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The atmospheric-pressure plasma jets (APPJs) are nonthermal plasma sources studied for their high potential in many medical applications where conventional solutions failed. In this paper, we show the influence of helium APPJ on pepsin structure and function. The APPJ source is characterized using voltage-current measurements, optical emission spectroscopy, and high-speed imaging. Pepsin powder was exposed to the action of the plasma jet, and then, spectroscopic investigations were carried out to obtain information on the structural modifications. Protein function was tested using an enzymatic assay.