Deciphering the chemical basis of traditional Chinese medicine (TCM) is of far-reaching significance for revealing its pharmacodynamic mechanism, metabolic transformation, and drug development. However, the complexity of chemical compositions and the large number of isomers in TCM make it difficult to achieve comprehensive detection and identification. Taking
Codonopsis Radix as a case, we proposed a reverse molecular assembly (RMA) analysis strategy for rapid discovery of potential new compounds in the complex system of TCM: the paired diagnostic product ions (pDPIs) were designed based on the structural characteristics and characteristic cleavage pathways of taxa-compounds. First, the reported compounds were categorized into different taxa based on different core structures. Second, pDPIs belonging to a certain taxon were designed according to different core structures, branch chains, and cleavage pathways. Third, the accuracy of pDPIs in positive and negative ion modes was verified by comparing mass spectrometry data, literature reports, and standards. Finally, the RMA analysis strategy was used to accurately identify the chemical components of
Codonopsis Radix extract. In this study, 209 compounds were preliminarily characterized, 128 of which are potential new compounds that have not been reported yet in
Codonopsis Radix. This study provides an important reference for in-depth elucidation of the chemical basis of the complex system of TCM.
