Garcinia mangostana L. (mangosteen) seed is recalcitrant, prone to low temperature and drying which limit its long-term storage. Therefore, it is imperative to understand the metabolic changes throughout its development, to shed some light into the recalcitrant nature of this seed. We performed metabolomics analysis on mangosteen seed at different stages of development; six, eight, ten, twelve and fourteen weeks after anthesis. Seed samples were subjected to methanol extraction prior analysis using liquid chromatography - mass spectrometry (LC-MS). The MS data acquired were analyzed using ProfileAnalysis (version 2.1). This data article refers to the article entitled "Metabolomics analysis of developing Garcinia mangostana seed reveals modulated levels of sugars, organic acids and phenylpropanoid compounds" (Mazlan et al., 2018) .
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