Impact of ion magnetron motion on electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry

Electron capture dissociation (ECD) efficiency in a 9.4 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer varies periodically with the time interval between ion and electron injection. The observed modulation frequency correlates to within 1% with ion magnetron frequency, most probably due to misalignment between the ion beam and the electron beam. The optimum ECD conditions are obtained by correctly phasing electron injection with the ion magnetron motion. Displacement of the trapped ion cloud by variation of the ICR trap radial electric field decreases ECD efficiency modulation amplitude. Experiments directly suggest that only ions interacting with electrons at the moment of electron injection participate in ECD reactions.