© 2015 by Begell House, Inc. For biological and medical applications of low-temperature atmospheric-pressure plasmas (APPs), gas- and liquid-phase chemical reactions caused by the plasmas determine the effectiveness of the APP-based treatments of biological systems. In this study, ions generated by helium-based low-frequency APP jets were identified by mass spectrometry. It is shown that, among all positive ions generated by plasma jets in ambient air, hydronium ions (H3O+) are the dominant ions that form water clusters. The stability of a hydronium ion with water molecules suggests that all positive ions generated by plasma jets would transfer their charges to hydronium ions if water molecules were abundant, such as in humid air or water. Similarly, it is shown that, among all negative ions generated by the plasma jets in ambient air, relatively few, such as OH-, HO2-, NO2-, NO3-, HCO3-, and HCO4-, form water clusters stably. The densities of positive and negative ions generated in ambient air by the APP jet system, as well as the concentrations of H2O2 and NO2- generated in pure water exposed to the same plasma, have been also measured.