AI proteomics: from protein identification to virtual cells.

Sun, Yingying; A, Jun; Liu, Zhiwei; Sun, Rui; Qian, Liujia; Payne, Samuel H; Bittremieux, Wout; Ralser, Markus et al. · Nat Methods · 2026

other · Level V

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Abstract

Artificial intelligence (AI) is transforming scientific research, including proteomics. In this Perspective, we highlight key mass spectrometry (MS)-based proteomics areas where AI is driving innovation, ranging from protein identification to building AI virtual cells. These include improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and, ultimately, enabling AI virtual cells. Finally, we call for global collaboration among data producers, data consumers and other stakeholders to establish an AI-friendly ecosystem for MS-based proteomics, laying the foundation for transformative advancements in proteomics driven by AI.