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

Erwin M. Schoof*, Benjamin Furtwängler, Nil Üresin, Nicolas Rapin, Simonas Savickas, Coline Gentil, Eric Lechman, Ulrich Auf dem Keller, John E. Dick, Bo T. Porse*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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 ~1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we develop a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a foundation for implementing global single-cell proteomics studies across the world.
Original languageEnglish
Article number3341
JournalNature Communications
Volume12
Number of pages15
ISSN2041-1723
DOIs
Publication statusPublished - 2021

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