Ion mobility is emerging as a rapid and sensitive tool for structural characterization. Collision cross-section (Ω) values determined using ion mobility are often compared to values calculated for candidate structures generated through molecular modeling. Several methods exist for calculating Ω values, but the trajectory method explicitly includes contributions from long-range, ion–neutral interactions. Recent implementations of the trajectory method have significantly reduced its expense and have made applications to proteins far more tractable. Here, we use ion mobility experiments and trajectory method calculations to characterize the effects of charge state, charge distribution, and structure on the ion mobility of proteins in nitrogen gas. These results show that ion-induced dipole interactions contribute significantly to the Ω values of these ions with nitrogen gas, even for the modestly charged ions commonly observed in native mass spectrometry experiments. Therefore, these interactions contribute significantly to the values measured in most structural biology and biophysics applications of ion mobility using nitrogen gas. Comparisons between the reciprocal mobilities of protein ions in helium gas and in nitrogen gas show that there are significant, noncorrelated differences between these values. As a consequence, it is challenging to estimate the errors associated with interconverting between helium- and nitrogen-based mobilities without extensive characterization in both gases, even for ions of proteins with similar sequences. Therefore, we recommend reporting Ω and mobility values that are based on the predominant gas present in the separation and applying additional caution when comparing results from mobility experiments performed using different gases.

中文翻译：

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氮气中蛋白质的离子迁移性：电荷状态，电荷分布和结构的影响

离子迁移正在成为一种快速，灵敏的结构表征工具。通常将使用离子迁移率确定的碰撞截面（Ω）值与通过分子建模生成的候选结构的计算值进行比较。存在几种计算Ω值的方法，但是轨迹法明确包含了远程离子中性相互作用的贡献。轨迹法的最新实现已大大降低了其成本，并使对蛋白质的应用更加容易处理。在这里，我们使用离子迁移率实验和轨迹方法计算来表征电荷状态，电荷分布和结构对氮气中蛋白质离子迁移率的影响。这些结果表明，即使对于在天然质谱实验中通常观察到的带负电荷的离子，离子诱导的偶极子相互作用也显着地促进了这些离子与氮气的Ω值。因此，这些相互作用对使用氮气进行离子迁移的大多数结构生物学和生物物理学应用中测得的值有很大贡献。氦气和氮气中蛋白质离子的倒数运动之间的比较表明，这些值之间存在显着的，不相关的差异。结果，要想在不对两种气体（即使是具有相似序列的蛋白质的离子）进行广泛表征的情况下，估计与基于氦气和氮的迁移率之间的相互转换相关的误差就极具挑战性。所以，