NOVELTY - Enzyme based method (m1) of separating a protein from protein-containing material derived from plant seeds, fruits or other biomass comprises: (a) combining the protein-containing material with a liquid enzyme medium comprising at least one cellulase, at least one hemicellulase and at least one pectinase; (b) mixing, where the enzymes in the liquid enzyme medium will hydrolyze the polysaccharides and oligosaccharides contained in the protein-containing material into saccharides that are soluble in the liquid enzyme medium; and (c) collecting the protein material.    USE - The method is useful for separating a protein from protein-containing material derived from plant seeds, fruits or other biomass to form a protein-containing powder (all claimed) that is useful in high-quality feed, food and industrial uses.    ADVANTAGE - The method: is simple; and produces soy products having a high protein content and low level of indigestible components, while generating and capturing the monosaccharide-rich liquid byproduct that can be converted by fermentation to various valuable bioproducts such as arabitol and other sugar derivatives, enzymes, xanthan gums, alginates, microbial polyesters such as polyhydroxyalkanoates and other biopolymers, rhamnolipids, sophorolipids and other biosurfactants, succinic acid, citric acid and other organic acids, pharmaceuticals including antibiotics, specialty chemicals, lipids, nutritional compounds, products from heterotrophic algae and bioethanol.    DETAILED DESCRIPTION - INDEPENDENT CLAIMS are also included for:    (1) a method (m2) of producing enzymes for use in the hydrolysis of polysaccharides and oligosaccharides in soybean meal, soy flour, soy flake and soy powder comprising: (a1) forming a seed culture by placing at least one fungus, a first carbon source, and a first nitrogen source in a container and agitating for 72 hours; (b1) transferring the contents of the seed culture to a fermentation vessel and adding at least a second carbon source, a second nitrogen source and water; (c1) adjusting the pH of the contents of the fermentation vessel to a pH of 3-8; (d1) growing the fungus in the fermentation vessel; and (e1) collecting the product of step (d1) which comprises a mixture of a solid waste material and an enzyme-containing liquid;    (2) a method (m3) of making monosaccharide-containing liquid for use in fermentation comprising: step (a) as above per se; (b2) stirring or agitating the mixture of step (a), where the enzymes in the liquid enzyme medium will hydrolyze the polysaccharides and oligosaccharides contained in the protein-containing material into monosaccharides and other sugars that are soluble in the liquid enzyme medium; (c2) collecting the monosaccharide-containing liquid and precipitating out the dissolved proteins and other biopolymers; and (d2) collecting the monosaccharide-containing liquid;    (3) a method (m4) of making a soy protein isolate comprising: (a3) combining the protein-containing material with the liquid enzyme medium; step (b2) as above per se, and dissolving any water soluble proteins; (c3) collecting the dissolved protein-containing liquid and heating it to a temperature of 60-100 degrees C to precipitate out the dissolved proteins; and (d3) collecting the precipitated proteins as a soy protein isolate;    (4) a protein-containing powder;    (5) a liquid enzyme medium;    (6) a soy-based monosaccharide-containing liquid made; and    (7) a soy protein isolate.