In this application note we have demonstrated that ECD fragmentation is useful in providing extensive backbone fragmentation of intact proteins, which is valuable for the protein characterization particularly when combined with the high mass accuracy of the LTQ FT.

With the configuration of both ECD and IRMPD available on the LTQ FT, it is possible to do “activated ion ECD” (AI-ECD) by first activating the ions with the IR laser and then dissociate them by ECD. This enables ECD to provide more extensive, and complementary sequence information.

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