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Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis

  • Research Article
  • Published:
Journal of The American Society for Mass Spectrometry

Abstract

The gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined by ion mobility spectrometry (IMS) and hydrogen deuterium exchange (HDX)-tandem mass spectrometry (MS/MS) techniques. [M+4H]4+ ions exhibit two conformers with collision cross sections of 418 Å2 and 471 Å2. [M+3H]3+ ions exhibit a predominant conformer with a collision cross section of 340 Å2 as well as an unresolved conformer (shoulder) with a collision cross section of ~367 Å2. Maximum HDX levels for the more compact [M+4H]4+ ions and the compact and partially-folded [M+3H]3+ ions are ~12.9, ~15.5, and ~14.9, respectively. Ion structures obtained from molecular dynamics simulations (MDS) suggest that this ordering of HDX level results from increased charge-site/exchange-site density for the more compact ions of lower charge. Additionally, a new model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) for the computer-generated structures is shown to better correlate to the experimentally determined per-residue deuterium uptake. Future comparisons of IMS-HDX-MS data with structures obtained from MDS are discussed with respect to novel experiments that will reveal the HDX rates of individual residues.

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Acknowledgments

The authors are grateful for financial support from the Eberly College of Arts and Sciences at West Virginia University for providing laboratory research startup funds as well as the Brodie Discovery and Innovation Award. Additionally, partial support has been provided by the 2012–2013 Starter Grant Award from the Society of Analytical Chemists of Pittsburgh (SACP) as well as the 2012–2013 Ralph E. Powe Junior Faculty Advancement Award from Oak Ridge Associated Universities (ORAU).

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  1. C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA

    Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Hossein Maleki, James R. Arndt, Gregory C. Donohoe & Stephen J. Valentine

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  1. Mahdiar Khakinejad
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  2. Samaneh Ghassabi Kondalaji
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  3. Hossein Maleki
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Correspondence to Stephen J. Valentine.

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Mahdiar Khakinejad and Samaneh Ghassabi Kondalaji contributed equally to this work.

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Khakinejad, M., Kondalaji, S.G., Maleki, H. et al. Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis. J. Am. Soc. Mass Spectrom. 25, 2103–2115 (2014). https://doi.org/10.1007/s13361-014-0990-0

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