Mass Analysis Using Alternating Fragmentation Modes

A method for the analysis of mixtures of components, comprising:

• (a) separating or partially separating different components of a mixture of a first sample by means that causes the components to elute sequentially over a period of time;
• (b) forming precursor ions from the components in the eluent, during the period of time;
• (c) receiving the precursor ions in an Electron Capture Dissociation fragmentation device, during the period of time;
• (d) repeatedly switching, altering or varying the Electron Capture Dissociation fragmentation device back and forth, during the period of time, between a hi-fragmentation mode and a low-fragmentation mode, to alternately produce product ions in the hi-fragmentation mode and to produce substantially fewer product ions in the low-fragmentation mode;
• and
• (e) obtaining mass spectra, during the period of time, from precursor and product ions received from the Electron Capture Dissociation fragmentation device, wherein at least one of the mass spectra is obtained in association with the Electron Capture Dissociation fragmentation device in the hi-fragmentation mode, and at least one of the mass spectra is obtained about a second later in association with the Electron Capture Dissociation fragmentation device in the low-fragmentation mode.