A method of mass spectrometry is disclosed wherein an Electron Capture Dissociation, Electron Transfer Dissociation or Surface Induced Dissociation fragmentation device is repeatedly switched between a high fragmentation or reaction mode and a low fragmentation or reaction mode. Parent ions from a first sample are passed through the device and parent ion mass spectra and fragmentation ion mass spectra are obtained. Parent ions from a second sample are then passed through the device and a second set of parent ion mass spectra and fragmentation ion mass spectra are obtained. The mass spectra are then compared and if either certain parent ions or certain fragmentation ions in the two samples are expressed differently then further analysis is performed to seek to identify the ions which are expressed differently in the two different samples.