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Atmospheric pressure nonthermal plasmas have demonstrated rapid deactivation of bacterial spores on surfaces. For example, the lethal Ames strain of Bacillus anthracis, known as anthrax, has been deactivated after 1 min of ionized gas exposure. The hypothesized plasma-produced spore deactivation processes, such as ultraviolet light, hot gases, and intense electric fields, were isolated. Exposure to each of these assumed deactivation mechanisms has demonstrated little to no effect on the sterilization of bacterial spores at plasma discharge exposure levels. The focus of this study has therefore, been on the determination of the mechanism of spore lysis and resultant deactivation from the interaction of the ionized gas with the biological substances within the spore. The rapid lysis of bacterial spores and other cells by nonthermal plasma has led to the integration of this approach with pathogen detection instruments, such as mass spectrometers. The identification by mass spectrometry of the extracted proteins from plasmalyzed spores has facilitated the discovery and subsequent sequencing of small acid soluble proteins (SASP) within the spore responsible for protecting bacterial spores. The identified SASP surrounds the nucleic acids providing some measure of protection from insult in the environment. The plasma discharge rapidly interacts with this SASP causing deactivation of the spore.