Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry

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,T-vib. Our results demonstrate significant fragmentation upstream and inside the TIMS tunnel that corresponds to T-eff,(vib) approximate to 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,T-vib data previously acquired on traveling-wave (TWIMS) ion mobility in the context of native mass spectrometry and conformational landscape exploration.