A method is disclosed of identifying parent ions by matching daughter ions found to be produced at substantially the same time that the parent ions elute from a mixture. Ions emitted from an ion source (1) are transmitted to a fragmentation device (4) comprising an Electron Capture Dissociation, an Electron Transfer Dissociation or a Surface Induced Dissociation fragmentation device. The fragmentation device (4) is alternately and repeatedly switched between a first mode wherein the ions are substantially fragmented to produce daughter ions and a second mode wherein the ions are not substantially fragmented. Mass spectra are taken in both modes. At the end of an experimental run parent and daughter ions are recognized by comparing the mass spectra obtained in the two different modes. Daughter ions are matched to particular parent ions on the basis of the closeness of fit of their elution times, and this enables parent ions then to be identified.