Abstract: An ion trap mass spectrometer uses electrospray ionization to introduce multiply-charged positive ions in an axial direction into a quadrupole ion trap and glow discharge ionization to introduce singly-charged negative ions in a radial direction into the ion trap. Methods of controlling ion-to-ion charge transfer reactions include applying a combination of a dipolar DC voltage and a dipolar RF voltage across endcap electrodes to allow partial charge state neutralization reactions to occur between the positive and negative ions and then control suspension and resumption of further charge state neutralization reactions. The remaining ions can be further processed and transformed and a mass spectrum created by scanning a quadrupolar RF field.