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This work consists of two parts that are concerned with different aspects of the ion dynamics in quadrupole ion trap (QIT) mass spectrometers. The first part describes the development and application of a method for detecting changes of ion kinetic energy distributions (KED), based on the interaction of ions with a variable potential barrier in the ion transfer stage. The potential barrier is introduced by applying a deceleration potential at the transfer stage exit. Deceleration potential response (DPR) curves are measured with a Faraday cup electrode and an ion trap. The Faraday cup measurements allow direct evaluation of the KED, because the data reflect the direct interaction of the ion charge with the potential barrier. In contrast, the DPR curves measured with the ion trap exhibit complex shapes. Modeling of the ion injection process confirmed that this is the result of the energy-dependent ion acceptance function of the ion trap which is superimposed on the DPR. The fringe field between the transfer stage exit and ion trap entrance electrodes introduces an RF-phase-dependent modulation of the ion kinetic energy. As conclusion, the absolute KED cannot be precisely determined from the ion trap data; however, the method is sensitive to changes of the KED. Further characterization of the method demonstrated that changes of the transfer voltages are conserved in the kinetic energy distribution only downstream of the second vacuum stage in Bruker HCT and amaZon mass spectrometers. Collisional re-equilibration of the kinetic energy occurs in the first and second vacuum stages. The RF voltage, or more generally, the stability parameter qz, was found to have a systematic impact on the shape of the DPR curves. The effect of different incident KEDs was studied in simulations to support interpretation of experimentally observed shifts of the DPR. It was demonstrated that the method supports the investigation of the ion evolution with electrospray ionization (ESI). The combination with survival yield experiments revealed that ion activation in the ion transfer stage impacts on the observed ion distribution due to changes of the KED. Finally, the method was applied to study the impact of experimental parameters on the KED of ions generated with ESI. It was found that the ESI tip voltage as well as the addition of chemical modifiers to the background gas strongly impacts on the ion formation process, likely due to a change of the drop-let formation and evolution dynamics. The results support the hypothesis that gas phase ion formation with ESI is not completed within the ion source but occurs downstream within the ion transfer stage. In the second part, the formation and storage of ions in a Fourier transform (FT) QIT with in-trap electron ionization (EI) is described. Ionization is carried out in a transient gas pulse within the quadrupolar field, which introduces nonlinear dependencies of the ionization rate on controllable ionization parameters. Modeling of the gas pulse suggests that chemical ionization (CI) conditions can easily be attained during ionization, i.e., ion-molecule chemistry is invoked. In combination with the RF-modulated electron beam energy, this renders the interpretation of mass spectra difficult and thus compromises compound identification with EI databases. Ionization rates, as determined from electron beam simulations, suggest that the trap is easily overloaded with ions. The controlled ejection of matrix ions, e.g., by instability ejection or selective excitation techniques, is thus a prerequisite for detection of compounds present at low mixing ratios. Collisions of ions with the background gas during the sample gas pulse adversely affect the ion lifetime in the ion trap. Collision-induced ion loss was found to significantly contribute to suppression of low-mass ions. This effect distorts the observed ion population significantly and leads to pronounced loss of spectral information. The simulation framework IDSimF, concurrently developed in a separate major research effort, was successfully applied in this work. The simulation results were in very good agreement with literature data. The capability of simulating realistic ion numbers, i.e., on the order of several ten thousand ions, in ion trap applications with consideration of space charge effects renders IDSimF a valuable tool for future complex ion dynamics studies.