A method for determining a mass-to-charge ratio of an analyte is described that accounts for space charge limitations when there are relatively high concentrations of ions in an ion trap. The method includes calibrating a mass spectrometer for the space charge effects caused by the analyte ion itself and also for adjacent ions that have a mass-to-charge ratio different than the analyte ion. A mass spectrum can be measured for both an analyte ion and an adjacent ion where there is a relatively high concentration of ions in the ion trap. A corrected mass-to-charge ratio can be calculated for an analyte ion based on the measured analyte mass-to-charge ratio, the measured analyte abundance, the first mass-to-charge ratio difference, and the measured first adjacent ion abundance. The resulting corrected mass-to-charge ratio has an increased accuracy and at the same time improves the dynamic range of the ion trap mass analyzer.