From fragments to function: a review of AI-driven mass spectrometry and fragment-based strategies

Traditional Chinese medicine (TCM) possesses unique advantages in disease prevention and treatment, yet its inherent complexity and diversity pose tremendous challenges for structural elucidation, mechanism research, and bioactivity characterization. High-resolution mass spectrometry (HRMS) technology demonstrates immense potential in TCM analysis due to its high sensitivity, high resolution, high throughput, and high efficiency. However, its application in TCM research remains constrained by the lack of intelligent analytical methods and unified standardized databases. Therefore, this paper focuses on the integration of artificial intelligence (AI) and mass spectrometry, providing a systematic review of the applications and potential of AI-driven mass spectrometry analysis in structural elucidation, data resource integration, multi-omics mechanism studies, and chemical biology. Furthermore, this article emphasizes that by leveraging AI models to learn the complex mapping from chemical structures to biological functions, fragment-based characterization has emerged as the bridge connecting chemical structures with biological activities. Molecular fragments themselves serve as the core “knowledge units” that carry bioactive information. Future research will focus on establishing high-quality mass spectrometry databases for the complete chemical profiles of TCM and promoting the standardization and open sharing of mass spectrometry databases, thereby advancing the integration of AI and mass spectrometry in TCM analysis and providing new tools for TCM research.