The present invention is directed to enzyme based methods for separating protein from protein-rich materials derived from plant seeds, fruit, or other biomass and products made therefrom. The protein content in the resulting products is improved by separating and removing the carbohydrates from around the proteins in, for example, soybean meal. This removal is facilitated by the enzymatic hydrolysis of poly- and oligomeric carbohydrates into monosaccharides and other water soluble sugars. The present invention provides for the production of three streams of useful materials. The first is an enriched protein material comparable to the known SPCs but without significant quantities of undigestible oligosaccharides and polysaccharides. The second is an SPI made from the soluble protein in the hydrolysate which is valuable for high-quality feed, food and industrial uses. The third is the soluble saccharides and hydrolyzed carbohydrates (releasing sugars) that can be converted by fermentation to various valuable bioproducts.