Metabolomics data of root and stem tissues in five-year-old Sophora flavescens

This dataset provides full metabolomic data for root and stem samples of Sophora flavescens, a commonly used Chinese medicine. Metabolites were extracted separately from root and stem samples and subjected to high-resolution LC-MS in positive and negative modes. Raw spectral data were used for peak detection, alignment, normalization, and metabolite annotation using established metabolomic pipelines and public databases. Principal component analysis and partial least-squares discriminant analysis were used to obtain tissue-specific metabolic profiles. Differential metabolite analysis was conducted to determine the metabolites that were more enriched and depleted in roots and stems, and pathway enrichment analysis was performed to determine the metabolic pathways related to these metabolites. The dataset contains raw LC–MS files, processed feature tables, annotated metabolite lists, and statistical analysis results in a standard format. In these data, there are important materials for studying the tissue-specific metabolism different of S. flavescens, as well as for conducting research on the different distribution of medicine materials and studying biosynthesis routes and quality identification of medicinal plants. The same will be helpful for comparative metabolomics, integrative multi-omics, and natural products.