Scutellaria baicalensis Georgi (SG) and Scutellaria rehderiana Diels (SD) belong to the same genus of Scutellaria in the Labiatae (Lamiaceae) family. SG is confirmed as the medicinal source according to the Chinese Pharmacopeia, but SD is often used as a substitute for SG due to its abundant plant resources. However, the current quality standards are far from sufficient to judge the quality differences between SG and SD. In this study, an integrated strategy of “biosynthetic pathway (specificity) - plant metabolomics (difference) - bioactivity evaluation (effectiveness)” was established to evaluate this quality differences. First, an ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF-MS/MS) method was developed for the identification of chemical components. The abundant components information was obtained and the characteristic constituents were screened according to the location in the biosynthetic pathway as well as species specificity. Then, plant metabolomics combined with multivariate statistical analysis to find differential components between SG and SD. The chemical markers for quality analysis were determined based on the differential and characteristic components, and the content of each marker was tentatively evaluated through the semi-quantitative analysis of UHPLC-Q/TOF-MS/MS. Finally, the anti-inflammatory activity of SG and SD was compared by measuring the inhibitory effect on the release of NO from lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. Under this analytical strategy, a total of 113 compounds were tentatively identified in both SG and SD, among which baicalein, wogonin, chrysin, oroxylin A 7-O-β-D-glucuronoside, pinocembrin and baicalin were selected as chemical markers due to their species characteristics and differentiation. The contents of oroxylin A 7-O-β-D-glucuronoside and baicalin was higher in SG, and the others were higher in SD. In addition, both SG and SD exhibited prominent anti-inflammatory activity, but SD was less effective. The analysis strategy combining phytochemistry and bioactivity evaluation realized the scientific evaluation of the intrinsic quality differences between SG and SD, which provides a reference for fully utilizing and expanding the medicinal resources, and also provides a reference for the comprehensive quality control of herbal medicines.
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