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Peer-reviewedCC BYNature communications

Extending single-cell proteomics from HeLa to small primary human immune cells.

  • Ivo Alexander Hendriks1,2
  • Sara Charlotte Buch-Larsen1,2
  • Martin Rykær1,2
  • Maico Y. Lechner1,2
  • Anders Handrup Kverneland1,3,2
  • Tabiwang N. Arrey4
  • Daniel J. Hermanson4
  • Eugen Damoc4
  • Jesper Velgaard Olsen5,6
6 affiliations
  1. 1Copenhagen Center for Glycocalyx Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
  2. 2Proteomics program, Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
  3. 3National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
  4. 4Thermo Fisher Scientific, 11 Hanna-Kunath Strasse, Bremen, Germany
  5. 5Copenhagen Center for Glycocalyx Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [email protected]
  6. 6Proteomics program, Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [email protected]
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Abstract

Single-cell proteomics (SCP) holds the promise of decoding cellular heterogeneity at the functional level, yet achieving deep and reproducible proteome coverage from individual cells has remained a formidable challenge. Here, we establish a high-sensitivity, label-free SCP platform that extends current depth and reproducibility. By integrating optimized low-input sample processing, refined liquid chromatography, and the Orbitrap Astral Zoom mass spectrometer, our approach routinely quantifies up to 7000 proteins per individual HeLa cell at over 100 samples-per-day (SPD), capturing thousands of low-abundance proteins that eluded prior SCP studies. Applied to very small human peripheral blood mononuclear cells (PBMCs), we identify up to 4000 proteins per cell, including key markers that distinguish monocytes, T cells, and activated lymphocytes within heterogeneous populations, underscoring that single-cell proteomics can now directly elucidate clinically relevant primary samples with both depth and precision.

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Cite

BibTeXRIS
BibTeX
@article{hendriks2026extending,
  title = {{Extending single-cell proteomics from HeLa to small primary human immune cells.}},
  author = {Ivo Alexander Hendriks and Sara Charlotte Buch-Larsen and Martin Rykær and Maico Y. Lechner and Anders Handrup Kverneland and Tabiwang N. Arrey and Daniel J. Hermanson and Eugen Damoc and Jesper Velgaard Olsen},
  journal = {Nature communications},
  year = {2026},
  month = sep,
  doi = {10.1038/s41467-026-77675-x},
  url = {https://europepmc.org/article/MED/42901897},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Extending single-cell proteomics from HeLa to small primary human immune cells.
AU  - Ivo Alexander Hendriks
AU  - Sara Charlotte Buch-Larsen
AU  - Martin Rykær
AU  - Maico Y. Lechner
AU  - Anders Handrup Kverneland
AU  - Tabiwang N. Arrey
AU  - Daniel J. Hermanson
AU  - Eugen Damoc
AU  - Jesper Velgaard Olsen
PY  - 2026
DA  - 2026/09/19
JO  - Nature communications
DO  - 10.1038/s41467-026-77675-x
UR  - https://europepmc.org/article/MED/42901897
AB  - Single-cell proteomics (SCP) holds the promise of decoding cellular heterogeneity at the functional level, yet achieving deep and reproducible proteome coverage from individual cells has remained a formidable challenge. Here, we establish a high-sensitivity, label-free SCP platform that extends current depth and reproducibility. By integrating optimized low-input sample processing, refined liquid chromatography, and the Orbitrap Astral Zoom mass spectrometer, our approach routinely quantifies up to 7000 proteins per individual HeLa cell at over 100 samples-per-day (SPD), capturing thousands of low-abundance proteins that eluded prior SCP studies. Applied to very small human peripheral blood mononuclear cells (PBMCs), we identify up to 4000 proteins per cell, including key markers that distinguish monocytes, T cells, and activated lymphocytes within heterogeneous populations, underscoring that single-cell proteomics can now directly elucidate clinically relevant primary samples with both depth and precision.
SN  - 2041-1723
ER  -