Functional proteomic signatures of bovine milk across Chinese dairy regions: quantitative comparison of casein, whey, and MFGM fractions

Milk proteins are major determinants of the nutritional, technological, and bioactive properties of dairy systems, yet region-associated molecular variation under standardized production conditions remains insufficiently characterized. In this study, we performed fraction-resolved, label-free quantitative proteomic analysis of casein, whey, and milk fat globule membrane (MFGM) proteins from bovine milk collected across three major dairy regions of China under controlled production conditions, including standardized breed background, feeding and management practices, lactation stage, milking schedule, and hygiene. A total of 597 proteins were identified, indicating that the overall proteome identity was broadly conserved across regions. In contrast, region-associated differences were observed mainly at the protein abundance level, with whey and MFGM fractions showing greater variation than the casein fraction. Functional enrichment analyses further suggested fraction-dependent differences in immune-, metabolism-, and membrane-related categories. These findings indicate that region-associated variation in bovine milk is reflected primarily by quantitative remodeling superimposed on a conserved proteomic background. Under standardized large-scale production conditions, the study provides a comparative molecular description of bovine milk proteomes across regions and offers a basis for future studies on dairy functionality and nutrition-related applications at the farm-composite level. • Region-associated abundance variation in milk proteomes under standardized production. • A conserved proteomic backbone was shared across dairy regions. • Whey and MFGM fractions exhibited greater quantitative plasticity than casein. • Region-associated abundance differences formed coherent molecular modules. • The study establishes a region-resolved molecular baseline for bovine milk.