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  Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

Brunner, A.-D., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., et al. (2022). Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Molecular Systems Biology, 18(3): e10798. doi:10.15252/msb.202110798.

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 Creators:
Brunner, Andreas-David1, Author              
Thielert, Marvin1, Author              
Vasilopoulou, Catherine1, Author              
Ammar, Constantin1, Author              
Coscia, Fabian2, Author
Mund, Andreas2, Author
Hoerning, Ole B.2, Author
Bache, Nicolai2, Author
Apalategui, Amalia2, Author
Lubeck, Markus2, Author
Richter, Sabrina2, Author
Fischer, David S.2, Author
Raether, Oliver2, Author
Park, Melvin A.2, Author
Meier, Florian1, Author              
Theis, Fabian J.2, Author
Mann, Matthias1, Author              
Affiliations:
1Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565159              
2external, ou_persistent22              

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Free keywords: RNA-SEQ; PEPTIDE IDENTIFICATION; REVEALS; PLATFORMBiochemistry & Molecular Biology; drug perturbation; low-flow LC-MS; proteomics at single-cell resolution; single-cell heterogeneity; systems biology;
 Abstract: Single-cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular function and in-depth characterization of individual cells by mass spectrometry (MS)-based proteomics would thus be highly valuable and complementary. Here, we develop a robust workflow combining miniaturized sample preparation, very low flow-rate chromatography, and a novel trapped ion mobility mass spectrometer, resulting in a more than 10-fold improved sensitivity. We precisely and robustly quantify proteomes and their changes in single, FACS-isolated cells. Arresting cells at defined stages of the cell cycle by drug treatment retrieves expected key regulators. Furthermore, it highlights potential novel ones and allows cell phase prediction. Comparing the variability in more than 430 single-cell proteomes to transcriptome data revealed a stable-core proteome despite perturbation, while the transcriptome appears stochastic. Our technology can readily be applied to ultra-high sensitivity analyses of tissue material, posttranslational modifications, and small molecule studies from small cell counts to gain unprecedented insights into cellular heterogeneity in health and disease.

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Language(s): eng - English
 Dates: 2022
 Publication Status: Published online
 Pages: 15
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: ISI: 000776291700003
DOI: 10.15252/msb.202110798
 Degree: -

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Title: Molecular Systems Biology
Source Genre: Journal
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Publ. Info: London : Nature Pub. Group
Pages: - Volume / Issue: 18 (3) Sequence Number: e10798 Start / End Page: - Identifier: ISSN: 1744-4292
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000021290