Seeing Things That Have Never Been Observed Before: Pushing the Limits of Mass Spectrometry

Apr 15, 2014
By Spectroscopy Editors

Mass spectrometry is a powerful analytical tool. Yet researchers and instrument makers continue to push the limits of its resolving power. One such researcher is
David E. Clemmer, the Robert & Marjorie Mann Chair and Distinguished Professor of Chemistry at Indiana University in Bloomington, Indiana and the 2014 Anachem Award winner. Clemmer’s group has done extensive research to develop and improve ion trapping techniques and ion mobility spectrometry–mass spectrometry (IMS–MS) instruments to analyze biomolecular mixtures and structures. Spectroscopy recently spoke with Clemmer about this work.

Your laboratory performs highly resolved measurements of biomolecular structures. How did you become interested in ion mobility spectrometry for use in this research?

Clemmer: We began thinking about the development of nested IMS-MS measurements in the mid 1990s — about the time that many people were becoming excited about the emerging fields of genomics and proteomics. At that time, it was a bit of a stretch to think about measurements of peptides from a proteome with IMS or MS alone. But the combination seemed quite natural and there were several advantages that we could imagine.  For example, because drift times are on the order of milliseconds, the measurement could be sandwiched between a liquid chromatography (LC) measurement and an MS measurement at no additional cost in analysis time. Also, we could see that it was possible to carry out collision-induced dissociation experiments in parallel with the combined technologies. So, we began trying to see if we could develop instruments with these advantages. In the end, I believe we tried perhaps a dozen different combinations of drift tubes, ion traps, and mass spectrometers as we worked on complex mixtures.
In a recent article (1), you discuss a new ion-trapping technique that involves the accumulation of ions in a cyclical drift tube as a means of enhancing ion signals for scanning ion cyclotron mobility measurements. Can you tell us more about this technique?  What are the advantages of the cyclical drift tube compared to linear drift tubes?

Clemmer: Circular IMS instruments allow one to take advantage of very long distances for separations. This is realized by allowing the ions to go around the circle many times. We recently described a technique called overtone mobility spectrometry. This is an approach that looks promising for improving the resolving power of diffusion measurements while still providing absolute mobilities (or cross sections), something other techniques like field asymmetric ion mobility spectrometry (FAIMS) can’t do (at least not yet). We believe that a circular instrument operated in an overtone mode would allow us to carry out what we are calling a zoom scan — a very high resolving power measurement designed to separate ions with nearly identical mobilities. To advance this, we’ve changed our thinking some. We operate the circle as a new type of ion trap (one based on diffusion) and take advantage of the overtones as ions migrate around the circle. This looks very promising as a means of pushing these methods to very high resolving power while maintaining the fundamental information that is useful for characterizing ion structures.

What applications do you expect the cyclical drift tube ion-trapping technique to be used for in the future?

Clemmer: This instrument is already capable of separating mixtures of ions that cannot be pulled apart with any existing technology. So, I see it as a way to see things that have never been observed before. I have some wild ideas about what we might see. But, I try to keep them largely within my research group until we are closer to trying the experiments.

Your laboratory has also published work using IMS-MS with a temperature-variable drift cell or a drift tube divided into sections to obtain information on the molecular dynamics of polyatomic ions in the absence of a solvent (2). How does this approach enable examination of structural changes?

Clemmer: Hybrid IMS-IMS-MS and IMS-IMS-IMS-MS measurements allow one to take a mixture of conformations, separate them, isolate a subset, activate the subset, and see what new structures are observed. One might think about this as a way of landing on difficult spots of potential energy landscapes. Effectively, it allows  researchers to test if they can get from one place to another. In our case the question is: Can we convert a selected conformation into a new structure? By doing this, we learn what types of transitions require solvent and which can occur when only intramolecular interactions are possible. Careful studies of this type are beginning to provide insight into what types of conformations might dissociate differently from one another. Most of the ions we have worked with so far go through a quasi-equilibrium distribution of states prior to dissociation, and thus there are no differences in fragmentation from specifically selected conformers. Those cases where different precursor ion conformations dissociate differently give us insight into the details of conformer structures.

How has computer simulation been used in your lab to investigate new instrument designs?

Clemmer: In the last few years, it is the case that we often design instruments on a computer and then calculate how ions move and are separated in these instruments under different conditions. This is a little different than our use of SIMION or other commercial codes because we write our own code to test the instruments. The calculations are so good now that we often run computer simulations of multiple electrode geometries under different pressure and field conditions prior to converging on the design of our next generation of instruments. 

What are the next steps in your research?

Clemmer: We are very interested in using gas-phase data to probe solution conformations. We have been careful about not assuming that they are the same.  But clearly, under some conditions it is possible to transfer elements of structure from solution into the gas phase. With our collaborator (David Russel), we recently published a paper where we found evidence for ~10 solution conformations of the nonapeptide bradykinin. Some of these appear to arise from different cis–trans configurations of proline residues. Bradykinin is a peptide that has been studied for more than 50 years; new technologies that allow multiple populations of solution structures that were unknown to date are quite exciting to us.  So, we’ll work in this area as next steps.  

(1) R.S. Glaskin, M.A. Ewing, and D.E. Clemmer, Anal. Chem. 85, 7003–7008 (2013).
(2) T. Wyttenbach, N.A. Pierson, D.E. Clemmer, and M.T. Bowers, Annu. Rev. Phys. Chem. 65, 175–196 (2014).

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