Dynamic DIA proteomics of mare's milk reveals distinct colostrum signatures and stage-specific lactation profiles

This study used data-independent acquisition (DIA) proteomics to analyze the changing protein content of mare's milk (n = 3) throughout the entire lactation period (days 1-120), with samples taken at seven different times. Principal component analysis (PCA) revealed that the protein composition of colostrum on day 1 differed markedly from that of later lactation stages. Colostrum-specific proteins such as IgG, IgM, IgE, AGPAT1, NPVF and CAMK2G were associated with rapid energy supply, neurodevelopment and immune defense. In contrast, mature milk was enriched in proteins involved in sustained nutrient metabolism and cellular homeostasis. Notably, the concentrations of key functional proteins, such as lactoferrin and lysozyme, increased progressively throughout lactation. PRM-based targeted quantification validated key DIA results. Overall, this study refines the definition of mare's colostrum and provides important insights into the stage-specific functional roles of milk proteins throughout lactation.