Electron capture dissociation (ECD) is performed by transmitting an electron beam through a cell along an electron beam axis, generating plasma in the cell by energizing a gas with the electron beam, and transmitting an ion beam through the interaction region along an ion beam axis to produce fragment ions. Generating the plasma forms an interaction region in the cell spaced from and not intersecting the electron beam, and including low-energy electrons effective for ECD. The ion beam axis may be at an angle to and offset from the ion beam axis, such that the electron beam does not intersect the ion beam.