Quantitative Food Biomarkers Enable Dietary Ontology Referencing Across 500 Foods and Human Plasma

Accurate and reproducible dietary assessment remains a persistent challenge in clinical and nutritional sciences. We present a validated, liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for the absolute quantification of 200 literature-curated food biomarkers across 500 single-ingredient food extracts and human plasma samples. The assay uses external matrix-matched calibration and robust quality control, including post-extraction recovery, matrix effect assessment, and intra/inter-day precision validation, demonstrating high linearity (R² > 0.99), low coefficients of variation (<15%), and recovery within 100 ± 15% for >75% of analytes. Using 200 authentic food standards against 500 complex food items resulted in reproducible detection and quantification of 102 food biomarkers across diverse food classes. Their specificity and distribution was evaluated at multiple levels of dietary ontology. Supervised multivariate analysis (PLS-DA) identified discriminative biomarker panels that classify foods such as citrus, dairy, and vegetables with high accuracy. Key markers - e.g., hesperidin, hypaphorine, piperine - showed strong source-specificity and were applied to human plasma samples from an inflammatory bowel disease (IBD) cohort on a Mediterranean diet. Biomarker concentrations tracked with dietary intake, confirming hypaphorine’s association with hummus and piperine’s correlation with black pepper–containing meals. This study demonstrates the utility of a rigorously validated targeted metabolomics workflow for both food chemistry and translational dietary biomarker research. The framework enables quantitative mapping of food molecules to dietary exposures and supports the development of more objective, chemistry-based dietary assessment strategies in clinical contexts.