Supplementary information.xlsx

Traditional Chinese medicine (TCM) has a wide range of clinical applications and good efficacy. However, due to the inherent multi-level, multi-linked, and multi-dimensional non-linear synergistic action characteristics, explaining the mechanism of action (MOA) of TCM in the treatment of diseases still faces great challenges. Therefore, a systematic and applicable research strategy that suits the therapeutic characteristics of TCM is urgently needed. Liu <em>et al.</em> proposed the Quality marker (Q-marker) opinion to monitor and evaluate the qualities of TCM products, which has significantly promoted the development of TCM in recent years. In this study, a Q-marker screening strategy for TCM formula which emphasizes efficacy and biological activities was proposed. In principle, we have integrated absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification in the Q-marker screening workflow. Qianghuo Shengshi decoction (QHSSD) in treating rheumatoid arthritis (RA) was taken as an example to screen Q-markers. As a result, five Q-markers with significant<em> in vitro</em> anti-inflammatory effects were screened out from 159 compounds in QHSSD for treating RA, including notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Moreover, much instructive information on pharmacological mechanisms was obtained through the integrated analysis of network pharmacology and metabolomics, such as the main targets and pathways that QHSSD plays important roles in the treatment of RA, which provided a research foundation for the further in-depth study of QHSSD. In conclusion, this work illustrates that the strategy is feasible and offers a practical reference model for the systematic research of TCM formula