Proteoform profiling of endogenous single cells from rat hippocampus at scale

Pei Su¹, Michael A R Hollas², Indira Pla², Stanislav Rubakhin^{3

4}, Fatma Ayaloglu Butun², Joseph B Greer², Bryan P Early², Ryan T Fellers², Michael A Caldwell², Jonathan V Sweedler^{3

4

5}, Jared O Kafader², Neil L Kelleher^{6

7

8

9

10

11}

Affiliations

¹ Department of Chemistry, Northwestern University, Evanston, IL, USA.
² Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
³ Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁴ Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁵ Chan Zuckerberg Biohub Chicago, Chicago, IL, USA.
⁶ Department of Chemistry, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
⁷ Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
⁸ Chan Zuckerberg Biohub Chicago, Chicago, IL, USA. n-kelleher@northwestern.edu.
⁹ Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. n-kelleher@northwestern.edu.
¹⁰ Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
¹¹ Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.

PMID: 40374954
DOI: 10.1038/s41587-025-02669-x

Proteoform profiling of endogenous single cells from rat hippocampus at scale

Pei Su et al. Nat Biotechnol. 2025.

. 2025 May 15.

doi: 10.1038/s41587-025-02669-x. Online ahead of print.

Authors

Affiliations

¹ Department of Chemistry, Northwestern University, Evanston, IL, USA.
² Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
³ Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁴ Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁵ Chan Zuckerberg Biohub Chicago, Chicago, IL, USA.
⁶ Department of Chemistry, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
⁷ Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
⁸ Chan Zuckerberg Biohub Chicago, Chicago, IL, USA. n-kelleher@northwestern.edu.
⁹ Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. n-kelleher@northwestern.edu.
¹⁰ Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
¹¹ Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.

PMID: 40374954
DOI: 10.1038/s41587-025-02669-x

Abstract

We perform intact proteoform profiling of 10,809 endogenous single cells from the rat hippocampus using single-cell proteoform imaging mass spectrometry (scPiMS). scPiMS directly extracts whole proteins and demonstrates high throughput for MS-based single-cell proteomics compared with existing approaches. We develop an informatics workflow dedicated to this datatype and use it to assign neurons, astrocytes or microglia cell types according to their proteoform signatures.

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Conflict of interest statement

Competing interests: J.O.K. and N.L.K. report a conflict of interest with I2MS technology, being commercialized by Thermo Fisher Scientific. R.T.F., J.B.G. and N.L.K. are involved in commercialization of software. N.L.K. is a paid consultant for Thermo Fisher Scientific. The other authors declare no competing interests.

References

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Proteoform profiling of endogenous single cells from rat hippocampus at scale

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Proteoform profiling of endogenous single cells from rat hippocampus at scale

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