Comparative Proteomics Profiling of Milk Fat Globule Membrane Protein Powders from Bovine Buttermilk and Cheese Whey

The milk fat globule membrane (MFGM), derived from dairy byproducts, possesses numerous beneficial physiological functions. However, systematic comparisons of MFGM protein powders (MFGMPs) from different raw materials and processing conditions remain limited. This study employed Astral-DIA-based label-free quantitative proteomics to characterize four MFGMPs: sweet buttermilk-MFGMP (SBMP), acid buttermilk-MFGMP (ABMP), sweet cheese whey-MFGMP (SWMP), and acid cheese whey-MFGMP (AWMP). A total of 1624 proteins were identified, including 487 significant differential abundance proteins (DAPs), demonstrating that both raw material and processing method significantly influence protein composition. SBMP exhibited the highest retention of immune-related proteins, whereas acid-treated samples (ABMP, AWMP) were enriched in lipid metabolism-associated proteins. Conversely, cheese whey-based ingredients (SWMP, AWMP) showed greater susceptibility to protein loss during thermal and enzymatic processing. These findings provide a theoretical basis for optimizing dairy byproducts valorization and developing tailored MFGMP ingredients for functional foods targeting immune, metabolic, and gut health.