A method for the analysis of mixtures of components includes separating or partially separating different components of a mixture of a sample by means that causes the components to elute sequentially over a period of time, forming precursor ions from the components in the eluent, repeatedly switching, altering or varying an Electron Capture Dissociation fragmentation device back and forth between a hi-fragmentation mode and a low-fragmentation mode to alternately produce product ions from the precursor ions in the hi-fragmentation mode and to produce substantially fewer product ions in the low-fragmentation mode, and obtaining mass spectra during the period of time from the precursor and product ions received from the Electron Capture Dissociation fragmentation device.