The high catalytic activity and specificity of enzymes can be used to pretreat biomass. Herein, the resourceful, reproducible, cheap, and crude protein-rich cottonseed meal (CM) is selected as a precursor and the protease in the K2CO3–KHCO3 buffer solution is used as the enzyme degradation substance to pretreat CM. The crude protein content is significantly reduced by the protease degradation, and, meanwhile, it results in a looser and porous structure of CM. What is more, it significantly reduces the amount of activator. In the subsequent carbonization process, the K2CO3–KHCO3 in the buffer solution is also used as an activating agent (the mass ratio of CM to activator is 2:1), and after carbonization, the O, S, and N doped porous carbon is obtained. The optimized PCM-800-4 exhibits high heteroatom contents and a hierarchical porous structure. The specific capacitance of the prepared porous carbon reaches up to 233 F g−1 in 6M KOH even when 10 mg of active material is loaded. In addition, a K2CO3–KHCO3/EG based gel electrolyte is prepared and the fabricated flexible capacitor exhibits an energy density of 15.6 Wh kg−1 and a wide temperature range (−25 to 100 °C). This study presents a simple enzymatic degradation and reduced activator dosage strategy to prepare a cottonseed meal derived carbon material and looks forward to preparing porous carbon using other biomass.

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