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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

Nature Methods volume 20, pages 363–374 (2023)Cite this article

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Abstract

In the last decade, single-cell RNA sequencing routinely performed on large numbers of single cells has greatly advanced our understanding of the underlying heterogeneity of complex biological systems. Technological advances have also enabled protein measurements, further contributing to the elucidation of cell types and states present in complex tissues. Recently, there have been independent advances in mass spectrometric techniques bringing us one step closer to characterizing single-cell proteomes. Here we discuss the challenges of detecting proteins in single cells by both mass spectrometry and sequencing-based methods. We review the state of the art for these techniques and propose that there is a space for technological advancements and complementary approaches that maximize the advantages of both classes of technologies.

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Fig. 1: Key areas of development for mass spectrometry-based single-cell proteomics.
Fig. 2: Single-cell antibody-based proteomics in combination with RNA transcript detection.
Fig. 3: Single-cell PTM and proteomic-detection methods using antibody complexes.

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Acknowledgements

We thank J.R. Lill, Z. Modrusan, O. Rozenblatt-Rosen, K. Geiger-Schuller, S. Klaeger, W.R. Mathews and T.K. Cheung for their insight, guidance and comments.

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Authors and Affiliations

  1. Department of Next Generation Sequencing and Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA

    Hayley M. Bennett, William Stephenson, Christopher M. Rose & Spyros Darmanis

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  1. Hayley M. Bennett
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  2. William Stephenson
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Contributions

H.M.B. and S.D. were responsible for leading the draft manuscript preparation. H.M.B., S.D., W.S. and C.M.R. all contributed to the preparation of the final version of the text and figures.

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Correspondence to Spyros Darmanis.

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Competing interests

H.M.B., S.D., W.S. and C.M.R. are currently employees and shareholders of Genentech, a member of the Roche Group.

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Nature Methods thanks Andreas Mund and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Allison Doerr, in collaboration with the Nature Methods team.

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Bennett, H.M., Stephenson, W., Rose, C.M. et al. Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods 20, 363–374 (2023). https://doi.org/10.1038/s41592-023-01791-5

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