The genus Scutellaria L., Lamiaceae family, Scutellarioideae sub-family is known as the most important medicinal plant in the world. This research aimed to investigate the flavonoid content of seven Scutellaria species from the center, southwest, and west of Iran. Via thin layer and column chromatography, the flavonoid was extracted from leaves and then purified. To screen the flavonoid compositions, a chromatographic method was applied by liquid chromatography mass spectrometry on a triple quadrupole mass spectrometer (LC/TQMS/MS). Fingerprint analysis was implemented so as to characterize a total of 73 chemical compounds, from which 71 compounds were flavonoids belonging to different classes. Flavone with 37 derivatives possessed major values. The most abundant flavonoid compounds were observed in S. multicaulis (23 compounds) and S. patonii (22 compounds). Flavonoid composition, including apigenin, kaempferol, quercetin, and hydroxyl- flavones represented remarkable derivatives. A total of 45 flavonoids, one tannin and one anthraquinone compound, were observed to be primarily separated and identified for Scutellaria species. Moreover, six categorized chemical groups were identified in this genus and proposed as chemical barcodes. The specific chemical groups strongly provided the boundaries of Scutellaria species, the pharmacological value enhancement, breeding programs, and comprehensive documents of the species. According to the results, LC/TQMS/MS was proven a dominant method regarding genus Scutellaria.

The report demonstrates that plenty of methylated flavones of the plant, as the end product of the flavone biosynthesis pathway, are concentrated in the root bark, which largely remains in the waste that makes up 7% w/w of the commercial root and is discarded. The study of the waste extract showed that the last enriched with monomethylated flavones wogonin and oroxylin A, along with some polymethylated ones represent an end of the biosynthesis pathway of flavones in the plant. In addition to wogonin, 7 known methylated flavones were found for the first time in the root bark. Due to a high content of wogonin and oroxylin A in the extract, these flavones were concentrated using preparative liquid chromatography. As a result, the obtained complex of these two target flavones turned out to be 0.8% w/w of the waste. Such morphologically specific accumulation of methylated flavones at the root boundary raises the question of their role in plant life.