A metabolome dataset of different parts of Gynura formosana Kitam.

(three biological replicates per organ; nine samples collected in October 2025 from Zhangzhou, Fujian Province, China). It consists of three organ-specific files (leaf, stem and root) and one integrated workbook.

In total, 1515 metabolites were annotated (corresponding to 1293 unique chromatographic features) and classified into 10 classes, with 1455, 1492 and 1460 metabolites detected in the leaf, stem and root, respectively. Each organ-specific compound table provides metabolite ID, compound name in English and Chinese, molecular formula, molecular weight, retention time, ion mode, identification level, MS2 score, class I and class II annotation, CAS number, HMDB ID, KEGG ID, PubChem CID, SMILES, InChIKey, and the relative abundance of each biological replicate together with the mean value.