Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

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<jats:p>Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω<jats:sub>EXP</jats:sub>. Molecular modelling is used to visualize what ion three‐dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω<jats:sub>CALC</jats:sub> are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω<jats:sub>EXP</jats:sub> determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G‐quadruplex [dTGGGGT]<jats:sub>4</jats:sub>, and we will present these detailed investigation in this tutorial. © 2015 The Authors. <jats:italic>Journal of Mass Spectrometry</jats:italic> published by John Wiley & Sons Ltd.</jats:p>

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