Comparative analysis of whey protein in goat milk throughout the lactation cycle using data-independent acquisition and data-dependent acquisition based proteomics methods

We have investigated whey proteome of goat milk at 1, 3, 30, 90, 150, and 240 d using data-independent acquisition and data-dependent acquisition quantitative proteomics approaches. The clustering and principal component analysis revealed that the protein components in goat milk was associated with specific lactation stages. Protein-protein interaction showed that fibronectin had more interaction with other proteins and was considered as a central node. Our results can provide a better understanding of the whey proteome during the lactation cycle of dairy goats and indicate which proteins are important for the development of newborns and mammary gland.