Scrophulariae Radix (SR) has been extensively used in traditional Chinese medicine (TCM) for thousands of years. However, the processing methods and production areas of Scrophularia ningpoensis have undergone notable historic changes. Thus, their effects on the bioactive constituents of SR still need to be studied further. This study aimed to establish an objective and comprehensive method to identify the correlation of bioactive constituents of SR with variety, place of origin and processing method for evaluating their qualities. An accurate and rapid high-performance liquid chromatography-diode array detector (HPLC-DAD) method for the simultaneous determination of 11 marker components (aucubin, harpagide, 6-O-methyl-catalpol, harpagoside, verbascoside, isoverbascoside, angoroside C, cinnamic acid, l-tyrosine, l-phenylalanine, and l-tryptophan) was established to evaluate the quality of SR for the first time. In addition, the effects of different production areas and processed methods on the target compounds were studied by analysing 66 batches of SR samples with chemometrics methods, including similarity evaluation of chromatographic fingerprints of TCM, principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA). Compared with "sweating", short-term "steaming" and "slice-drying" could largely preserve the bioactive constituents of SR. When using the model established through PLS-DA, five components were identified as the most significant variables for discrimination. Furthermore, the score plots of PCA and the similarity evaluation revealed that variety had a more notable influence on the quality of SR than the place of origin. An objective approach of HPLC fingerprint coupled with chemometrics analysis and quantitative assessment could be applied to discriminate different processed SR and evaluate the qualities of SR rapidly.
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