Modern
ion mobility instrumentation is typically operated above
the low field limit, which may activate the ions and cause structural
rearrangement or fragmentation during analysis. Here, we quantitatively
assessed the internal heating experienced by ions during trapped ion
mobility spectrometry (TIMS) experiments. To this end, the fragmentation
yields of fragile benzylpyridinium “thermometer” ions
were monitored during both the accumulation and analysis steps inside
the TIMS tunnel. The corresponding fragmentation rate constants were
translated into a vibrational effective temperature T
eff,vib. Our results demonstrate significant fragmentation
upstream and inside the TIMS tunnel that corresponds to T
eff,vib ≈ 510 K during both the accumulation and
analysis steps. Broadening our scope to cytochrome c and lysozyme, we showed that although compact “native”
folds can be preserved, the collision cross section distributions
are highly sensitive to the transmission voltages and the analysis
time scale. Our results are discussed with regard to T
eff,vib data previously acquired on traveling-wave (TWIMS)
ion mobility in the context of native mass spectrometry and conformational
landscape exploration.