The invention referres to analytic methods, the accuracy of which is increased by relating signals of analyte ions to those of reference ions, or by relating ion signals from measuring methods under special conditions to those of reference methods. If such "comparative" analysis procedures are performed in ion trap mass spectrometers, problems arise with the low dynamic measuring range covered by one spectrum in such mass spectrometers and, if different spectra are compared, with the control of the space charge within the ion trap. The invention consists in acquiring analyte spectra and reference spectra in different acquisition procedures, alternating between both types of spectrum acquisitions as fast as possible, whereby control of the space charge in the ion trap proceeds separately for the spectra of both types, the control being related to previously acquired spectra of the same type. A similar procedure can be set up, if measuring results of two different sets of measurement conditions have to be compared. The control variable for the space charge control is derived from the last respective individual spectra scanned under the same conditions. Due to this fast interchanging of individual spectra, time-saving control of the space charge is achieved on the one hand, and a large dynamic measurement range is available on the other.