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Indiana University Bloomington

Clemmer Group

IMS Theory

  1. Instrumental Simulations
  2. Intrinsic Size Parameters
  3. Molecular Modeling / CS Calculations
  4. Notes and References

Instrumental Simulations

Michael A. Ewing

We investigate new instrument designs by simulation of the instruments we have built or of those we propose. We use SIMION for calculation of the electric field and a separate program written in-house to simulate ion trajectories in the gas phase. This program adds the motion due to the electric field to a diffusive motion approximated as Brownian motion. These simulations have been helpful in understanding a variety of instruments from tandem IMS to OMS instruments, with recent work also aiding in the understanding of the kinetics of structural transitions in the gas phase. Current work in our lab uses instrumental simulations to understand new instruments we are developing and to assist in the design process.

Intrinsic Size Parameters

Jonathan M. Dilger

The cross section of an ion is a measure of its overall shape and thus is related to its structure. The relative contribution to cross section for an individual amino acid residue within a peptide sequence can be derived with intrinsic size parameters (ISPs).1 These ISPs are derived with each residue as a separate variable from the large number of measurements contained within the cross section database. The utility of ISPs are demonstrated with respect to prediction of cross section,2, 3 extraction of average volumes of amino acid residues,4 and sequence specificity.5 Current work with ISPs focuses on the structural analysis of metalated tryptic peptides.6 Comparisons of these metal-coordinated ISPs with protonated ISPs can display general trends in metal interactions with a given peptide sequence.

Molecular Modeling / CS Calculations

Nicholas A. Pierson

Ion mobility analyses are often combined with computational modeling approaches to aid in the interpretation of experimental data. Molecular dynamics (MD) simulations use Newtonian physics to theoretically model the structure and dynamics of molecules in a given system over time. Our group utilizes these methods to model biomolecules both in solution and in vacuo. Energy-minimized structures can be related to IMS data by submitting atomic coordinates to a program called MOBCAL, developed by Martin F. Jarrold. MOBCAL (freely available online from the Jarrold Group at Indiana University) calculates theoretical collision cross sections for the submitted molecular structures.7 These theoretical cross section values are then compared with calculated experimental cross sections from IMS to match the data with tentative low-energy structures.

Notes and References

Full-text formats for many of these references can be found on the Publications page. External links are provided as necessary and available.

  1. Valentine, S. J.; Counterman, A. E.; Hoaglund-Hyzer, C. S.; Clemmer, D. E. Intrinsic Amino Acid Size Parameters from a Series of 113 Lysine-Terminated Tryptic Digest Peptide Ions, J. Phys. Chem. B 1999, 103, 1203–1207. (Link)
  2. Valentine, S. J.; Counterman, A. E.; Clemmer, D. E. A Database of 660 Peptide Ion Cross Sections: Use of Intrinsic Size Parameters for Bona Fide Predictions of Cross Sections, J. Am. Soc. Mass Spectrom. 1999, 10, 1188–1211. (Link)
  3. 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., 2011, 10, 2318–2329. (Link)
  4. Counterman, A. E.; Clemmer, D. E. Volumes of Individual Amino Acid Residues in Gas-Phase Peptide Ions, J. Am. Chem. Soc. 1999, 121, 4031–4039. (Link)
  5. Hilderbrand, A. E.; Clemmer, D. E. Determination of Sequence-Specific Intrinsic Size Parameters from Cross Sections for 162 Tripeptides J. Phys. Chem B 2005, 109, 11802–11809. (Link)
  6. Dilger, J. M.; Valentine, S. J.; Glover, M. S.; Ewing, M. A.; Clemmer, D. E. A Database of Alkali Metal-Containing Peptide Cross Sections: Influence of Metals on Size Parameters for Specific Amino Acids. Accepted to Int. J. Mass Spectrom. (Link)
  7. MOBCAL calculates theoretical collision cross sections by three methods:
    1. Projection approximation (PA): Mack, E. Average cross-sectional areas of molecules by gaseous diffusion methods, J. Am. Chem. Soc. 1925, 47, 2468–2482.
    2. Exact hard-spheres scattering model (EHS): Shvartsburg, A. A.; Jarrold, M. F. An exact hard-spheres scattering model for the mobilities of polyatomic ions, Chem. Phys. Lett. 1996, 261, 86–91.
    3. Trajectory method (TM): Mesleh, M. F.; Hunter, J. M.; Shvartsburg, A. A.; Schatz, G. C.; Jarrold, M. F. Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential, J. Phys. Chem. 1996, 100, 16082–16086.