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Faculty & Research

James Prell

Profile picture of James Prell
Associate Professor
Biophysics, Materials Chemistry, Physical Chemistry & Analytical/Bioanalytical Chemistry
Chemistry and Biochemistry
Phone: 541-346-2597
Office: 141 Klamath Hall


Postdoctoral scholar, University of California, Berkeley, Jan 2011-July 2014 (Research adviser: Professor Stephen R. Leone). Ph.D., University of California, Berkeley, Chemistry, May 2011 (Research adviser: Professor Evan R. Williams). Coursework, University of California, Berkeley, Germanic Literatures and Linguistics, 2005-2006. B.A. (summa cum laude), Washington University in Saint Louis, Chemistry, Mathematics, and German, with minors in Music and Religious Studies, 2005. Awards and Honors: Florence Moog Honorary Fellow at WUStL (2001-2005), Barry M. Goldwater Scholar (2003-2005), Andrew W. Mellon Fellow (2005), Regents Intern Fellow at UC Berkeley (2005), National Science Foundation CAREER Award (2018), American Society for Mass Spectrometry Research Award (2018).

Prell Group website


The Prell laboratory uses state-of-the-art mass spectrometry and ion mobility techniques to investigate the physical and chemical properties that govern the organization of macromolecular assemblies at the nanoscale, including those found in biological membranes.  At the scale of a few nanometers, chemical interactions (from covalent bonds to hydrogen bonds and van der Waals interactions) collectively give rise to material properties, such as surface tension, viscosity, and phase separation behavior, in many condensed phase "soft-matter" systems.  Biological cells, for instance, likely exploit delicate balances of these interactions to regulate signalling, endocytosis, and many other processes, although a precise characterization of the nanoscale structures that are involved can be extremely challenging.  Mass spectrometry and allied techniques have proved invaluable for studying the structure and organization of many kinds of matter, from simple molecules to megadalton-sized cytosolic and even membrane protein assemblies.  Our lab uses newly developed methods capable of transferring and analyzing intact macromolecular assemblies in the gas phase while retaining much of their condensed-phase tertiary and quaternary structure.  We learn complementary information about their composition, shape, and folding state in these same experiments using ion mobility spectrometry.  Combined with computational modeling and results from other bioanalytical experiments, data obtained with these methods can be used to construct detailed models of the assemblies, ligand binding, and other properties.  Assembly structures and their dependence on the condensed-phase environment in which they arise enable us to paint a vivid picture of how biological and other nanoscale systems bridge the gap from chemical to material properties, with a view toward biochemical, pharmaceutical, and technological applications.  These experiments are informed by our in-house Fourier Transform-based spectral analysis tools (iFAMS), collisional cross section modeling software (Collidoscope), and MD simulations of ion heating, unfolding, and dissociation. iFAMS and Collidoscope are available by request as well as on Github as open-source, free, publicly available software (see github.com/prellgoup/Collidoscope and github.com/seanpatcleary/iFAMS). Our research is supported generously by the National Institute of Allergy and Infectious Disease, National Science Foundation CAREER Award, and an American Society for Mass Spectrometry Research Award.


At the University of Oregon (the list below may be outdated; please see prellgroup.uoregon.edu or visit Jim Prell's Google Scholar page for most current list)

  1. Prell, J.S. Modelling Collisional Cross Sections, in Comprehensive Analytical Chemistry 83: Ion Mobility Spectrometry, Elsevier, Amsterdam, 2019, in press
  2. Cleary, S.P.; Li, H.; Bagal, D.; Loo, J.A.; Campuzano, I.D.G.; Prell, J.S. Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics. J. Am. Soc. Mass Spectrom., 2018, DOI: 10.1007/s13361-018-2018-7 (download iFAMS here)
  3. Hartle, M.D.; Tillotson, M.R.; Prell, J.S.; Pluth, M.D. Spectroscopic Investigation of the Reaction of Metallo-Protoporphyrins with Hydrogen Sulfide. J. Inorg. Bio., 2017, 173, 152-157 DOI: 10.1016/j.jinorgbio.2017.04.021
  4. Donor, M.T.; Ewing, S.A.; Zenaidee, M.A.; Donald, W.A.; Prell, J.S. Extended Protein Ions are Formed by the Chain Ejection Model in Chemical Supercharging Electrospray Ionization. Anal. Chem. 2017, 89, 5107-5114 DOI: 10.1021/acs.analchem.7b00673
  5. Ewing, S.A.; Donor, M.T.; Wilson, J.W.; Prell, J.S. Collidoscope: An Improved Tool for Computing Collisional Cross Sections with the Trajectory Method. J. Am. Soc. Mass Spectrom.201728, 587-596 DOI: 10.1007/s13361-017-1594-2 [Focus Issue: Emerging Investigators] (download Collidoscope here)
  6. Wheeler, L.C.; Donor, M.T.; Prell, J.S.; Harms, M. J. Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family. PLOS ONE 2016, 11, e0164740 DOI: 10.1371/journal.pone.0164740
  7. Cleary, S.P.; Thompson, A.M.; Prell, J.S. Fourier Analysis Method for Analyzing Highly Congested Mass Spectra of Ion Populations with Repeated Subunits. Anal. Chem. 2016, 88, 6205-6213 DOI: 10.1021/acs.analchem.6b01088 (download iFAMS here)
  8. Taber, B.; Kislitsyn, D.A.; Gervasi, C.F.; Mills, J.M.; Rosenfield, A.E.; Zhang, L.; Mannsfeld, S.C.B.; Prell, J.S.; Briseno, A.L.; Nazin, G.V. Real-Space Visualization of Conformation-Dependent Oligothiophene Electronic Structure. J. Chem. Phys. 2016, 144, 194703 DOI: 10.1063/1.4949765
  9. Hartle, M.D.; Prell, J.S.; Pluth, M.D. Spectroscopic Investigations into the Binding of Hydrogen Sulfide to Synthetic Picket-Fence Porphyrins. J. Chem. Soc., Dalton Trans. 2016, 45, 4843-4853. DOI: 10.1039/C5DT04563K
  10. Kislitsyn, D.A.; Taber, B.; Gervasi, C.F.; Zhang, L.; Mannsfeld, S.C.B; Prell, J.S.; Briseno, A.; Nazin, G.Y. Oligothiophene Wires: Impact of Torsional Conformation on the Electron Structure. Phys. Chem. Chem. Phys. 2016, 18, 4842-4849. DOI: 10.1039/C5CP07092A

Earlier publications

  1. Zürch, M.; Chang, H.-T.; Kraus, P. M.; Cushing, S. K.; Borja, L. J.; Gandman, A.; Kaplan, C. J.; Oh, M. H.; Prell, J. S.; Prendergast, D.; Pemmaraju, C. D.; Neumark, D. M.; Leone, S. R. Carrier Trapping and Thermalization in Silicon-Germanium Alloy Probed by Attosecond XUV Transient Absorption Spectroscopy. Structural Dynamics 2017, 4, 044029 DOI: 10.1063/1.4985056
  2. Zürch, M.; Chang, H.-T.; Borja, L.J.; Kraus, P.M.; Cushing, S.K.; Gandman, A.; Kaplan, C.J.; Oh, M.H.; Prell, J.S.; Prendergast, D.; Pemmaraju, C.D.; Neumark, D.M.; Leone, S.R. Direct and Simultaneous Observation of Ultrafast Electron and Hole Dynamics in Germanium. Nature Comm. 2017, in press.
  3. Schultze, M.; Ramasesha, K.; Pemmaraju, C.D.; Sato, S.A.; Whitmore, D.; Gandman, A.; Prell, J.S.; Borja, L.; Prendergast, D.; Yabana, K.; Neumark, D.M.; Leone, S.R. Attosecond Band Gap Dynamics in Silicon. Science 2014, 346, 1348-1352. DOI: 10.1126/science.1260311
  4. Gomez, L.F.; Ferguson, K.R.; Cryan, J.P.; Bacellar, C.; Tanyag, R.M.P.; Jones, C.; Schorb, S.; Anielski, D.; Belkacem, A.; Bernando, C.; Boll, R.; Bozek, J.; Carron, S.; Chen, G.; Delmas, T.; Englert, L.; Epp, S.W.; Erk, B.; Foucar, L.; Hartmann, R.; Hexemer, A.; Huth, M.; Kwok, J.; Leone, S.R.; Ma, J.H.S.; Maia, F.R.N.C.; Malmerberg, E.; Marchesini, S.; Neumark, D.M.; Poon, B.; Prell, J.; Rolles, D.; Rudek, B.; Rudenko, A.; Seifrid, M.; Siefermann, K.R.; Sturm, F.P.; Swiggers, M.; Ulrich, J.; Weise, F.; Zwart, P.; Bostedt, C.; Gessner, O.; Vilesov, A.F. Shapes and Vorticities of Superfluid Helium Droplets. Science 2014, 345, 906-909. DOI: 10.1126/science.1252395
  5. Prell, J.S.; Borja, L.J.; Neumark, D.M.; Leone, S.R. Simulation of Attosecond-Resolved Imaging of the Plasmon Electric Field in Metallic Nanoparticles. Ann. Phys.—Berlin 2013, 525, 151-161.
  6. Nagel, P.M.; Robinson, J.S.; Harteneck, B.; Pfeifer, T.; Abel, M.J.; Prell, J.S.; Neumark, D.M.; Kaindl, R.A.; Leone, S.R. Surface Plasmon Assisted Electron Acceleration in Photoemission from Gold Nanopillars. Chem. Phys. 2013, 414, 106-111.
  7. Chang, T.M.; Prell, J.S.; Warrick, E.R.; Williams, E.R. Where’s the Charge? Protonation Sites in Gaseous Ions Change with Hydration. J. Am. Chem. Soc. 2012, 134, 15805-15813.
  8. Sterling, H.J; Prell, J.S.; Cassou, C.A.; Williams, E.R. Protein Conformation and Supercharging with DMSO from Aqueous Solution. J. Am. Soc. Mass Spectrom. 2011, 22, 1178–1186.
  9. Prell, J.S.; Chang, T.M.; Biles, J.A.; Berden, G.; Oomens, J.; Williams, E.R. Isomer Population Analysis of Gaseous Ions from Infrared Multiple Photon Dissociation Spectroscopy. J. Phys. Chem. A 2011, 115, 2745–2751.
  10. Prell, J.S.; O’Brien, J.T.; Williams, E.R. Structural and Electric Field Effects of Ions in Aqueous Nanodrops. J. Am. Chem. Soc. 2011, 133, 4810–4818.
  11. Prell, J.S.; Correra, T.C.; Chang, T.M.; Biles, J.A.; Williams, E.R. Entropy Drives a Water Molecule from the C- to N-Terminus on Protonated Proline. J. Am. Chem. Soc. 2010, 132, 14733–14735.
  12. O’Brien, J.T.; Prell, J.S.; Berden, G.; Oomens, J.; Williams, E.R. Effects of Anions on the Zwitterion Stability of Glu, His, and Arg Investigated by IRMPD Spectroscopy and Theory. Int. J. Mass Spectrom. 2010, 297, 116–123.
  13. O’Brien, J.T.; Prell, J.S.; Williams, E.R. Sulfate Ion Patterns Water at Long Distance. J. Am. Chem. Soc. 2010, 132, 8248–8249.
  14. Prell, J.S.; Chang, T.M.; O’Brien, J.T.; Williams, E.R. Hydration Isomers of Protonated Phenylalanine and Derivatives: Relative Stabilities from Infrared Photodissociation. J. Am. Chem. Soc. 2010132, 7811–7819.
  15. Prell, J.S.; O’Brien, J.T.; Williams, E.R. IRPD Spectroscopy and Ensemble Measurements: Effects of Different Data Acquisition and Analysis Methods. J. Am. Soc. Mass Spectrom. 2010, 21, 800–809.
  16. Prell, J.S.; Flick, T.G.; Oomens, J.; Berden, G.; Williams, E.R. Coordination of Trivalent Metal Cations to Peptides: Results from IRMPD Spectroscopy and Theory. J. Phys. Chem. A 2010, 114, 854–860.
  17. Bush, M.F.; O’Brien, J.T.; Prell, J.S.; Wu, C.; Saykally, R.J.; Williams, E. R. Hydration of Alkaline Earth Metal Dications: Effects of Metal Ion Size Determined Using Infrared Action Spectroscopy. J. Am. Chem. Soc. 2009, 131, 13270–13277.
  18. Donald, W.A.; Leib, R.D.; Demireva, M.; O’Brien, J.T.; Prell, J.S.; Williams, E.R. Directly Relating Reduction Energies of Gaseous Eu(H2O)n3+, n = 55-140, to Aqueous Solutions: The Absolute SHE Potential and Real Proton Solvation Energy. J. Am. Chem. Soc. 2009, 131, 13328–13337.
  19. Prell, J.S.; O’Brien, J.T.; Steill, J.D.; Oomens, J.; Williams, E.R. Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges. J. Am. Chem. Soc. 2009131, 11442–11449.
  20. Prell, J.S.; Williams, E.R. Structures of Thermal, Mass-Selected Water Clusters Probed with Hydrophobic Ion Tags and Infrared Photodissociation Spectroscopy. J. Am. Chem. Soc. 2009131, 4110–4119.
  21. O’Brien, J.T.; Prell, J.S.; Steill, J.D.; Oomens, J.; Williams, E.R. Changes in Binding Motif of Protonated Heterodimers Containing Valine Investigated Using IRMPD Spectroscopy between 800 and 3700 cm−1 and Theory. J. Am. Chem. Soc. 2009131, 3905-3912.
  22. Prell, J.S.; Demireva, M.; Williams, E.R. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J. Am. Chem. Soc. 2009131, 1232–1242.
  23. O’Brien, J.T.; Prell, J.S.; Steill, J.D.; Oomens, J.; Williams, E.R. Interactions of Mono- and Divalent Metal Cations with Aspartic and Glutamic Acid Investigated with Infrared Photodissociation Spectroscopy and Theory. J. Phys. Chem. A 2008112, 10823–10830.
  24. Prell, J.S.; O’Brien, J.T.; Holm, A.I.S.; Leib, R.D.; Donald, W.A.; Williams, E.R. Electron Capture Dissociation by a Hydrated Gaseous Peptide: Effects of Water on Fragmentation and Molecular Survival. J. Am. Chem. Soc. 2008130, 12680–12689.
  25. O’Brien, J.T.; Prell, J.S.; Holm, A.I.S.; Williams, E.R. Effects of Electron Kinetic Energy and Ion-Electron Inelastic Collisions in Electron Capture Dissociation Measured Using Ion Nanocalorimetry. J. Am. Soc. Mass Spectrom. 200819, 772–779.
  26. Bush, M.F.; Prell, J.S.; Saykally, R.J.; Williams, E.R. One Water Molecule Stabilizes the Cationized Arginine Zwitterion. J. Am. Chem. Soc. 2007129, 13544–13553.
  27. Bush, M.F.; O’Brien, J.T.; Prell, J.S.; Saykally, R.J.; Williams, E.R. Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition from Nonzwitterionic to Zwitterionic Structure. J. Am. Chem. Soc. 2007129, 1612–1622.
  28. Gaspar, P.P.; Liu, X.P.; Ivanova, D.; Read, D.; Prell, J.S.; Gross, M.L. Four Valence-Electron Reactive Intermediates and the Philicity of Charged Carbene Analogs. Modern Aspects of Main Group Chemistry 2006917, 52–65.