MassIVE MSV000099156

Partial Public PXD068359

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

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Description

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. [doi:10.25345/C58912422] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: rattus norvegicus ; medial prefrontal cortex ; acute brain slice ; pyramidal neuron ; patch-clamp electrophysiology ; single-cell proteomics ; neuron retrieval ; data-independent acquisition ; Orbitrap Astral ; ion channels ; GPCRs ; synaptic proteins ; DatasetType:Proteomics

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Principal Investigators:
(in alphabetical order) 		John Yates, The Scripps Research Institute, USA
Submitting User: lrodriguez
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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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