Data-independent acquisition quantitative proteomics analysis of milk fat globule membrane proteins in rabbit colostrum and mature milk

Proteomics has been widely used to identify proteins in the milk fat globule membrane (MFGM). However, the characteristics of MFGM proteins in rabbit colostrum (RC) and mature milk (RM) remain largely unexplored. This study aimed to profile the rabbit MFGM proteins and assess differences in component and functional profiles between RC and RM through data-independent acquisition (DIA) quantitative proteomics. We established the proteomic profile of rabbit MFGM, identifying 3,548 proteins across RC and RM. Notably, typical MFGM proteins, such as Perilipin 2 (PLIN2), Xanthine dehydrogenase/oxidase (XDH/XO), and Apolipoprotein, were detected in rabbit milk, and 10 of these were confirmed by Parallel reaction monitoring (PRM) detection. Comparative analysis revealed 480 differentially expressed MFGM proteins (DEMPs), with 379 up-regulated and 101 down-regulated DEMPs in RC compared to RM. This included 68 unique proteins in RC, 5 in RM, and 407 DEMPs expressed in both groups. The GO analysis indicated that DEMPs are predominantly involved in processes such as proteolysis, cell adhesion, and ion transport, with enrichments of 32, 14, and 14 DEMPs, respectively. KEGG analysis gathered 56 significant pathways, most of which were categorized into Human Diseases (20/56) and Metabolism (14/56). Protein–protein interaction (PPI) network analysis emphasized the core role of DEMPs (e.g., proteasome subunits and integrins) in human diseases (e.g., Alzheimer’s disease) and in signal transduction (e.g., the PI3K-Akt signaling pathway). These results offer theoretical insights into the components and functions of rabbit milk, suggesting a novel way to enhance the economic benefit of the rabbit industry.