Isomeric and Conformational Analysis of Small Drug and Drug-Like Molecules by Ion Mobility-Mass Spectrometry (IM-MS)

  • Shawn T. Phillips
  • James N. Dodds
  • Jody C. May
  • John A. McLeanEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1939)


This chapter provides a broad overview of ion mobility-mass spectrometry (IM-MS) and its applications in separation science, with a focus on pharmaceutical applications. A general overview of fundamental ion mobility (IM) theory is provided with descriptions of several contemporary instrument platforms which are available commercially (i.e., drift tube and traveling wave IM). Recent applications of IM-MS toward the evaluation of structural isomers are highlighted and placed in the context of both a separation and characterization perspective. We conclude this chapter with a guided reference protocol for obtaining routine IM-MS spectra on a commercially available uniform-field IM-MS.

Key words

Isomers Drugs Conformation Ion mobility spectrometry Ion mobility-mass spectrometry IM-MS 



This work was supported in part using the resources of the Center for Innovative Technology at Vanderbilt University. Financial support for aspects of this research was provided by The National Institutes of Health (NIH Grant R01GM092218) and under Assistance Agreement No. 83573601 awarded by the US Environmental Protection Agency (EPA). This work has not been formally reviewed by the EPA, and the EPA does not endorse any products or commercial services mentioned in this publication. Furthermore, the content is solely the responsibility of the authors and should not be interpreted as representing the official views and policies, either expressed or implied, of the funding agencies and organizations.


  1. 1.
    Chail H (2008) DNA sequencing technologies key to the human genome project. Nature Education 1:219Google Scholar
  2. 2.
    Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52:413–435CrossRefGoogle Scholar
  3. 3.
    Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67–73CrossRefGoogle Scholar
  4. 4.
    Takenaka T (2001) Classical vs reverse pharmacology in drug discovery. BJU Int 88:7–10CrossRefGoogle Scholar
  5. 5.
    Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14:111–129CrossRefGoogle Scholar
  6. 6.
    Vaidya ADB (2014) Reverse pharmacology-a paradigm shift for drug discovery and development. Curr Res Drug Discov 1:39–44CrossRefGoogle Scholar
  7. 7.
    Roses AD (2008) Pharmacogenetics in drug discovery and development: a translational perspective. Nat Rev Drug Discov 7:807–817CrossRefGoogle Scholar
  8. 8.
    Nageswara Rao R, Talluri MV (2007) An overview of recent applications of inductively coupled plasma-mass spectrometry (ICP-MS) in determination of inorganic impurities in drugs and pharmaceuticals. J Pharm Biomed Anal 43:1–13CrossRefGoogle Scholar
  9. 9.
    Kauppila TJ, Wiseman JM, Ketola RA, Kotiaho T, Cooks RG, Kostiainen R (2006) Desorption electrospray ionization mass spectrometry for the analysis of pharmaceuticals and metabolites. Rapid Commun Mass Spectrom 20:387–392CrossRefGoogle Scholar
  10. 10.
    Cooks RG (1995) Special feature: historical. Collision-induced dissociation: readings and commentary. J Mass Spectrom 30:1215–1221CrossRefGoogle Scholar
  11. 11.
    Wells JM, McLuckey SA (2005) Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol 402:148–185CrossRefGoogle Scholar
  12. 12.
    Nguyen LA, He H, Pham-Huy C (2006) Chiral drugs: an overview. Int J Biomed Sci 2:85–100PubMedPubMedCentralGoogle Scholar
  13. 13.
    McMurry J (2008) Organic chemistry, 7th edn. Cengage Learning, Stamford, CTGoogle Scholar
  14. 14.
    NCBI.NLM.NIH.Gov. Search terms “C8H9NO2.” Accessed 18 Apr 2017
  15. 15.
    Ferreres F, Giner JM, Tomás-Barberán FA (1994) A comparative study of hesperetin and methyl anthranilate as markers of the floral origin of citrus honey. J Sci Food Agric 65:371–372CrossRefGoogle Scholar
  16. 16.
    Groessl M, Graf S, Knochenmuss R (2015) High resolution ion mobility-mass spectrometry for separation and identification of isomeric lipids. Analyst 140:6904–6911CrossRefGoogle Scholar
  17. 17.
    Xiao Y, Vecchi MM, Wen D (2016) Distinguishing between leucine and isoleucine by integrated LC-MS analysis using Orbitrap fusion mass spectrometer. Anal Chem 88:10757–10766CrossRefGoogle Scholar
  18. 18.
    Takayama K, Kilburn JO (1989) Inhibition of synthesis of arabinogalactan by ethambutol in mycobacterium smegmatis. Antimicrob Agents Chemother 33:1493–1499CrossRefGoogle Scholar
  19. 19.
    Chatterjee VK, Buchanan DR, Friedmann AI, Green M (1986) Ocular toxicity following ethambutol in standard dosage. Br J Dis Chest 80:288–291CrossRefGoogle Scholar
  20. 20.
    Carey R (1996) Organic chemistry, 3rd edn. McGraw Hill, New York, pp 89–92Google Scholar
  21. 21.
    Kothiwale S, Mendenhall JL, Meiler J (2015) BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform 7:47CrossRefGoogle Scholar
  22. 22.
    Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson BO, Astarita G (2014) Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem 86:3985–3993CrossRefGoogle Scholar
  23. 23.
    Enders JR, McLean JA (2009) Chiral and structural analysis of biomolecules using mass spectrometry and ion mobility –mass spectrometry. Chirality 21:253–264CrossRefGoogle Scholar
  24. 24.
    Dodds JN, May JC, McLean JA (2017) Investigation of the complete suite of the leucine and isoleucine isomers: toward prediction of ion mobility separation capabilities. Anal Chem 89:952–959CrossRefGoogle Scholar
  25. 25.
    Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH (2007) An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom 261:1–12CrossRefGoogle Scholar
  26. 26.
    May JC, McLean JA (2015) Ion mobility-mass spectrometry: time-dispersive instrumentation. Anal Chem 87:1422–1436CrossRefGoogle Scholar
  27. 27.
    May JC, Goodwin CR, Lareau NM, Leaptrot KL, Morris CB, Ruwam T, Kurulugama RT, Mordehai A, Klein C, Barry W, Darland E, Overney G, Imatani K, Stafford GC, Fjeldsted JC, McLean JA (2014) Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer. Anal Chem 86:2107–2116CrossRefGoogle Scholar
  28. 28.
    Web of Science. Thomson Reuters. Search terms “Ion Mobility” AND “Mass Spectrometry.” Articles from 2002 to 2017. Accessed 15 May 2017Google Scholar
  29. 29.
    Paglia G, Astarita G (2017) Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry. Nat Protoc 12:797–813CrossRefGoogle Scholar
  30. 30.
    Stow SM, Lareau NM, Hines KM, McNees CR, Goodwin CR, Bachmann BO, McLean JA (2014) In: Havlíček V, Spížek J (eds) Natural products analysis: instrumentation, methods, and applications. John Wiley & Sons, Inc., Hoboken, NJ, pp 397–432Google Scholar
  31. 31.
    Sundarapandian S, May JC, McLean JA (2010) Dual source ion mobility mass-spectrometer for direct comparison of ESI and MALDI collision cross section measurements. Anal Chem 82:3247–3254CrossRefGoogle Scholar
  32. 32.
    Mason EA, McDaniel EW (1988) Transport properties of ions in gases. John Wiley and Sons, Indianapolis, INCrossRefGoogle Scholar
  33. 33.
    Glaskin RS, Valentine SJ, Clemmer DE (2010) A scanning frequency mode for ion cyclotron mobility spectrometry. Anal Chem 82:8266–8271CrossRefGoogle Scholar
  34. 34.
    Cumeras R, Figueras E, Davis CE, Baumbach JI, Grácia I (2015) Review on ion mobility spectrometry. Part 1: current instrumentation. Analyst 140:1376–1390CrossRefGoogle Scholar
  35. 35.
    Cumeras R, Figueras E, Davis CE, Baumbach JI, Grácia I (2015) Review on ion mobility spectrometry. Part 2: hyphenated methods and effects of experimental parameters. Analyst 140:1391–1410CrossRefGoogle Scholar
  36. 36.
    Adamov A, Mauriala T, Teplov V, Laakia J, Pedersen CS, Kotiaho T, Sysoev AA (2010) Characterization of a high resolution drift tube ion mobility spectrometer with a multi-ion source platform. Int J Mass Spectrom 298:24–29CrossRefGoogle Scholar
  37. 37.
    Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH Jr (2008) Ion mobility–mass spectrometry. J Mass Spectrom 43:1–22CrossRefGoogle Scholar
  38. 38.
    Jurneczko E, Kalapothakis J, Campuzano ID, Morris M, Barran PE (2012) Effects of drift gas on collision cross sections of a protein standard in linear drift tube and traveling wave ion mobility mass spectrometry. Anal Chem 84:8524–8531CrossRefGoogle Scholar
  39. 39.
    Ujma J, Giles K, Morris M, Barran PE (2016) New high resolution ion mobility mass spectrometer capable of measurements of collision cross sections from 150 to 520 K. Anal Chem 88:9469–9478CrossRefGoogle Scholar
  40. 40.
    Giles K, Williams JP, Campuzano I (2011) Enhancements in travelling wave ion mobility resolution. Rapid Commun Mass Spectrom 25:1559–1566CrossRefGoogle Scholar
  41. 41.
    Shvartsburg AA, Smith RD (2008) Fundamentals of traveling wave ion mobility spectrometry. Anal Chem 80:9689–9699CrossRefGoogle Scholar
  42. 42.
    Bush MF, Campuzano ID, Robinson CV (2012) Ion mobility mass spectrometry of peptide ions: effects of drift gas and calibration strategies. Anal Chem 84:7124–7130CrossRefGoogle Scholar
  43. 43.
    Hines KM, May JC, McLean JA, Xu L (2016) Evaluation of collision cross section calibrants for structural analysis of lipids by traveling wave ion mobility-mass spectrometry. Anal Chem 88:7329–7336CrossRefGoogle Scholar
  44. 44.
    Lanucara F, Holman SW, Gray CJ, Eyers CE (2014) The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem 6:281–294CrossRefGoogle Scholar
  45. 45.
    May JC, McLean JA (2015) A uniform field ion mobility of melittin and implications of low-field mobility for resolving fine cross-sectional detail in peptide and protein experiments. Proteomics 15:2862–2871CrossRefGoogle Scholar
  46. 46.
    Shvartsburg AA, Tang K, Smith RD (2009) Two-dimensional ion mobility analyses of proteins and peptides. Methods Mol Biol 492:417–445CrossRefGoogle Scholar
  47. 47.
    Kilman M, May JC, McLean JA (2011) Lipid analysis and lipidomics by structually selective ion mobility-mass spectrometry. Biochimica et Biophusica Acta (BBA)-Molecular and Cell Biology of Lipids 1811:935–945CrossRefGoogle Scholar
  48. 48.
    Gaye MM, Nagy G, Clemmer DE, Pohl NL (2016) Multidimensional analysis of 16 glucose isomers by ion mobility spectrometry. Anal Chem 88:2335–2344CrossRefGoogle Scholar
  49. 49.
    Fenn LS, McLean JA (2013) Structural separations by ion mobility-MS for glycomics and glycoproteomics. Methods Mol Biol 951:171–194CrossRefGoogle Scholar
  50. 50.
    Lalli PM, Corilo YE, Rowland SM, Marshall AG, Rodgers RP (2015) Isomeric separation and structural characterization of acids in petroleum by ion mobility mass spectrometry. Energy Fuel 29:3626–3633CrossRefGoogle Scholar
  51. 51.
    Barnett DA, Ells B, Guevremont R, Purves RW (1999) Separation of leucine and isoleucine by electrospray ionization-high field asymmetric waveform ion mobility spectrometry-mass spectrometry. J Am Chem Soc 10:1279–1284Google Scholar
  52. 52.
    Knapman TW, Berryman JT, Campuzano I, Harris SA, Ashcroft AE (2010) Considerations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry. Int J Mass Spectrom 298:17–23CrossRefGoogle Scholar
  53. 53.
    Li H, Bendiak B, Siems WF, Gang DR, Hill HH Jr (2013) Ion mobility mass spectrometry analysis of isomeric disaccharide precursor, product and cluster ions. Rapid Commun Mass Spectrom 27:2699–2709CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Shawn T. Phillips
    • 1
  • James N. Dodds
    • 1
  • Jody C. May
    • 1
  • John A. McLean
    • 1
    Email author
  1. 1.Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer CenterVanderbilt UniversityNashvilleUSA

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