This study aimed to comprehensively analyze primary and secondary metabolites of three different-colored (white, pale green, and green) pak choi cultivars (Brassica rapa subsp. chinensis) using gas chromatography attached with time-of-flight mass spectrometry (GC-TOFMS) and high-performance liquid chromatography (HPLC). In total, 53 primary metabolites were identified and subjected to partial least-squares discriminant analysis. The result revealed a significant difference in the primary and secondary metabolites between the three pak choi cultivars. In addition, 49 hydrophilic metabolites were detected in different cultivars. Total phenolic and glucosinolate contents were highest in the pale green and green cultivars, respectively, whereas total carotenoid and chlorophyll contents were highest in the white cultivar. Superoxide dismutase activity, 2,2-diphenyl-1-picrylhydraz scavenging, and reducing power were slightly increased in the white, pale green, and green cultivars, respectively. In addition, a negative correlation between pigments and phenylpropanoids was discovered by metabolite correlation analysis. This approach will provide useful information for the development of strategies to enhance the biosynthesis of phenolics, glucosinolates, carotenoids, and chlorophyll, and to improve antioxidant activity in pak choi cultivars. In addition, this study supports the use of HPLC and GC-TOFMS-based metabolite profiling to explore differences in pak choi cultivars.
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