Mass-spectrometry-based proteomics: from single cells to clinical applications

Tiannan Guo (), Judith A. Steen () and Matthias Mann ()
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Tiannan Guo: Westlake University
Judith A. Steen: Harvard Medical School
Matthias Mann: Max Planck Institute of Biochemistry

Nature, 2025, vol. 638, issue 8052, 901-911

Abstract: Abstract Mass-spectrometry (MS)-based proteomics has evolved into a powerful tool for comprehensively analysing biological systems. Recent technological advances have markedly increased sensitivity, enabling single-cell proteomics and spatial profiling of tissues. Simultaneously, improvements in throughput and robustness are facilitating clinical applications. In this Review, we present the latest developments in proteomics technology, including novel sample-preparation methods, advanced instrumentation and innovative data-acquisition strategies. We explore how these advances drive progress in key areas such as protein–protein interactions, post-translational modifications and structural proteomics. Integrating artificial intelligence into the proteomics workflow accelerates data analysis and biological interpretation. We discuss the application of proteomics to single-cell analysis and spatial profiling, which can provide unprecedented insights into cellular heterogeneity and tissue architecture. Finally, we examine the transition of proteomics from basic research to clinical practice, including biomarker discovery in body fluids and the promise and challenges of implementing proteomics-based diagnostics. This Review provides a broad and high-level overview of the current state of proteomics and its potential to revolutionize our understanding of biology and transform medical practice.

Date: 2025
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DOI: 10.1038/s41586-025-08584-0

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