AI Redefines Mass Spectrometry Chemicals Identification: Retention Time Prediction in Metabolomics and for a Human Exposome Project

Fenna Sille¹Carsten Prasse²Thomas Luechtefeld^1,3Thomas Hartung^1,4*

• ¹Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States
• ²Johns Hopkins University Whiting School of Engineering, Baltimore, United States
• ³Insilica, Rockville, MD, United States
• ⁴Universitat Konstanz, Konstanz, Germany

The comprehensive identification of environmental and endogenous chemicals in human biospecimens is a critical bottleneck for realizing the Human Exposome Project. Untargeted metabolomics, particularly liquid chromatography–high-resolution mass spectrometry (LC-HRMS), offers unparalleled coverage of small molecules, but most detected features remain unidentified due to limited spectral libraries and structural ambiguity. Retention time (RT) prediction—based on quantitative structure–retention relationships (QSRR) and enhanced by artificial intelligence (AI)—is an underutilized orthogonal parameter that can substantially improve metabolite annotation confidence. This review synthesizes advances in machine learning–based RT prediction, probabilistic calibration, and cross-platform harmonization for liquid chromatography and gas chromatography, including deep learning, graph neural networks, and transfer learning approaches. We evaluate workflows integrating RT prediction with mass-based searches and network-based annotation tools, highlighting their potential to refine candidate ranking and reduce false positives in environmental exposure assessment. The use of endogenous compounds as internal calibrants is discussed as a practical strategy for improving RT transferability across laboratories. We further outline how RT-aware annotation supports non-targeted screening of emerging contaminants, transformation products, and exposure biomarkers, thereby enhancing the interpretability and reproducibility of exposomics data. By integrating RT prediction, QSRR modeling, and AI into untargeted metabolomics pipelines, researchers can move from qualitative detection toward quantitative, inference-driven mapping of environmental influences on human health, strengthening the scientific foundation for environmental health policy and preventive public health strategies.