The novel application of a quadrupole ion trap mass spectrometer (QITMS) to permanent gas analysis was recently presented by our laboratory. The quantitative performance of the QITMS equaled or surpassed that of other mass analyzers evaluated; however, concern was raised as to the impact of ion-molecule reactions observed within the ion trap. Hydrogen, helium, oxygen, and argon, four permanent gases currently monitored during Space Shuttle launch preparations by the National Aeronautics and Space Administration, were examined in their reactions with common atmospheric and mass spectrometer background components. Rapid charge-exchange and protonation reactions occurred. Greater than 99.8% of hydrogen and 98% of helium ions trapped are lost during a scan cycle predominately through reactions with background nitrogen. The neutralization rate of argon ions varied with water concentration, while increased concentrations of all three gases inflated the oxygen ion signal intensity through charge-exchange. Although such dramatic effects challenge the analytical sensitivity and robustness of QITMS for permanent gas analysis, through proper understanding and control of relevant experimental conditions the QITMS can still function in monitoring applications.