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Indiana University Bloomington

David ClemmerDavid E. Clemmer

Professor, Chemistry Department
Robert & Marjorie Mann Chair, Chemistry Department

Office: Simon Hall 120E

Phone: 812/855-8259

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B.S. Chemistry (1987, with honors) Adams State College, Alamosa, CO

Ph.D. Physical Chemistry (1992), University of Utah; Salt Lake City, UT (Advisor: Peter B. Armentrout)

JSPS Postdoctoral Fellow (1992-93), Himeji Institute of Technology, Japan

Postdoctoral Associate (1993-95), Northwestern University, Evanston, IL (Advisor: Martin F. Jarrold)


Much of the research performed in our group is focused on the development of mass spectrometry (MS)-based instrumentation for examining complex mixtures of biomolecules. Efforts center on the development of techniques that employ high-efficiency gas-phase separations (ion mobility spectrometry –IMS) of mixture components prior to MS analysis. The use of IMS results in more than an order of magnitude improvement in mixture component resolution and requires shorter experimental run times. The dataset depicted below shows a two-dimensional drift time, m/z separation of peptide ion components from a human plasma digest. Current research efforts seek to improve the resolution and speed of the overall analysis by combining multiple stages of IMS separation prior to MS. This will provide the throughput necessary to perform comparative analyses (proteomics, glycomics, and metabolomics) for large populations of individuals. The aim of such work is to identify biomolecules that can be used as markers for a number of disease states.

A second research area in our group involves the use of IMS to perform conformational analyses of proteins and peptides. These studies can provide information regarding factors that influence the establishment of solution-phase structures of specific molecules. A number of experiments have shown that aspects of solution-phase conformation can be retained in the gas-phase. Thus, such experiments can also directly probe solution-phase conformations. One area of interest is that of macromolecular assembly ranging from small protein complexes to larger species such as those observed in viral assembly.

Representative Publications

Selected Publications (from 140+ peer-reviewed publications)

  1. Valentine, S. J.; Kurulugama, R. T.; Bohrer, B. C.; Merenbloom, S. I.; Sowell, R. A.; Clemmer, D. E. Developing IMS–IMS–MS for rapid characterization of abundant proteins in human plasma. International Journal of Mass Spectrometry 2009, 283, 149–160.
  2. Merenbloom, Samuel I.; Glaskin, Rebecca S.; Henson, Zachary B.; Clemmer, David E. High-Resolution Ion Cyclotron Mobility Spectrometry. Analytical Chemistry 2009, 81(4), 1482-1487.
  3. Valentine, S.J., Stokes, S.T. Kurulugama, R., Nachtigall, F.M., Clemmer, D.E. Overtone Mobility Spectrometry (Part2): Theoretical Considerations of Resolving Power. J. Am. Soc. Mass Spec, 20, 5, 2009, 738-750
  4. Kurulugama, R., Nachtigall, F.M., Lee, S., Valentine, S.J., Clemmer, D.E. Overtone Mobility Spectrometry (Part1): Experimental Observations. J. Am. Soc. Mass Spec., 20, 5, 2009, 729-737
  5. Plasencia, M. D. ; Isailovic, D. ; Merenbloom, S. I. ; Mechref, Y. ; Clemmer, D. E. Resolving and Assigning N-linked Glycan Structural Isomers from Ovalbumin by IMS-MS. J. Am. Soc. Mass Spectrom. 2008, 19 (11), 1706-1715.
  6. Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. Quantitative Proteomics of a Presymptomatic A53T {alpha}-Synuclein Drosophila Model of Parkinson Disease. Mol. Cell. Proteomics, 2008, 7, 1191-1203.
  7. Isailovic, D. ; Kurulugama, R. T. ; Plasencia, M. D. ; Stokes, S. T. ; Kyselova, Z. ; Goldman, R. ; Mechref, Y. ; Novotny, M. V. ; Clemmer, D. E. Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS-MS. J. Proteome Res. 2008, 7(3), 1109-1117.
  8. Sowell, R. A. ; Hersberger, K. E. ; Kaufman, T. C. ; Clemmer, D. E. Examining the Proteome of Drosophila Across Organism Lifespan. J. Proteome Res. 2007, 6(9), 3637-3647.
  9. Liu, X. ; Valentine, S. J. ; Plasencia, M. D. ; Trimpin, S. ; Naylor, S. ; Clemmer, D. E. Mapping the Human Plasma Proteome by SCX-LC-IMS-MS. J. Am. Soc. Mass Spectrom. 2007, 18(7), 1249-1264.
  10. Koeniger, S. L. ; Clemmer, D. E. Resolution and Structural Transitions of Elongated States of Ubiquitin, J. Am. Soc. Mass Spectrom. 2007, 18, 322-331
  11. Myung, S. ; Lorton, P. ; Merenbloom, S. I. ; Fioroni, M. ; Koeniger, S. L. ; Julian, R. R. ; Baik, M-H. ; Clemmer, D. E. Spontaneous Resolution of Icosahedral Proline J. Am. Chem. Soc. 2006, 28, 15988-9.
  12. Koeniger, S. L. ; Merenbloom, S. I. ; Valentine, S. J. Jarrold, M. F. ; Udseth, H. ; Smith, R. ; Clemmer, D. E. An IMS-IMS Analogue of MS-MS Anal. Chem. 2006, 78, 4161-4174.
  13. Merenbloom, S. I. ; Koeniger, S. L. ; Valentine, S. J. ; Plasencia, M. D. ; Clemmer, D. E. IMS-IMS and IMS-IMS-IMS/MS for Separating Peptide and Protein Fragment Ions, Anal. Chem. 2006, 78, 2802-2809.
  14. Koeniger, S. L. ; Merenbloom, S. I. ; Clemmer, D. E. Evidence for Many Resolvable Structures within Conformation Types of Electrosprayed Ubiquitin Ions, J. Phys. Chem B 2006, 110, 7017-7021.
  15. Myung, S. ; Badman, E. ; Lee, Y. J. ; Clemmer, D. E. Structural Transitions of Electrosprayed Ubiquitin Ions Stored in an Ion Trap over ~10 ms to 30s, J. Phys. Chem. A 2002, 106, 9976-9982.
  16. Hoaglund-Hyzer, C. S. ; Lee, Y. J. ; Counterman, A. E. ; Clemmer, D. E. Coupling Ion Mobility Separations, Collisional Activation Techniques, and Multiple Stages of MS for Analysis of Complex Peptide Mixtures, Anal. Chem. 2002, 74, 992-1006.
  17. Badman, E. R. ; Hoaglund-Hyzer, C. S. ; Clemmer, D. E. Monitoring Structural Changes of Proteins in an Ion Trap over ~10-200 ms: Unfolding Transitions in Cytochrome c Ions, Anal. Chem. 2001, 73, 6000-6007.
  18. Counterman, A. E. ; Clemmer, D. E. Large Anhydrous Polyalanine Ions: Evidence for Extended Helices and Onset of a More Compact State, J. Am. Chem. Soc. 2001, 123, 1490-1498.
  19. Hoaglund Hyzer, C. S. ; Counterman, A. E. ; Clemmer, D. E. Anhydrous Protein Ions, Chem. Rev. 1999, 99, 3037-3079 (invited).
  20. Henderson, S. C. ; Valentine, S. J. ; Counterman, A. E. ; Clemmer, D. E. ESI/Ion Trap/Ion Mobility/Time-of-Flight Mass Spectrometry for Rapid and Sensitive Analysis of Biomolecular Mixtures, Anal. Chem. 1999, 71, 291-301.
  21. Hoaglund, C. S. ; Valentine, S. J. ; Sporleder, C. R. ; Reilly, J. P. ; Clemmer, D. E. Three-Dimensional Ion Mobility/TOFMS Analysis of Electrosprayed Biomolecules, Anal. Chem. 1998, 70, 2236-2242.
  22. Hoaglund, C. S. ; Valentine, S. J. ; Clemmer, D. E. An Ion Trap Interface for ESI-Ion Mobility Experiments, Anal. Chem. 1997, 69, 4156-4161\Valentine, S. J. ; Anderson, J. G. ; Ellington, A. D. ; Clemmer, D. E. Disulfide-Intact and -Reduced Lysozyme in the Gas Phase: Conformations and Pathways of Folding and Unfolding, J. Phys. Chem. B 1997, 101, 3891-3900.