Dataset Information

Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies

ABSTRACT: Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses. By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying approximately 1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we developed a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a solid foundation for implementing global single-cell proteomics studies across the world.

INSTRUMENT(S): Orbitrap Fusion, Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Acute Leukemia

SUBMITTER: Erwin Schoof

LAB HEAD: Bo Porse

PROVIDER: PXD020586 | Pride | 2021-05-06

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20200514_MK_ES_E1200_precol_scMS_500ms_8227_P5_S1.raw	Raw
	20200514_MK_ES_E1200_precol_scMS_500ms_8227_P5_S11.raw	Raw
	20200514_MK_ES_E1200_precol_scMS_500ms_8227_P5_S2.raw	Raw
	20200514_MK_ES_E1200_precol_scMS_500ms_8227_P5_S3.raw	Raw
	20200514_MK_ES_E1200_precol_scMS_500ms_8227_P5_S4.raw	Raw

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Publications

Quantitative single-cell proteomics as a tool to characterize cellular hierarchies.

Schoof Erwin M EM Furtwängler Benjamin B Üresin Nil N Rapin Nicolas N Savickas Simonas S Gentil Coline C Lechman Eric E Keller Ulrich Auf dem UAD Dick John E JE Porse Bo T BT

Nature communications 20210607 1

Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses. By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell pop ...[more]

PMID: 34099695

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