Structurally Selective Imaging Mass Spectrometry by Imaging Ion Mobility-Mass Spectrometry

  • John A. McLean
  • Larissa S. Fenn
  • Jeffrey R. Enders
Part of the Methods in Molecular Biology book series (MIMB, volume 656)


This chapter describes the utility of structurally based separations combined with imaging mass spectrometry (MS) by ion mobility-MS (IM-MS) approaches. The unique capabilities of combining rapid (μs-ms) IM separations with imaging MS are detailed for an audience ranging from new to potential practitioners in IM-MS technology. Importantly, imaging IM-MS provides the ability to rapidly separate and elucidate various types of endogenous and exogenous biomolecules (e.g., nucleotides, carbohydrates, peptides, and lipids), including isobaric species. Drift tube and traveling wave IM-MS instrumentation are described and specific protocols are presented for calculating ion–neutral collision cross sections (i.e., apparent ion surface area or structure) from experimentally obtained IM-MS data. Special emphasis is placed on the use of imaging IM-MS for the analysis of samples in life sciences research (e.g., thin tissue sections), including selective imaging for peptide/protein and lipid distributions. Future directions for rapid and multiplexed imaging IM-MS/MS are detailed.

Key words

Ion mobility ion mobility-mass spectrometry IM-MS imaging mass spectrometry IMS MSI imaging ion mobility-mass spectrometry structural separations MALDI IM-MS/MS 



We thank Whitney B. Ridenour and Richard M. Caprioli (Vanderbilt University) for assistance and use of the Synapt HDMS (data shown in Figs. 21.6 and 21.7), which is supported by the Vanderbilt University Mass Spectrometry Research Core. Financial support for this work was provided by the National Institutes of Health-NIDA (#HHSN271200700012C), Vanderbilt University College of Arts and Sciences, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrated Biosystems Research and Education, the American Society for Mass Spectrometry (Research award to J.A.M), the Spectroscopy Society of Pittsburgh, Waters Corp., and Ionwerks Inc.


  1. 1.
    Fenn, L. S., McLean, J. A. (2008) Biomolecular structural separations by ion mobility-mass spectrometry. Anal Bioanal Chem, 391, 905–909.PubMedCrossRefGoogle Scholar
  2. 2.
    McLean, J. A., Ruotolo, B. T., Gillig, K. J., Russell, D. H. (2005) Ion mobility-mass spectrometry: a new paradigm for proteomics. Int J Mass Spectrom, 240, 301–315.CrossRefGoogle Scholar
  3. 3.
    Wyttenbach, T., Bowers, M. T. (2003) Gas-phase conformations: the ion mobility/ion chromatography method. Modern Mass Spectrom, 225, 207–232.CrossRefGoogle Scholar
  4. 4.
    Jarrold, M. F. (2000) Peptides and proteins in the vapor phase, Annu Rev Phys Chem, 51, 179–207.PubMedCrossRefGoogle Scholar
  5. 5.
    Clemmer, D. E. Jarrold, M. Fd. (1997) Ion mobility measurements and their applications to clusters and biomolecules. J Mass Spectrom, 32, 577–592.CrossRefGoogle Scholar
  6. 6.
    Eiceman, E. A., Karpas, Z. (2004) Ion Mobility Spectrometry, 2nd Ed., CRC Press, Boca Raton, FL,  http://Chapter 1.Google Scholar
  7. 7.
    McAfee, K. B., Jr., Edelson, D. (1963) Identification and mobility of ions in a townsend discharge by time-resolved mass spectrometry, Proc Phys Soc Lond, 81, 382–384.CrossRefGoogle Scholar
  8. 8.
    Barnes, W. S., Martin, D. W., McDaniel, E. W. (1961) Mass spectrographic identification of the ion observed in hydrogen mobility experiments, Phys Rev Lett, 6, 110–111.CrossRefGoogle Scholar
  9. 9.
    Gieniec, J., Mack, L. L., Nakamae, K., Gupta, C., Kumar, V., Dole, M. (1984) Electrospray mass spectroscopy of macromolecules: application of an ion-drift spectrometer. Biomed Mass Spectrom, 11, 259–268.CrossRefGoogle Scholar
  10. 10.
    Von Helden, G., Wyttenbach, T., Bowers, M. T. (1995) Inclusion of a MALDI ion source in the ion chromatography technique: conformation information on polymer and biomolecular ions. Int J Mass Spectrom Ion Process, 146/147, 349–364.CrossRefGoogle Scholar
  11. 11.
    Shelimov, K. B., Clemmer, D. E., Hudgins, R. R., Jarrold, M. F. (1997) Protein structure in vacuo: the gas phase conformations of BPTI and cytochrome c, J Am Chem Soc, 119, 2240–2248.CrossRefGoogle Scholar
  12. 12.
    Wyttenbach, T., Von Helden, G., Bowers, M. T. (1996) Gas-phase conformation of biological molecules: bradykinin. J Am Chem Soc, 118, 8355–8364.CrossRefGoogle Scholar
  13. 13.
    Von Helden, G., Wyttenbach, T., Bowers, M. T. (1995) Conformation of macromolecules in the gas phase: use of matrix-assisted laser desorption methods in ion chromatography. Science, 267, 1483–1485.CrossRefGoogle Scholar
  14. 14.
    Myung, S., Lee, Y. J., Moon, M. H., Taraszka, J., Sowell, R., Koeniger, S., Hilderbrand, A. E., Valentine, S. J., Cherbas, L., Cherbas, P., Kaufmann, T. C., Miller, D. F., Mechref, Y., Novotny, M. V., Ewing, M. A., Sporleder C. R., Clemmer, D. E. (2003) Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract. Anal Chem, 75, 5137–5145.PubMedCrossRefGoogle Scholar
  15. 15.
    Isailovic, D., Kurulugama, R. T., Plasencia, M. D., Stokes, S. T., Kyselova, Z., Goldman, R., Mechref, Y., Novotny, M. V. and Clemmer, D. E. (2008) Profiling of human serum glycans associated with liver cancer and cirrhosis by IMS-MS. J Proteome Res, 7, 1109–1117.PubMedCrossRefGoogle Scholar
  16. 16.
    Liu, X., Valentine, S. J., Plasencia, M. D., Trimpin, S., Naylor, S., Clemmer, D. E. (2007) Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom, 18, 1249–1264.PubMedCrossRefGoogle Scholar
  17. 17.
    Valentine, S. J., Plasencia, M. D., Liu, X., Krishnan, M., Naylor, S., Udseth, H. R., Smith, R. D., Clemmer, D. E. (2006) Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res, 5, 2977–2984.PubMedCrossRefGoogle Scholar
  18. 18.
    Liu, X., Plasencia, M., Ragg, S., Valentine, S. J., Clemmer, D. E. (2004) Development of high throughput dispersive LC–ion mobility–TOFMS techniques for analysing the human plasma proteome. Brief Funct Genomic Proteomic, 3, 177–186.PubMedCrossRefGoogle Scholar
  19. 19.
    Liu, X., Miller, B. R., Rebec, G. V., Clemmer, D. E. (2007) Protein expression in the striatum and cortex regions of the brain for a mouse model of Huntington’s disease.J Proteome Res, 6, 3134–3142.PubMedCrossRefGoogle Scholar
  20. 20.
    Taraszka, J. A., Kurulugama, R., Sowell, R. A., Valentine, S. J., Koeniger, S. L., Arnold, R. J., Miller, D. F., Kaufman, T. C., Clemmer, D. E. (2005) Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods. J Proteome Res, 4, 1223–1237.PubMedCrossRefGoogle Scholar
  21. 21.
    Benesch, J. L. P., Ruotolo, B. T., Simmons, D. A., Robinson, C. V. (2007) Protein complexes in the gas phase: technology for the structural genomics and proteomics. Chem Rev, 107, 3544–3567.PubMedCrossRefGoogle Scholar
  22. 22.
    Ruotolo, B. T., Hyung, S.-J., Robinson, P. M., Giles, K., Bateman, R. H., Robinson, C. V. (2007) Ion mobility-mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. Angew Chem Int Ed, 46, 8001–8004.CrossRefGoogle Scholar
  23. 23.
    Ruotolo, B. T., Giles, K., Campuzano, I., Sandercock, A. M., Bateman, R. H., Robinson, C. V. (2005) Evidence for macromolecular rings in the absence of bulk water. Science, 310, 1658–1661.PubMedCrossRefGoogle Scholar
  24. 24.
    Jackson, S. N., Ugarov, M., Egan, T., Post, J. D., Langlais, D., Schultz, J. A., Woods, A. S. (2007) MALDI-ion mobility-TOFMS imaging of lipids in rat brain tissue. J Mass Spectrom, 42, 1093–1098.PubMedCrossRefGoogle Scholar
  25. 25.
    McLean, J. A., Ridenour, W. B., Caprioli, R. M. (2007) Profiling and imaging of tissues by imaging ion mobility-mass spectrometry. J Mass Spectrom, 42, 1099–1105.PubMedCrossRefGoogle Scholar
  26. 26.
    Mason, E. A., McDaniel, E. W. (1988) Transport Properties of Ions in Gases. John Wiley & Sons, New York, NY.Google Scholar
  27. 27.
    Mason, E. A. (1984) Ion mobility: its role in plasma chromatography, in Plasma Chromatography, (Carr, T. W. ed.), Plenum Press, New York, NY, 43–93.Google Scholar
  28. 28.
    Revercomb, H. E. and Mason, E. A. (1975) Theory of plasma chromatography/gaseous electrophoresis – a review. Anal Chem, 47, 970–983.CrossRefGoogle Scholar
  29. 29.
    Ruotolo, B. T., Benesch, J. L. P., Sandercock, A. M., Hyung, S.-J. Robinson, C. V. (2008) Ion mobility-mass spectrometry analysis of large protein complexes. Nat Protoc, 3, 1139–1152.PubMedCrossRefGoogle Scholar
  30. 30.
    Williams, J. P., Scrivens, J. H. (2008) Coupling desorption electrospray ionization and neutral desorption/extractive electrospray ionization with a travelling-wave based ion mobility mass spectrometer for the analysis of drugs. Rapid Commun Mass Spectrom, 22, 187–196.PubMedCrossRefGoogle Scholar
  31. 31.
    Gidden, J., Bowers, M. T. (2003) Gas-phase conformations of deprotonated and protonated mononucleotides determined by ion mobility and theoretical modeling. J Phys Chem B, 107, 12829–12837.CrossRefGoogle Scholar
  32. 32.
    Gidden, J., Bowers, M. T. (2003) Gas-phase conformations of deprotonated trinucleotides (dGTT(–), dTGT(–), and dTTG (–)): the question of zwitterion formation. J Am Soc Mass Spectrom, 14, 161–170.PubMedCrossRefGoogle Scholar
  33. 33.
    Wyttenbach, T., Witt, M., Bowers, M. T. (2000) On the stability of amino acid zwitterions in the gas phase: the influence of derivatization, proton affinity, and alkali ion addition. J Am Chem Soc, 122, 3458–3464.CrossRefGoogle Scholar
  34. 34.
    Shvartsburg, A. A., Jarrold, M. F. (1996) An exact hard-spheres scattering model for the mobilities of polyatomic ions. Chem Phys Lett, 261, 86–91.CrossRefGoogle Scholar
  35. 35.
    Dwivedi, P., Wu, P., Klopsch, S. J., Puzon, G. J., Xun, L., Hill, H. H. (2008) Metabolic profiling by ion mobility mass spectrometry (IMMS). Metabolomics, 4, 63–80.CrossRefGoogle Scholar
  36. 36.
    Tao, L., McLean, J. R., McLean, J. A., Russell, D. H. (2007) A collision cross-section database of singly-charged peptide ions. J Am Soc Mass Spectrom, 18, 1232–1238.PubMedCrossRefGoogle Scholar
  37. 37.
    Ruotolo, B. T., Verbeck, G. F., Thomson, L. M., Woods, A. S., Gillig, K. J., Russell, D. H. (2002) Distinguishing between phosphorylated and nonphosphorylated peptides with ion mobility-mass spectrometry. J Proteome Res, 1, 303–306.PubMedCrossRefGoogle Scholar
  38. 38.
    Furche, F., Ahlrichs, R., Weis, P., Jacob, C., Gilb, S., Bierweiler, T., Kappes, M. M. (2002) The structures of small gold cluster anions as determined by a combination of ion mobility measurements and density functional calculations. J Chem Phys, 117, 6982–6990.CrossRefGoogle Scholar
  39. 39.
    Shvartsburg, A. A., Smith, R. D. (2008) Fundamentals of traveling wave ion mobility spectrometry. Anal Chem, 80, 9689–9699.PubMedCrossRefGoogle Scholar
  40. 40.
    Mason, E. A., McDaniel, E. W. (1988) Measurement of drift velocities and longitudinal diffusion coefficients, in Transport Properties of Ions in Gases, John Wiley & Sons, New York, NY, 31–102. Google Scholar
  41. 41.
    Kanu, A. B., Dwivedi, P., Tam, M., Matz, L., Hill, H. H., Jr. (2008) Ion mobility-mass spectrometry, J Mass Spectrom, 43, 1–22.PubMedCrossRefGoogle Scholar
  42. 42.
    Steiner, W. E., Clowers, B. H., English, W. A., Hill, H. H., Jr. (2004) Atmospheric pressure matrix-assisted laser desorption/ionization with analysis by ion mobility-mass spectrometry. Rapid Commun Mass Spectrom, 18, 882–888.PubMedCrossRefGoogle Scholar
  43. 43.
    McLean, J. A., Russell, D. H. (2003) Sub-femtomole peptide detection in ion-mobility-time-of-flight mass spectrometry measurements. J Proteome Res, 2, 427–430.PubMedCrossRefGoogle Scholar
  44. 44.
    McLean, J. A., Ridenour, W. B., Caprioli, R. M. (2007) Imaging ion mobility mass spectrometry: advantages, challenges, and future prospects. Proceedings of the 55th Annual Meeting of the American Society for Mass Spectrometry, Indianapolis, IN.Google Scholar
  45. 45.
    Merenbloom, S. I., Glaskin, R. S., Clemmer, D. E. (2009) High resolution ion cyclotron mobility spectrometry. Anal Chem, 81, 1482–1487.Google Scholar
  46. 46.
    Wyttenbach, T., Kemper, P. R., Bowers, M. T. (2001) Design of a new electrospray ion mobility mass spectrometer. Int J Mass Spectrom, 212, 13–23.CrossRefGoogle Scholar
  47. 47.
    Dugourd, Ph., Hudgins, R. R., Clemmer, D. E., Jarrold, M. F. (1997) High-resolution ion mobility measurements. Rev Sci Instrum, 68, 1122–1129.CrossRefGoogle Scholar
  48. 48.
    Giles, K., Pringle, S. D., Worthington, D. L., Wildgoose, J. L., Bateman, R. H. (2004) Applications of travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Commun Mass Spectrom, 18, 2401–2414.PubMedCrossRefGoogle Scholar
  49. 49.
    Pringle, S. D., Giles, K., Wildgoose, J. L., Williams, J. P., Slade, S. E., Thalassinos, K., Bateman, R. H., Bowers, M. T., Scrivens, J. H. (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, 1–12.CrossRefGoogle Scholar
  50. 50.
    Vakhrushev, S. Y., Langridge, J., Campuzano, I., Hughes, C., Peter-Katalinic, J. (2008) Ion mobility mass spectrometry analysis of human glycourinome. Anal Chem, 80, 2506–2513.PubMedCrossRefGoogle Scholar
  51. 51.
    Riba-Garcia, I., Giles, K., Bateman, R.H., Gaskell, S.J. (2008) Evidence for structural variants of a- and b- type peptide fragment ions using combined ion mobility/mass spectrometry. J Am Soc Mass Spectrom, 19, 609–613.PubMedCrossRefGoogle Scholar
  52. 52.
    Trim, P. J., Henson, C. M., Avery, J. L., McEwen, A., Snel, M. F., Claude, E., Marshall, P. S., West, A., Princivalle, A. P., Clench, M. R. (2008) Matrix-assisted laser desorption/ionization-ion mobility separation-mass spectrometry imaging of vinblastine in whole body tissue sections. Anal Chem, 80, 8628–8634.PubMedCrossRefGoogle Scholar
  53. 53.
    Reyzer, M. L., Hsieh, Y., Ng, K., Korfmacher, W .A., Caprioli, R. M. (2003) Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom, 38, 1081–1092.PubMedCrossRefGoogle Scholar
  54. 54.
    Domon, B., Costello, C. E. (1988) A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates. Glycoconjugate J, 5, 397–409.CrossRefGoogle Scholar
  55. 55.
    Karas, M., Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem, 60, 2299–2301.PubMedCrossRefGoogle Scholar
  56. 56.
    Henderson, S. C., Valentine, S. J., Counterman, A. E., Clemmer, D. E. (1999) ESI/ion trap/ion mobility/time-of-flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures. Anal Chem, 71, 291–301.PubMedCrossRefGoogle Scholar
  57. 57.
    Hoaglund, C. S., Valentine, S. J., Sporleder, C. R., Reilly, J. P., Clemmer, D. E. (1998) Three-dimensional ion mobility/TOFMS analysis of electrosprayed biomolecules. Anal Chem, 70, 2236–2242.PubMedCrossRefGoogle Scholar
  58. 58.
    Clemmer cross section database (2006) (Assessed January 28th, 2009 at∼clemmer/Research/crosssection database/cs database.htm)
  59. 59.
    Fenn, L. S., Kliman, M., Mahsutt, A., Zhao, S. R., McLean, J. A. (2009) Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples. Anal Bioanal Chem, 394, 235–244.Google Scholar
  60. 60.
    Theories and analysis of IM-MS data (Assessed January 28th, 2009 at
  61. 61.
    Wyttenbach, T., von Helden, G., Batka, J. J., Jr., Carlat, D., Bowers, M. T. (1997) Effect of the long-range interaction potential on ion mobility measurements. J Am Soc Mass Spectrom, 8, 275–282.CrossRefGoogle Scholar
  62. 62.
    Mesleh, M. F., Hunter, J. M., Shvartsburg, A. A., Schatz, G. C., Jarrold, M. F. (1996) Structural information from ion mobility measurements: effects of the long-range potential. J Phys Chem, 100, 16082–16086.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • John A. McLean
    • 1
  • Larissa S. Fenn
    • 1
  • Jeffrey R. Enders
    • 1
  1. 1.Department of ChemistryVanderbilt Institute of Chemical Biology, and Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt UniversityNashvilleUSA

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