Advances in Proteomics and Functional Foods from Fermentation and Bioencapsulation of Andean Grains and Tubers: Applications and Perspectives

The transformation of Andean grains and tubers through fermentation and bioencapsulation has emerged as a key strategy to enhance their nutritional, functional, and biotechnological value, driven by advances in proteomic and metabolomic techniques. This study aimed to systematize recent evidence on the biochemical and functional modifications induced by these processes and their potential application in the development of functional foods. The methodology integrated 67 studies analyzed using tools such as R 4.5.1 with the JupyterLab interface 4.5.2, SCImago Graphica Beta 1.0.53, and VOSviewer 1.6.20, incorporating data generated through LC-MS/MS, UHPLC-QTOF, Orbitrap platforms, transcriptomics, and combined omics approaches, considering original studies published between 2020 and 2025. The main findings indicate substantial increases in free amino acids (up to 64.8%), phenolic compounds (2.9–5.2%), and antioxidant activity (up to 45%), along with the identification of 430 polyphenols, 90 flavonoids, 14 novel oxindole acetates, and bioactive peptides with IC50 values ranging from 0.51 to 0.78 mg/mL. Bioencapsulation showed controlled release of bioactive compounds, highlighting nanocapsules of 133–165 nm with a maximum release of 9.86 mg GAE/g. In conclusion, the combination of fermentation and encapsulation enhances the stability, bioavailability, and functionality of Andean crops, supporting their industrial adoption for the development of sustainable nutraceutical foods that improve health and promote the valorization of traditional resources.