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Single-cell and spatial proteomics

We adapt quantitative proteomic workflows to low-input samples and single cells, and localize proteins within tissues to understand their spatial distribution across tissues and within individual cells.

RECENT HIGHLIGHTS

Three recent papers from the group

Single-cell proteomics workflow and benchmarking results, Hendriks et al. 2026
01
Nature Communications · 19 September 2026

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

Ivo A. Hendriks, Sara C. Buch-Larsen, Martin Rykær, Maico Y. Lechner, Anders H. Kverneland, Tabiwang N. Arrey, Daniel Hermanson, Eugen Damoc, Jesper V. Olsen

A high-sensitivity, label-free single-cell proteomics platform that combines optimised low-input sample processing, refined liquid chromatography and the Orbitrap Astral Zoom. It quantifies up to 7,000 proteins per HeLa cell at over 100 samples per day, currently a record for single-cell proteomics, and up to 4,000 proteins in small primary immune cells, enough to distinguish monocytes, T cells and activated lymphocytes.

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02
Cell · March 2025

Global analysis of protein turnover dynamics in single cells

Pierre Sabatier, Maico Lechner, Ulises H. Guzmán, Christian M. Beusch, Xinlei Zeng, Longteng Wang, Fabiana Izaguirre, Anjali Seth, Olga Gritsenko, Sergey Rodin, Karl-Henrik Grinnemo, Zilu Ye, Jesper V. Olsen

Single-cell proteomics has mostly measured how much of each protein a cell contains. Using pulsed SILAC (SC-pSILAC), this study measures protein abundance and turnover together, detecting both labels on around 4,000 proteins in single HeLa cells. Across more than 1,000 cells from differentiating stem cells, turnover dynamics separated dividing from non-dividing cells and revealed co-regulated protein complexes.

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SC-pSILAC workflow and example spectra showing slow, medium and fast protein turnover, Sabatier et al. 2025
Chip-Tip single-cell proteomics workflow and protein identifications, Ye et al. 2025
03
Nature Methods · January 2025

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics

Zilu Ye, Pierre Sabatier, Leander van der Hoeven, Maico Y. Lechner, Teeradon Phlairaharn, Ulises H. Guzman, Zhen Liu, Haoran Huang, Min Huang, Xiangjun Li, David Hartlmayr, Fabiana Izaguirre, Anjali Seth, Hiren J. Joshi, Sergey Rodin, Karl-Henrik Grinnemo, Ole B. Hørning, Dorte B. Bekker-Jensen, Nicolai Bache, Jesper V. Olsen

Chip-Tip is a high-sensitivity, label-free workflow that identifies more than 5,000 proteins in individual HeLa cells at up to 120 samples per day. It detects post-translational modifications directly, without enrichment, and in differentiating stem cells it quantified pluripotency markers such as OCT4 and SOX2 alongside lineage markers for all three germ layers.

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