Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow named Chip-Tip, identifying >5,000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications in single cells, making the need for specific post-translational modification-enrichment unnecessary. Our study demonstrates the feasibility of processing up to 120 label-free SCP samples per day. An optimized tissue dissociation buffer enabled effective single-cell disaggregation of drug-treated cancer cell spheroids, refining overall SCP analysis. Analyzing nondirected human-induced pluripotent stem cell differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in human-induced pluripotent stem cells and lineage markers such as GATA4 (endoderm), HAND1 (mesoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a benchmark in SCP for sensitivity and throughput, with broad applications in basic biology and biomedicine for identification of cell type-specific markers and therapeutic targets.
Authors
- Hiren J. Joshi (ORCID: https://orcid.org/0000-0002-8192-2829)
- Ole B. Hørning
- Zilu Ye (ORCID: https://orcid.org/0000-0001-8829-6579)
- Karl‐Henrik Grinnemo (ORCID: https://orcid.org/0000-0002-6100-6209)
- David Hartlmayr (ORCID: https://orcid.org/0000-0002-1436-2841)
- Anjali Seth (ORCID: https://orcid.org/0000-0003-4701-2562)
- Ulises H. Guzmán (ORCID: https://orcid.org/0000-0003-1665-7659)
- Leander van der Hoeven (ORCID: https://orcid.org/0000-0003-4005-580X)
- Fabiana Izaguirre (ORCID: https://orcid.org/0009-0008-5335-0780)
- Pierre Sabatier (ORCID: https://orcid.org/0000-0002-2734-1791)
- Jesper Velgaard Olsen (ORCID: https://orcid.org/0000-0002-4747-4938)
- Teeradon Phlairaharn (ORCID: https://orcid.org/0000-0001-6031-0578)
- Sergey Rodin (ORCID: https://orcid.org/0000-0002-6954-1986)
- Nicolai Bache (ORCID: https://orcid.org/0000-0003-2306-9943)
- Dorte B. Bekker‐Jensen (ORCID: https://orcid.org/0000-0002-7932-079X)
- Maico Lechner (ORCID: https://orcid.org/0009-0006-7471-6003)
- Zhen Liu (ORCID: https://orcid.org/0000-0002-3678-1465)
- Min Huang (ORCID: https://orcid.org/0000-0002-2844-5680)
- Xiangjun Li (ORCID: https://orcid.org/0000-0001-9919-1238)
- Haoran Huang (ORCID: https://orcid.org/0009-0000-1921-738X)
Institutions
- Uppsala University (SE)
- University of Copenhagen (DK)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Novo Nordisk Foundation (DK)
- Suzhou Institute of Systems Medicine (CN)
- Thermo Fisher Scientific (China) (CN)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-01-16
- DOI
- https://doi.org/10.1038/s41592-024-02558-2
- Citations
- 76
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 60.45
Funders
- Innovationsfonden
- Government of Jiangsu Province
- Novo Nordisk
- Vetenskapsrådet
- Natural Science Foundation of Jiangsu Province
- Chinese Academy of Medical Sciences
- Novo Nordisk Fonden