Improved enzyme based methods of separating protein from protein-rich material are provided. A method can include utilizing a modeling equation to more effectively hydrolyze the various types of carbohydrates present in a protein-rich material. A method can include a fed-batch method of incrementally adding a protein-rich material, an enzyme broth, or both a protein-rich material and an enzyme broth. A method can also include partially or completely recycling the hydrolysate.