Dataset Information

Electrophoresis-Correlative Framing of Ion Mobility Deepens Single-Cell Mass Spectrometry Proteomics

ABSTRACT: This project developed electrophoresis-correlative (Eco) mass spectrometry (MS) to measure the proteome of single cells on a trapped ion mobility mass spectrometer (timsTOF PRO). Eco-MS identified 962 protein groups in a <20 min of electrophoresing a single-HeLa-cell-equivalent (~200 pg) proteome amount. Match-between-runs improved this number to 2,139 protein groups on the same dataset. We demonstrate the approach to measure the proteome of single cells in X. laevis embryos at stage 8 (blastula). Single cells were isolated from the animal cap and their proteomes digested on a fluorosilane-coated microplate. Less than 4% of the available single-cell proteome was analyzed on a custom-built capillary electrophoresis (CE) platform under classical and Eco-driven ddaPASEF. Eco-MS returned ~51% of more protein groups than the control, identifying 1,157 proteins from N = 9 different single cells (biological replicates) of the animal cap. Eco-MS deepens the detectable coverage of the single-cell proteome using ddaPASEF on a timsTOF MS.

INSTRUMENT(S): timsTOF

ORGANISM(S): Homo Sapiens (human) Xenopus Laevis (african Clawed Frog)

TISSUE(S): Cell Culture

SUBMITTER: Peter Nemes

LAB HEAD: Peter Nemes

PROVIDER: PXD057685 | Pride | 2025-05-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	200pgHeLa_processing.zip	Other
	200pgHeLa_raw.zip	Other
	2023-05-13-decoys-contam-2023-Human.fasta.fas	Fasta
	500pgHeLa_dataProcessing.zip	Other
	500pgHeLa_raw.zip	Other

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Publications

Electrophoresis-Correlative Ion Mobility Deepens Single-Cell Proteomics in Capillary Electrophoresis Mass Spectrometry.

Shen Bowen B Zhou Fei F Nemes Peter P

Molecular & cellular proteomics : MCP 20241219 2

Detection of trace-sensitive signals is a current challenge in single-cell mass spectrometry (MS) proteomics. Separation prior to detection improves the fidelity and depth of proteome identification and quantification. We recently recognized capillary electrophoresis (CE) electrospray ionization (ESI) for ordering peptides into mass-to-charge (m/z)-dependent series, introducing electrophoresis-correlative (Eco) data-independent acquisition. Here, we demonstrate that these correlations based on e ...[more]

PMID: 39674510

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