During cocoa processing, there can be the formation of bioactive amines, which are compounds that play relevant roles not only in plant development but also in human health. Thus, we aimed to investigate the presence and levels of bioactive amines during the processing of two important varieties of cocoa (PS 1319 and Parazinho). The seeds were fermented using five different pulp proportions: 100% (E1), 80% (E2), 60% (E3), and 0% (total pulp removal) (E4). The beans were fermented and dried on a farm following traditional procedures. Soon after, they were roasted and processed into chocolates with 60% cocoa in the laboratory. Bioactive amine contents were determined by ion-pair reversed-phase HPLC and fluorometric detection in the samples before, during, and after fermentation, after drying and roasting (nibs), and in the liquor and chocolate. The only amines found before processing in PS 1319 and Parazinho, respectively, in dry weight basis (dwb), were putrescine (pulp, 13.77 and 12.31; seed, 5.88 and 4.58) and serotonin (seed, 2.70 and 2.54). Fermentation was shorter for Parazinho (156 h) compared to PS 1319 (180 h). The changes in amines were affected by the cocoa variety. During drying, the presence of cadaverine stood out, appearing in all treatments of the PS 1319 variety, reaching 17.96 mg/kg dwb, and in two treatments of the Parazinho variety (100 and 60% pulp). During roasting, most of the amines decreased, except for phenylethylamine, which increased up to 2.47 mg/kg dwb for Parazinho and 1.73 mg/kg dwb for PS 1319. Most of the amines formed and built up (e.g., tyramine, putrescine, and cadaverine) during fermentation were not available or were at low levels in the nibs. Most of the amines found during processing did not reach the final product (chocolate), except for cadaverine in PS 1319 without pulp (7.54 mg/kg dwb). Finally, we confirmed how pulp content, processing, and variety influence the content of bioactive amines in cocoa and chocolate. These changes can be better demonstrated through a heatmap and principal component analysis.
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