Currently in America the biofuel ethanol is primarily being produced by the dry grind technique to obtain the starch contained in the corn grains and subsequently subjected to fermentation. This so-called 1st generation technology has two setbacks; first the lingering debate whether its life cycle contributes to a reduction of fossil fuels and the animal feed sectors future supply/demand imbalance caused by the co-product dry distillers grains (DDGS). Additional utilization of the cellulosic components and separation of the proteins for use as chemical precursors have the potential to alleviate both setbacks. Several different corn feedstock layouts were treated with 2nd generation ammonia fiber expansion (AFEX) pre-treatment technology and tested for protein separation options (protease solubilization). The resulting system has the potential to greatly improve ethanol yields with lower bioprocessing energy costs and satisfy a significant portion of the organic chemical industry.