Red yeast rice (RYR) is a popular food product with significant quality control challenges. This study first established a gradient elution tower plate theory suitable for gradient elution and proposed a dual-label system calibration method to monitor and correct chromatographic systems for changes. Subsequently, high-performance liquid chromatography as the analytical method, and a five-wavelength maximization profile was employed to obtain comprehensive chromatographic information on RYR. A novel multi-marker assay by monolinear method (MAML) was employed for the accurate quantitative determination of quality markers. A differential scanning calorimetry (DSC) quantized fingerprint was established to study complete thermal changes. The comprehensive linear quantitative fingerprint method (CLQFM) was also developed to evaluate fingerprints. Results showed that the CLQFM divides the samples into four quality grades, MAML yielded better results than quantitative analysis of multi-components by a single marker method. Thermal analysis revealed that treatment temperatures higher than 193.7 °C for extended periods should be avoided to maintain sample quality. This study promotes the dual control of the quality and thermal stability of RYR, providing a new direction for food control.
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