Milk of different species may vary in protein quality and quantity. A proteomic approach for high-resolution analyses of the complex mixture of milk proteins by SDS polyacrylamide gel electrophoresis (PAGE) is of great importance due to its exceptional resolving capacity. Degreased milk samples (non-infected) of Nili-Ravi buffaloes, Sahiwal and cross-bred cows were used for comparative protein profiling using 12% SDS polyacrylamide gels. Protein profiling clearly resolved the major milk peptides. Qualitative differences were observed in high, medium and low molecular weight (MW) zones. In high molecular weight (M. wt.) zone, proteins of ~208 kDa and ~190 kDa were detected in all tested samples. In medium M. wt. zone, three peptides i.e. lactoferrin (78.2kDa), serum albumen (66.2kDa) and heavy chain of immunoglobulin (IgG) (54 kDa) were detected in all samples while a prominent band of ovalbumen (45kDa) was also detected mainly in cow milk samples. In low M. wt. zone, clear bands of milk caseins were detected. All four casein (CN) bands i.e. αS₂ – CN (29 kDa), αS₁ – CN (27 kDa), β - CN (24 kDa) and κ- CN (22 kDa) were detected in cross-bred and Sahiwal cows. However, in milk of Nili-Ravi buffaloes, three casein protein i.e. αS₂ – CN (29 kDa), β - CN (25 kDa) and κ- CN (22 kDa) were detected. In milk of Nili-Ravi buffaloes, αS₁ – CN (27 kDa) was not detected. Moreover, a band of β-lactoglobulin (~18 kDa) was detected in milk of cross-bred cows and not in other samples especially Nili-Ravi buffaloes. As the αS₁-casein and β-lactoglobulin are the major allergens, milk of Nili-Ravi buffaloes that lacks these peptides can be used for development of non-allergic or hypoallergenic dairy products. Deferential peptides may also help to distinguish the milk from different tested breeds.

Key words: kDa, Lactoferrin, αS₁-casein, β-lactoglobulin