A mass spectrometer is disclosed comprising a liquid chromatography device for separating ions. A gas phase ion-neutral reaction device is arranged downstream to perform a gas phase ion-neutral reaction such as Hydrogen-Deuterium exchange. A control system is arranged to automatically and repeatedly switch the reaction device back and forth between a first mode of operation and a second mode of operation, wherein in the first mode of operation at least some parent or precursor ions are caused to react within the reaction device and wherein in the second mode of operation substantially fewer or no parent or precursor ions are caused to react.