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

Professor Clemmer received a Ph.D. in Chemistry from the University of Utah and did postdoctoral work at the Himeji Institute of Technology (Japan) and Northwestern University before coming to IU in 1995.  His research involves the development of methods for studying the structures of complex low-symmetry systems in the gas phase.  These methods are being applied to several types of problems including elucidation of fundamental issues associated with how a protein folds, as well as studies of complex mixtures of proteins – the emerging field of proteomics. 

Professor Clemmer has published more than 135 papers and his work has been recognized with several awards, including the Fresenius Chemistry Award.  He has been a member of the US Defense Science Study group.

Research

We are interested in the structures of large low-symmetry molecules in the gas phase and the step-by-step motions explaining the connectivity of the various isomers. We are using and developing a variety of techniques—including ion mobility spectrometry, mass spectrometry, lasers, and computer modeling—to separate gas-phase isomers, discern structural information, and follow isomerization processes.

A major area of interest to our group is protein structure. Although the "native" solution structures of many proteins are known, little is known about how denatured forms fold into the native state. This is because isolating and determining structures for a large number of solutions-phase intermediates is difficult. We are approaching this problem quite differently by studying the structures of naked proteins in the gas phase. Although it seems unlikely that proteins in the gas phase will have structures that are identical to those found in solution, it is straightforward to separate gas-phase intermediates and follow the dynamics associated with folding.

It is worth explaining briefly how shape information about biological systems in the gas phase is obtained. The mobility of a charge protein through a high-pressure buffer gas depends on the protein's average collision cross-section, a property defined by its confirmation. By comparing measured mobilities to those calculated for trail conformations, structural information about the gas-phase species can be extracted.

Another area of interest is the rapid and sensitive analysis of mixtures such as those that arise in the field of proteomics. Electrospray ionization provides an efficient means of ionizing many different types of samples. By combining ion mobility methods with mass spectrometry and other separation techniques, we can examine isomers or variations in conformations that are inaccessible by conventional mass spectrometry methods. Current projects include fundamental studies of the fly and human urinary proteomes and analyses of combinational libraries.

Two-dimensional drift(flight) dataset of the digest mixture from m/z ranges of 510 to 610. The white circles indicate the location of fragment peaks that were observed in the tryptic digestion of horse albumin. Peaks labeled with sequence assignments correspond to tryptic fragments expected from digestion of horse albumin. All peaks that were identified in the individual protein were identified in the mixture except for the peak at m/z=543.8 corresponding to [KQSALAWLVK 2H]2 . This peak cannot be unambiguously identified because of spectral congestion in this region.

Publications

PubMed

Valentine, S.J.; Ewing, M.; Dilger, J.M.; Glover, M.; Geromanos, S.; Hughes, C.; Clemmer, D.E. Using Ion Mobility Data to Improve Peptide Identification: Cross Section Databases and Intrinsic Amino Acid Size Parameters. J. Proteome Res., Article ASAP, Web Publication Date: March 21, 2011

Valentine, S.J.; Kurulugama, R.T.; Clemmer, D. E. Overtone Mobility Spectrometry: Part 3. On the Origin of Peaks. J Am Soc Mass Spectrom. 2011, 22(5), 804-16.

Li, Z.; Valentine, S.J.; Clemmer, D.E. Complexation of Amino Compounds by 18C6 Improves Selectivity by IMS-IMS-MS: Application to Petroleum Characterization. J Am Soc Mass Spectrom. 2011, 22(5), 817-27.

Bohrer, B.; Atlasevich, N.; Clemmer, D.E. Transitions between Elongated Conformations of Ubiquitin [M+11H]11+ Enhance Hydrogen/Deuterium Exchange. J. Phys. Chem. B 2011, 115 (15), 4509–4515.

Bohrer, B.C.; Li, Y. F.; Reilly, J.P.; Clemmer, D. E.; Di Marchi, R.D.; Radivojac, P.; Tang, H.; Arnold, R.J. Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics. Analytical Chemistry 2010, 82(15), 6559-6568.

Kim, T.-Y.; Valentine, S.J.; Clemmer, D.E.; Reilly, J.P. Gas-Phase Conformation-Specific Photofragmentation of Proline-Containing Peptide Ions. Journal of the American Society for Mass Spectrometry 2010, 21(8), 1455-1465.

Trimpin, S., Clemmer, D.E., and Larsen, B.S. Snapshot, Conformation, and Bulk Fragmentation of Polymeric Architectures using ESI-IMS-MS, Ion Mobility Spectrometry: Theory and Applications, Taylor and Francis Group, 2010. (Book Chapter)

Glaskin, R.S.; Valentine, S.J.; Clemmer, D. E. A Scanning Frequency Mode for Ion Cyclotron Mobility Spectrometry. Analytical Chemistry 2010, 82(19), 8266-8271.

Shvartsburg, A.A.; Clemmer, D.E.; Smith, R.D. Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry. Analytical Chemistry 2010, 82(19), 8047-8051

Lee, S.; Ewing, M.A.; Nachtigall, F.M.; Kurulugama, R.T.; Valentine, S.J.; Clemmer, D.E. Determination of Cross Sections by Overtone Mobility Spectrometry: Evidence for Loss of Unstable Structures at Higher Overtones. Journal of Physical Chemistry B 2010, 114(38), 12406-12415.

Robinson, R.A.S.; Kellie, J. F.; Kaufman, T.C.; Clemmer, D. E. Insights into aging through measurements of the Drosophila proteome as a function of temperature. Mechanisms of Ageing and Development 2010, 131(9), 584-590.

Pierson, N.; Valentine, S.J.; Clemmer, D.E.. Evidence for a Quasi-Equilibrium Distribution of States for Bradykinin [M+3H]3+ Ions in the Gas Phase. J. Phys. Chem. B, 2010, 114, 7777–7783

Liu, X., Afrane, M., Clemmer, D.E., Zhong, G., Nelson, D.E. Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomics. J Bacteriol. 2010, 192(11), 2852-2860

Xun, Z., Kaufman, T.C., Clemmer, D.E. Stable Isotope labeling and label-free proteomics of Drosophila parkin null mutants . J. Proteome Research, 2009, 8(10), 4500-4510.

Valentine, S. J.; Clemmer, D. E. Protein oligomers frozen in time. Nature Chemistry 2009, 1 (4), 257-258

Valentine, S. J.; Clemmer, D. E. Treatise on the Measurement of Molecular Masses with Ion Mobility Spectrometry Anal. Chem. 2009, 81(14), 5876-5880

Trimpin, S., Tan, B., Bohrer, B.C., O’Dell, D.K., Merenbloom, S.I., Pazos, M.X., Clemmer, D.E., Walker, J.M. Profiling of Phospholipids and Related Lipid Structures using Multidimensional Ion Mobility Spectrometry-Mass Spectrometry. International Journal of Mass Spectrometry 2009, 287, 58-69.

Valentine, S. J.; Kurulugama, R. T.; Bohrer, B. C.; Merenbloom, S. I.; Sowell, R. A.; Mechref, Y.; 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.

Merenbloom, S.I.; Glaskin, R.S.; Henson, Z.B.; Clemmer, D. E. High-Resolution Ion Cyclotron Mobility Spectrometry. Analytical Chemistry 2009, 81(4), 1482-1487.

Valentine, S.J., Stokes, S.T. Kurulugama, R., Nachtigall, F.M., Clemmer, D.E. Overtone Mobility Spectrometry (Part2): Theoretical Considerations of Resolving Power. Journal of the American Society for Mass Spectrometry, Volume 20, Issue 5, 2009, 738-750

Kurulugama, R., Nachtigall, F.M., Lee, S., Valentine, S.J., Clemmer, D.E. Overtone Mobility Spectrometry (Part1): Experimental Observations Journal of the American Society for Mass Spectrometry, Volume 20, Issue 5, 2009, 729-737

Awards

• Japanese Society for the Promotion of Science (JSPS) Fellowship (2011-12)
• Outstanding Alumnus, Adams State College (2010)        
  
• Tracy M. Sonneborn Award (2009)
  
• ACS Akron award (2007)
  
• Biemann Medal (2006, Am. Soc. for Mass Spectrom.)
  
• Fellow of the Royal Society of Chemistry –FRSC (2005)
  
• NSF Special Creativity Award (2003-05)
  
• Pittcon Achievement Award (2002)
  
• Named on Popular Science 10 Most Brilliant List (2002)
  
• Phi Lambda Upsilon National Fresenius Award (2000)
  
• Eli Lilly Analytical Chemistry Award (2000-02)
  
• TR-100 research innovation award -Technology Review Magazine, MIT (2000)
  
• Camille Dreyfus Teacher-Scholar Award (1999-2004)
  
• ACS Findeis Award (1999)
  
• Teaching Excellence Recognition Award (1999, IU)
  
• Alfred P. Sloan Research Fellow (1998-2001)
  
• Outstanding Junior Faculty Award (1998, IU)
  
• Finnegan Award (1997, Am. Soc. for Mass Spectrom.)
  
• NSF Early Career Award -Gas-Phase Proteins (1996-2000)
  
• IU Summer Faculty Research Fellowship (1995)

Highlights

Indiana University chemist named one of nation's most "brilliant"

Chemistry Chair David Clemmer has been named one of Popular Science magazine's "Brilliant 10" scientists. Full Story