Chemical drivers of bioactivity in fermented whey and pea proteins assessed by proteomics.

Lactic acid fermentation is a promising strategy to valorize dairy by-products and plant proteins by modifying composition and enhancing functionality; however, links between microbial metabolism, chemical profiles, and bioactivity remain poorly understood. In this study, whey, pea, and their mixture were used as model systems for fermented beverages to investigate how substrate composition influences metabolic pathways and shapes chemical profiles during fermentation by Lacticaseibacillus paracasei AF43. Proteomic and metabolite profiling were integrated to link metabolism to compound formation and bioactivity. Substrate composition drove distinct pathways, shifting from homolactic fermentation in whey to phosphoketolase-mediated metabolism in pea, with intermediate behavior in the hybrid matrix. Whey fermentates accumulated low-molecular-weight peptides (<3 kDa, 0.51 mg/mL) and showed ACE-inhibitory and antimicrobial activity. Pea fermentates exhibited enhanced antioxidant capacity linked to citrate production (0.55 g/L). The hybrid substrate enhanced ACE inhibition, highlighting synergistic effects. These findings provide mechanistic insights for designing functional fermented protein beverages.