Electron transfer dissociation (ETD) in the Thermo Scientific LTQ XL™ linear ion trap mass spectrometer takes less than 350 ms per experiment, which is fast enough to allow alternating CID and ETD scans for every selected precursor ion in a chromatographic time scale. ETD is an activation method that is complementary to CID. It not only favors multiply charged peptides, but also preserves labile post translational modifications (PTMs). Recent studies indicate that increased identification confidence is obtained using a combined CID and ETD approach for peptide/protein identification.