Targeted metabolomics for quantitative assessment of polyphenols and methylxanthines in fermented and unfermented cocoa beans from 18 genotypes of the Brazilian Amazon

The bioactive compounds present in cocoa, such as polyphenols and methylxanthines, are known for their health benefits. The concentration of these compounds in cocoa beans is influenced by genotype and post-harvest processing. This study utilized a targeted metabolomics approach using UPLC-MS/MS to quantify polyphenols (flavan-3-ols, anthocyanins, flavonols, and phenolic acids) and methylxanthines in fermented and unfermented cocoa beans from 18 genotypes largely cultivated in the Brazilian Amazon region. The major compounds identified were theobromine, (-)-epicatechin, procyanidin C1, procyanidin B2, and caffeine. Fermentation significantly reduced the concentration of most compounds, except for protocatechuic acid, which increased. Principal component analysis revealed that chemical differences between fermented and unfermented cocoa beans are more pronounced than those between genotypes, mainly due to flavan-3-ols and anthocyanins. The concentrations of bioactive compounds varied significantly among the 18 genotypes both before and after fermentation. The fermented beans were grouped into three distinct clusters, the genotype CAB214 exhibited the lowest concentrations of bioactive compounds, while CCN51 had the highest. The observed chemical diversity has important implications for the selection of genotypes aimed at producing chocolate with high levels of bioactive compounds and for formulating products in other industries.