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      Recommendations for reporting ion mobility Mass Spectrometry measurements

      review-article
      1 , , 2 , , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 15 , 16 , 17 , 18 , 19 , 20 , 12 , 21 , 17 , 22 , 22 , 23 , 18 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 7
      Mass Spectrometry Reviews
      John Wiley and Sons Inc.

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          Abstract

          Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values ( K 0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/ N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method‐dependent results) only if the gas nature, temperature or E/ N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

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          Ion mobility-mass spectrometry analysis of large protein complexes.

          Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry.
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            Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology.

            Collision cross sections in both helium and nitrogen gases were measured directly using a drift cell with RF ion confinement inserted within a quadrupole/ion mobility/time-of-flight hybrid mass spectrometer (Waters Synapt HDMS, Manchester, U.K.). Collision cross sections for a large set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ions are reported here, forming a database of collision cross sections that spans over 2 orders of magnitude. The average effective density of the native-like ions is 0.6 g cm(-3), which is significantly lower than that for the solvent-excluded regions of proteins and suggests that these ions can retain significant memory of their solution-phase structures rather than collapse to globular structures. Because the measurements are acquired using an instrument that mimics the geometry of the commercial Synapt HDMS instrument, this database enables the determination of highly accurate collision cross sections from traveling-wave ion mobility data through the use of calibration standards with similar masses and mobilities. Errors in traveling-wave collision cross sections determined for native-like protein complexes calibrated using other native-like protein complexes are significantly less than those calibrated using denatured proteins. This database indicates that collision cross sections in both helium and nitrogen gases can be well-correlated for larger biomolecular ions, but non-correlated differences for smaller ions can be more significant. These results enable the generation of more accurate three-dimensional models of protein and other biomolecular complexes using gas-phase structural biology techniques.
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              Structural Information from Ion Mobility Measurements:  Effects of the Long-Range Potential

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                Author and article information

                Contributors
                v.gabelica@iecb.u-bordeaux.fr
                alexandre.shvartsburg@wichita.edu
                Journal
                Mass Spectrom Rev
                Mass Spectrom Rev
                10.1002/(ISSN)1098-2787
                MAS
                Mass Spectrometry Reviews
                John Wiley and Sons Inc. (Hoboken )
                0277-7037
                1098-2787
                01 February 2019
                May-Jun 2019
                : 38
                : 3 ( doiID: 10.1002/mas.v38.3 )
                : 291-320
                Affiliations
                [ 1 ] University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site 2 rue Robert Escarpit, 33600 Pessac France
                [ 2 ] Department of Chemistry Wichita State University 1845 Fairmount St. Wichita Kansas 67620
                [ 3 ] Université de Rouen Mont‐Saint‐Aignan France
                [ 4 ] Michael Barber Centre for Collaborative Mass Spectrometry Manchester Institute for Biotechnology, University of Manchester Manchester UK
                [ 5 ] Department of Chemistry, Chemistry Research Laboratory University of Oxford, Mansfield Road, OX1 3TA Oxford UK
                [ 6 ] Department of Chemistry and Biochemistry Florida State University Tallahassee Florida 32311
                [ 7 ] University of California Santa Barbara California
                [ 8 ] Biological Sciences Division Pacific Northwest National Laboratory Richland Washington
                [ 9 ] Department of Chemistry University of Washington Seattle Washington
                [ 10 ] SCIEX, Concord Ontario Canada
                [ 11 ] Amgen Discovery Research Thousand Oaks California
                [ 12 ] University of Natural Resources and Life Sciences (BOKU) Department of Chemistry, Division of Analytical Chemistry Vienna Austria
                [ 13 ] Department of Chemistry Washington State University Pullman Washington
                [ 14 ] Centre for Analytical Science Department of Chemistry, Loughborough University Loughborough UK
                [ 15 ] Laboratoire de spectrométrie de masse (L.S.M.) − Molecular Systems Université de Liège Liège Belgium
                [ 16 ] Department of Chemistry and Biochemistry Florida International University Miami Florida
                [ 17 ] Agilent Technologies Santa Clara California
                [ 18 ] Waters Corporation Wilmslow UK
                [ 19 ] Department of Nephrology and Hypertension and Department of BioMedical Research Inselspital, Bern University Hospital, University of Bern, Switzerland and Tofwerk Thun Switzerland
                [ 20 ] Department of Mechanical Engineering University of Minnesota Minneapolis Minnesota
                [ 21 ] Department of Chemistry Korea University Seoul Korea
                [ 22 ] Department of Chemistry Center for Innovative Technology, Vanderbilt University Nashville Tennessee
                [ 23 ] Freie Universitaet Berlin Institute for Chemistry and Biochemistry Berlin Germany
                [ 24 ] Bruker Daltonics Billerica Massachusetts
                [ 25 ] CNRS, INSERM and University of Bordeaux Institut Européen de Chimie et Biologie Pessac France
                [ 26 ] Antwerp University Biomolecular & Analytical Mass Spectrometry Antwerp Belgium
                [ 27 ] Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
                [ 28 ] School of Molecular and Cellular Biology University of Leeds Leeds UK
                [ 29 ] Institute of Structural and Molecular Biology, Division of Biosciences University College London London WC1E 6BT UK
                [ 30 ] United Kingdom and Institute of Structural and Molecular Biology Department of Biological Sciences, Birkbeck College, University of London London WC1E 7HX UK
                [ 31 ] C. Eugene Bennett Department of Chemistry West Virginia University Morgantown West Virginia
                Author notes
                [*] [* ] Correspondence to: Valérie Gabelica, University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France. E‐mail: v.gabelica@ 123456iecb.u-bordeaux.fr

                Correspondence to: Alexandre A. Shvartsburg, Department of Chemistry, Wichita State University, 1845 Fairmount St., Wichita, KS 67260, USA. E‐mail: alexandre.shvartsburg@ 123456wichita.edu

                Article
                MAS21585
                10.1002/mas.21585
                6618043
                30707468
                8ce57507-9c41-40f2-92d0-7917fbad2999
                © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 25 September 2018
                : 01 November 2018
                : 02 November 2018
                Page count
                Figures: 7, Tables: 3, Pages: 30, Words: 24719
                Categories
                Review Article
                Review Articles
                Custom metadata
                2.0
                mas21585
                May/June 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.5 mode:remove_FC converted:10.07.2019

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