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Ultra-high performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS) was applied for the non-targeted metabolomic characterization of Paeoniae Radix Alba and Paeoniae Radix Rubra decoction pieces. Differential metabolites were identified through multivariate statistical analysis. Interpretable machine learning methods, including random forest (RF), adaptive boosting (AdaBoost), and extreme gradient boosting (XGBoost), were further employed to build classification models, and the Shapley additive explanations (SHAP) algorithm was used to evaluate the contributions of characteristic metabolites. A total of 44 metabolites were identified, including 9 flavonoids, 8 phenolic acids, and other types of metabolites, among which 12 showed significant differences between the two kinds of decoction pieces. In the test set, the RF model exhibited superior performance. SHAP analysis indicated that gluconic acid, quercetin, kaempferol, L-aspartic acid, taxifolin, and oxypaeoniflorin significantly contributed to model discrimination, with L-aspartic acid showing elevated levels in Paeoniae Radix Alba, while the other metabolites were relatively higher in Paeoniae Radix Rubra. The metabonomics-machine learning strategy established in this study provides potential chemical evidence for elucidating the efficacy differences between Paeoniae Radix Alba and Paeoniae Radix Rubra and offers new insights into the identification, origin traceability, and characteristic marker discovery of other easily confused traditional Chinese medicines.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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