Characterization and potential functions of milk fat globule membrane and exosome proteins in donkey and bovine milk: A comparative data-independent acquisition proteomic analysis

Milk fat globule membrane (MFGM) and milk exosome proteins represent two significant categories of functional membrane proteins in milk. This study aimed to identify and compare the potential biological functions of MFGM and exosome proteins between donkey milk (DM) and bovine milk (BM) by data-independent acquisition (DIA) proteomics technology. As a result, 1,441 and 1,491 proteins were identified in DM and BM MFGM proteins, and 1,486 and 1,579 proteins were identified in their respective exosome proteins. The differentially expressed proteins in the MFGM and milk exosomes of DM and BM were all mainly associated with immune regulation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the differentially expressed and species-specific proteins in DM and BM. The core potential functions of MFGM proteins in BM were primarily associated with host defense and immune regulation, whereas those in DM emphasized protein metabolism and local immune regulation. BM exosome proteins were predominantly involved in signal transduction and molecular transport, while DM exosome proteins played prominent roles in immune activation and metabolic homeostasis. These findings could systematically clarify the potential functional properties of MFGM and milk exosome proteins in both DM and BM, contribute to expanding the foundational dataset for milk-derived proteomics research, and support innovation in the dairy industry.