Electron-based fragmentation methods have revolutionized biomolecular mass 
spectrometry, in particular native and top-down protein analysis. Here, we 
report the use of a new electromagnetostatic cell to perform electron capture 
dissociation (ECD) within a quadrupole/ion mobility/time-of-flight mass 
spectrometer. This cell was installed between the ion mobility and 
time-of-flight regions of the instrument, and fragmentation was fast enough to 
be compatible with mobility separation. The instrument was already fitted with 
electron transfer dissociation (ETD) between the quadrupole and mobility regions 
prior to modification. We show excellent fragmentation efficiency for denatured 
peptides and proteins without the need to trap ions in the gas phase. 
Additionally, we demonstrate native top-down backbone fragmentation of 
noncovalent protein complexes, leading to comparable sequence coverage to what 
was achieved using the instrument's existing ETD capabilities. Limited 
collisional ion activation of the hemoglobin tetramer before ECD was reflected 
in the observed fragmentation pattern, and complementary ion mobility 
measurements prior to ECD provided orthogonal evidence of monomer unfolding 
within this complex. The approach demonstrated here provides a powerful platform 
for both top-down proteomics and mass spectrometry-based structural biology 
studies.