The underappreciated diversity of functional pigments in red yeast rice revealed by an integrated multi-engine mining strategy (IMMS).

Red yeast rice (RYR) is a popular functional food, while its functional components remain severely understudied. This study developed an integrated multi-engine mining strategy (IMMS) ingeniously combining feature-based molecular networking, building blocks-based molecular networking, SIRIUS, PEAKS, and BUDDY to comprehensively analyze RYR components. Employing IMMS, 219 pigments (208 red, 6 orange, 5 yellow) and 104 peptides were first identified, including 185 potential new pigments, with red and yellow pigments showing higher contents. Notably, red pigments demonstrated optimal plasma exposure and brain distribution in rats after oral RYR. Bioactivity analysis first revealed that six typical pigments, especially red, suppressed oxidative stress and neuroinflammation related to Alzheimer's disease in L-Glu-induced HT-22 cells and LPS-induced BV-2 cells, potentially via the Keap1-Nrf2 and IDO1 pathways, respectively. These findings significantly expanded the pigment diversity and RYR components, facilitating the discovery of functional components and providing a foundation for RYR's development as an anti-Alzheimer's functional food.