Identification and comparison of milk fat globule membrane and whey proteins from Selle Francais, Welsh pony, and Tieling Draft horse mares milk

•773 MFGM proteins and 596 whey proteins were found in horse’s milk using label-free quantitative proteomics.•Physiological differences were observed in MFGM and whey proteins among different horse breeds.•β-lactoglobulin had the lowest concentration in Selle Français mare’s milk.