While all three proteins have different functions to perform, when combined together, they yield results like never before. The difference between these three types of proteins is in the way they are processed. The difference between individual proteins also lies in the way amino acids unite into peptides. The nutritional content varies across the types of Whey Protein. Whey Protein Concentrate contains 35-89% of Protein whereas Whey Protein Isolate contains more than 90% of Protein. Whey Protein Hydrolysate, on the other hand, contains 80-90% of Protein.