Strategies for structural annotation of food-derived flavonoids based on biosynthetic networks and mass spectrometry fragmentation patterns.

Plant flavonoids possess diverse structures and broad bioactivities, making reliable structural annotation essential for evaluating their nutritional and health effects. However, conventional LC-HRMS workflows depend heavily on empirical fragment interpretation, resulting in low throughput and substantial subjectivity. This review presents a tailored annotation framework that integrates flavonoid biosynthesis with Q-TOF MS fragmentation behavior. It maps enzyme-induced structural changes to characteristic mass shifts and fragmentation patterns, thereby linking biochemical mechanisms with mass spectrometric behavior. The review also evaluates the limitations of this dual-track strategy, including uncertainty in mass spectral data and interference from non-enzymatic transformations during food processing. In addition, emerging cheminformatics approaches, including molecular networking and computer-assisted spectral prediction, are critically assessed regarding their data requirements, applicability, and limitations in complex food matrices. Overall, this review provides a systematic and objective methodological reference for improving the structural annotation of food-derived flavonoids and supporting more confident food-related metabolomic investigations.