An ultra performance liquid chromatography (UPLC) coupled with quadrupole time-of-flight mass spectrometry (QTOF/MS) method is established for the rapid analysis of isoflavones, saponins and flavones in 16 samples originated from the flowers of Pueraria lobata and P. thomsonii. A total of 25 isoflavones, 13 saponins and 3 flavones were identified by co-chromatography of sample extract with authentic standards and comparing the retention time, UV spectra, characteristic molecular ions and fragment ions with those of authentic standards, or tentatively identified by MS/MS determination along with Mass Fragment software. Moreover, the method was validated for the simultaneous quantification of 29 components. The samples from two Pueraria flowers significantly differed in the quality and quantity of isoflavones, saponins and flavones, which allows the possibility of showing their chemical distinctness, and may be useful in their standardization and quality control. Dataset obtained from UPLC-MS was processed with principal component analysis (PCA) and orthogonal partial least squared discriminant analysis (OPLS-DA) to holistically compare the difference between both Pueraria flowers.
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