Effect of Genotypic and Processing on Antioxidant and Chemical Characteristics of Indonesian Cocoa Beans as Revealed by ATR-FTIR Fingerprint and Multivariate Data Analysis

Indonesia has a diverse range of cocoa genotypes. However, research on how these genotypes and post-harvest processing affect the antioxidant activity of cocoa beans remains limited. This research aimed to identify the infrared (IR) spectral regions of Indonesian cocoa beans affected by genotype and post-harvest treatments (fermentation and roasting) and to determine which IR regions are associated with in vitro antioxidant activity (DPPH, ABTS, and FRAP assays). The study combined an ATR-FTIR spectrophotometer, antioxidant assays, and multivariate analyses (PCA, OPLS-DA, and OPLS). PCA revealed significant variation due to post-harvest processing, whereas genotypic differences were not distinguishable in the IR spectra. OPLS-DA and OPLS identified IR spectral markers for unfermented, fermented, roasted, and antioxidant-rich cocoa beans. C–H out-of-plane deformation (986–989 cm−1) marked unfermented and antioxidant-rich samples. Fermented beans showed alkyl ketones (1222–1230 cm−1), aromatic aldehydes (1387–1389 cm−1), and carboxylic acid C=O vibrations (1649–1651 cm−1) signals. Roasted beans exhibited alkyl pyrazine peaks at 1508, 1518, 1557, and 1598–1600 cm−1. These findings confirm that ATR-FTIR fingerprinting combined with multivariate analysis effectively identifies antioxidant-related functional groups and processing-specific markers. This approach provides a practical tool for quality control in the cocoa industry across various genotypes and post-harvest treatments.