Time Dependent Tandem Ion Mobility to Assess the Stability of Biomolecules

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In a new study, researchers delve into the structural stability of native-like protein ions, using a technique known as time-dependent, tandem ion mobility mass spectrometry (IM-MS).

In the realm of structural biology and mass spectrometry, the stability of biomolecules in the gas phase is of paramount importance. In a new study published in Analytical Chemistry, researchers delve into the structural stability of native-like protein ions, using a technique known as time-dependent, tandem ion mobility mass spectrometry (IM-MS). The ions of interest are selectively isolated after the first dimension of IM and then confined for up to approximately 14 seconds. The subsequent step involves determining time-dependent, collision cross section distributions based on separations in a second dimension of IM.

Time-dependent tandem ion mobility mass spectrometry (IM-MS) is an analytical technique that combines multiple ion mobility separations with varying time intervals, followed by mass spectrometry analysis, to enhance the separation and identification of complex mixtures of ions. By applying different drift times or voltage settings in consecutive IM stages and then measuring mass-to-charge ratios, this method improves the resolution and specificity of ion separation.

Notably, monomeric protein ions exhibited specific structural changes influenced by both the nature of the protein and its charge state. However, in contrast, large protein complexes did not display any discernible structural alterations within the timeframes of these experiments.

To gain further insights into the extent of unfolding, the research team conducted energy-dependent experiments, known as collision-induced unfolding. This comparison with time-dependent experiments yielded remarkable findings. The collision cross section values observed in the energy-dependent experiments, where high collision energies were employed, were notably larger than those seen in the time-dependent experiments. This suggests that the structures observed in the time-dependent experiments are kinetically trapped and retain some memory of their solution-phase structure.

While it's crucial to consider structural changes in highly charged, monomeric protein ions, the research underscores the kinetic stability exhibited by higher-mass protein ions in the gas phase. This study paves the way for advancements in our comprehension of biomolecules and their stability in various environments. The potential to preserve the memory of solution-phase structures during gas-phase analysis opens new horizons for research and the development of innovative techniques and technologies in structural biology and mass spectrometry.


In summary, researchers used a specialized instrument to study the stability of different protein ions in the gas phase. They found that smaller proteins changed their shape over a few seconds but still retained their original structure from the solution phase. Larger proteins remained stable for longer, indicating that they may be better suited for certain experiments. These findings offer insights for designing experiments in structural mass spectrometry.

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Zercher, B. P.; Hong, S.; Roush, A. E.; Feng, Y.; Bush, M. F. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Anal. Chem.2023, 95 (25), 9589–9597. DOI:10.1021/acs.analchem.3c01222.