophysiological outcome. Retrieval outcomes included neurons with preserved gigaseals, neurons that lost the gigaseal during soma withdrawal, neurons without gigaseals (collected without electrophysiological recordings), and torn/aspirated neurons. Electrophysiological parameters such as capacitance, resistance, and spiking were recorded where possible. Each retrieved soma was processed using a single-cell surfactant-based workflow (DDM lysis, one-pot digestion in low-bind plates) and analyzed by nanoLC coupled to an Orbitrap Astral mass spectrometer operating in DIA mode. The dataset contains raw DIA files, DIA-NN search outputs, and annotated metadata linking each cell to its retrieval outcome and electrophysiological properties. Together, these data provide a resource for evaluating how neuron size, retrieval quality, and physiological characterization influence single-cell proteomic recovery in acute brain slices.

INSTRUMENT(S): Orbitrap Astral

ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116)

SUBMITTER: John Yates

PROVIDER: MSV000099156 | MassIVE |

SECONDARY ACCESSION(S): PXD068359

REPOSITORIES: MassIVE

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