Application of molecular networking to improve the compound annotation in liquid chromatography–mass spectrometry–based metabolomics analysis: A case study of Bupleuri radix

Abstract Introduction Compound annotation is always a challenging step in metabolomics studies. The molecular networking strategy has been developed recently to organize the relationship between compounds as a network based on their tandem mass (MS2) spectra similarity, which can be used to improve compound annotation in metabolomics analysis. Objective This study used Bupleuri Radix from different geographic areas to evaluate the performance of molecular networking strategy for compound annotation in liquid chromatography‐mass spectrometry (LC–MS)–based metabolomics. Methodology The Bupleuri Radix extract was analyzed by LC‐quadrupole time‐of‐flight MS under MSe acquisition mode. After raw data preprocessing, the resulting dataset was used for statistical analysis, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS‐DA). The chemical makers related to the sample growth place were selected using variable importance in projection (VIP) > 2, fold change (FC) > 2, and p < 0.05. The molecular networking analysis was applied to conduct the compound annotation. Results The score plots of PCA showed that the samples were classified into two clusters depending on their growth place. Then, the PLS‐DA model was constructed to explore the chemical changes of the samples further. Sixteen compounds were selected as chemical makers and tentatively annotated by the feature‐based molecular networking (FBMN) analysis. Conclusion The results showed that the molecular networking method fully exploits the MS information and is a promising tool for facilitating compound annotation in metabolomics studies. However, the software used for feature extraction influenced the results of library searching and molecular network construction, which need to be taken into account in future studies.