Abstract: Two-dimensional gel electrophoresis (2DGE) was applied in protein fingerprinting of cow and goat milk products. First of all, the protein profiles of cow and goat milk were compared to find out the differential proteins. Afterwards, the specificity of this method was tested by applying it to infant formula and whey protein powder from cow and goat milk and the sensitivity was evaluated by using different proportion mixtures of cow milk infant formula and goat milk infant formula. Finally, commercialized infant formula, liquid milk and yoghurt samples were tested. 2DGE method was confirmed to be highly informative and highly repeatable and it could visually present protein profiles. As proved by our data, liquid milk, whey protein and infant formula could be distinguished clearly by 2DGE and the detection limit reached 5%. Of 8 commercialized samples, one labelled as fermented goat milk was identified as cow milk with a clear protein fingerprint which could visually reflect the authenticity of the product

Key words: two-dimensional gel electrophoresis, goat milk, cow milk, protein