Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
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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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New molecular measurements such as single-cell proteomics are becoming available.
“Moreover, new molecular measurements are becoming available such as the young and fast-evolving field of single-cell proteomics243.”
From Best practices for single-cell analysis across modalities (2023) · cites this paper as [243]
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- Demichev V, Yu F, Teo GC, Szyrwiel L, Rosenberger GA, Decker J, Kaspar‐Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI et al (2021) High sensitivity dia‐PASEF proteomics with DIA‐NN and FragPipe. bioRxiv 10.1101/2021.03.08.434385 [PREPRINT] · DOI
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- Authors
- Brunner, A., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O. B., Bache, N., Apalategui, A., Lubeck, M., Richter, S., Fischer, D. S., Raether, O., Park, M. A., Meier, F., Theis, F. J., & Mann, M.
- Affiliations
- Max Planck Institute of Biochemistry (DE)
- University of Copenhagen (DK)
- Bruker (Germany) (DE)
- Helmholtz Munich (DE)
- Bruker (United States) (US)
- Jena University Hospital (DE)
- Corresponding author
- Mann, Matthias
- ORCID
- Venue
- Molecular Systems Biology
- Published
- 2022-02-28
- Volume
- 18
- Issue
- 3
- Pages
- e10798-e10798
- ISSN
- 1744-4292 (ISSN-L)
- PMC
- PMC8884154
- OpenAlex
- W4214546240
- Cited by
- 544
- References
- 71
- Citations by year
- 2026: 69 · 2025: 104 · 2024: 106 · 2023: 147 · 2022: 66 · 2021: 50 · 2020: 2
- FWCI
- 38.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Molecular Systems Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Site cant be reached (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Max‐Planck‐Gesellschaft
- Novo Nordisk Fonden (NNF14CC0001, NNF15CC0001)
- Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München (HIDSS‐006)
- Marie Curie individual fellowship (846795)
- Graduate School of Quantitative Biosciences Munich (GSC 1006)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- single-cell proteomics, miniaturized sample preparation, cell cycle arrest, cellular heterogeneity, post-translational modification, small molecule analysis
- MeSH terms
- Protein Processing, Post-Translational, Mass Spectrometry, Proteome, Proteomics, Workflow
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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