Fast multiple electron capture dissociation in a linear radio frequency quadrupole ion trap

We developed a fast electron capture dissociation (ECD) device using a linear radio frequency-quadrupole (RFQ) ion trap. The device dissociated peptides and proteins using a focused electron beam with an intensity of 0.5 mu A and a diameter of 1 mm. The electron capture rate was 13%/ms for doubly charged peptides, and the total amount of ECD products was identical to the theoretical limit, i.e., 50% of incident precursor ions were observed as maximum ECD products by electron irradiation of 7 ms in a pulse counting detection scheme. Coupling this ECD device to a time-of-flight mass spectrometer, we applied multiple ECD. Protonated ubiquitin precursor ions with a charge state of 10 were repeatedly cleaved by ECD, i.e., charge-reduced species and their highly charged fragments were cleaved again and again, creating lower charged products, leaving only singly to triply charged states among the final products. Meanwhile with the amount of electron irradiated, lower charged products increased. Applying an electron beam for 8 ms, we obtained 96% of the total sequence coverage using a 40 fmol sample except at three proline sites. This fast ECD device should be widely applicable to proteomics including post-translational modification analysis and top-down analysis.