Differentiation of Indonesian Specialty Cocoa (Theobroma cacao) Varieties and Origins Using Phenolic Contents, Antioxidant Activities, and Spectrometric Fingerprints for Traceability

Abstract

This study investigated the influence of geographical origin and genetic variety in differentiating specialty cocoa (Theobroma cocoa) from various regions across Indonesia. By leveraging intrinsic markers such as antioxidant activity, total phenolic (TPC) and total flavonoid contents (TFC), infrared (IR), gas chromatography-mass spectrometry (GC-MS) fingerprints, and sensory profiles, we successfully distinguished cocoa origins and varieties through principal component analysis (PCA) and hierarchical cluster analysis (HCA). Among 27 samples from five provinces, the West Papua beans exhibited the highest antioxidant activity, TPC, and TFC. In addition, the PCA analysis reduced 63 intrinsic quality markers into two principal components (PC1 and PC2), explaining 84.8% of the variance, while HCA categorized samples into three distinct groups. The primary discriminating intrinsic markers included volatile compounds like 2- and 3-methyl butanoic acids, 2-methyl propanoic acid, 2,3-butanediol, 5-butyl nonane, phenylethyl alcohol, 2-nonanol, and 4,6-dimethyl dodecane, alongside with sensory attributes (acidity, floral notes) and total phenolic content. These results highlighted the importance of incorporating intrinsic markers into grading systems to enhance the traceability and classification of Indonesian specialty cocoa.