A method of operating a Fourier Transform (FT) mass analyzer, which has a plurality of selectable resolving power settings, includes storing an optimized voltage value in association with each one of the plurality of selectable resolving power settings. More particularly, the optimized voltage values for at least two of the selectable resolving power settings differ from one another. When a user selects one of the plurality of selectable resolving power settings, the optimized voltage value that is stored in association therewith is retrieved. At least one voltage setting of the FT mass analyzer is controlled, based on the retrieved optimized voltage value, and an analytical scan is performed at the selected one of the plurality of selectable resolving power settings for a population of ions within the FT mass analyzer.