A mass spectrometer is disclosed wherein a z-lens upstream of an orthogonal acceleration Time of Flight mass analyser is repeatedly switched between a first mode wherein ions are transmitted to the mass analyser for subsequent mass analysis with a relatively high transmission and a second mode wherein ions are transmitted with a relatively low transmission. If it is determined that mass spectral data obtained when the mass analyser is in the first mode is suffering from saturation, then suitably scaled mass spectral data obtained when the mass analyser is in the second mode is used instead. If the saturation is severe then the mass spectral data obtained in the first mode may be replaced in its entirety with mass spectral data obtained in the second mode.