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Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure
Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections o...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Blackwell Publishing Ltd
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440389/ https://www.ncbi.nlm.nih.gov/pubmed/26259654 http://dx.doi.org/10.1002/jms.3590 |
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author | D'Atri, Valentina Porrini, Massimiliano Rosu, Frédéric Gabelica, Valérie |
author_facet | D'Atri, Valentina Porrini, Massimiliano Rosu, Frédéric Gabelica, Valérie |
author_sort | D'Atri, Valentina |
collection | PubMed |
description | Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). 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(CALC) 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(EXP) 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](4), and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. |
format | Online Article Text |
id | pubmed-4440389 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Blackwell Publishing Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-44403892015-05-27 Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure D'Atri, Valentina Porrini, Massimiliano Rosu, Frédéric Gabelica, Valérie J Mass Spectrom Special Feature: Tutorial Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). 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(CALC) 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(EXP) 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](4), and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. Blackwell Publishing Ltd 2015-05 2015-04-20 /pmc/articles/PMC4440389/ /pubmed/26259654 http://dx.doi.org/10.1002/jms.3590 Text en © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
spellingShingle | Special Feature: Tutorial D'Atri, Valentina Porrini, Massimiliano Rosu, Frédéric Gabelica, Valérie Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title | Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title_full | Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title_fullStr | Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title_full_unstemmed | Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title_short | Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure |
title_sort | linking molecular models with ion mobility experiments. illustration with a rigid nucleic acid structure |
topic | Special Feature: Tutorial |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440389/ https://www.ncbi.nlm.nih.gov/pubmed/26259654 http://dx.doi.org/10.1002/jms.3590 |
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