Multivariate Integration of Functional and Compositional Transitions in Gluten-Free Composite Flours Based on Amaranthus caudatus and Lupinus mutabilis

The transition from starch-dominated to protein-enriched gluten-free systems represents a critical step in improving the functional and nutritional quality of composite flours. This study investigated the effects of progressive substitution of Amaranthus caudatus (amaranth) with Lupinus mutabilis (Andean lupin) on the physicochemical, rheological, and antioxidant properties of gluten-free flour blends. A multimodal dataset comprising 33 variables across six measurement domains (proximal composition, hydration properties, thermomechanical behavior, pasting profiles, particle size, and antioxidant activity) was analyzed using an integrated framework combining univariate inference (FDR-adjusted p-values), PCA, Multiple Factor Analysis (MFA), and sparse Partial Least Squares Discriminant Analysis (sPLS-DA). Results revealed that increasing lupin content (10–40%) significantly increased protein and fiber levels while decreasing starch content, leading to higher water absorption capacity and reduced peak viscosity and setback. Multivariate models showed that the protein/fiber–starch trade-off was the principal axis of compositional differentiation (PC1, ~41% variance), while PC2 captured rheological and antioxidant variability, with formulations containing higher proportions of amaranth exhibiting greater antioxidant activity. The sPLS-DA model achieved 72% separation accuracy with moisture, protein, water absorption, and torque parameters as top discriminants. These findings provide an evidence-based framework for gluten-free flour optimization using Andean crops and highlight how statistical modeling can inform targeted formulation decisions. The approach is transferable to other compositional transitions in food systems, underscoring the utility of multivariate analytics in applied food research. The multivariate framework further suggests that intermediate substitution levels may offer an optimal balance between nutritional enrichment and rheological functionality.