Value of the Data •The atlas provides the presence of proteins within a milk fraction to facilitate extraction and quantification. •The atlas provides information on the lactation stage at which a protein of interest is secreted into milk. •The applied output is for nutrition researchers interested in milk protein allergy and/or digestibility in humans, and for dairy industry. •The atlas may be used to identify potential biochemical properties of proteins/peptides in bovine milk, or to isolate proteins of interest. •This atlas provides information about the molecular signatures of metabolic adaptations that occur throughout lactation. •This computational approach to obtain an atlas of milk proteins using publicly available data may be an elegant alternative or complementary to animal experiments.