Journal of the American Society for Mass Spectrometry

, Volume 17, Issue 9, pp 1216–1228

Ion trajectory simulation for electrode configurations with arbitrary geometries



A multi-particle ion trajectory simulation program ITSIM 6.0 is described, which is capable of ion trajectory simulations for electrode configurations with arbitrary geometries. The electrode structures are input from a 3D drawing program AutoCAD and the electric field is calculated using a 3D field solver COMSOL. The program CreatePot acts as interface between the field solver and ITSIM 6.0. It converts the calculated electric field into a field array file readable by ITSIM 6.0 and ion trajectories are calculated by solving Newton’s equation using Runge-Kutta integration methods. The accuracy of the field calculation is discussed for the ideal quadrupole ion trap in terms of applied mesh density. Electric fields of several different types of devices with 3D geometry are simulated, including ion transport through an ion optical system as a function of pressure. Ion spatial distributions, including the storage of positively charged ions only and simultaneous storage of positively/negatively charged ions in commercial linear ion traps with various geometries, are investigated using different trapping modes. Inelastic collisions and collision induced dissociation modeled using RRKM theory are studied, with emphasis on the fragmentation of n-butylbenzene inside an ideal quadrupole ion trap. The mass spectrum of 1,3-dichlorobenzene is simulated for the rectilinear ion trap device and good agreement is observed between the simulated and the experimental mass spectra. Collisional cooling using helium at different pressures is found to affect mass resolution in the rectilinear ion trap.


  1. 1.
    March, R. E. Quadrupole Ion Trap Mass Spectrometry: Theory, Simulation, Recent Developments, and Applications. Rapid Commun. Mass Spectrom. 1998, 12, 1543–1554.CrossRefGoogle Scholar
  2. 2.
    Diaz, J. A.; Giese, C. F.; Gentry, W. R. Sub-Miniature EXB Sector-Field Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2001, 12, 619–632.CrossRefGoogle Scholar
  3. 3.
    Marinach, C.; Brunot, A.; Beaugrand, C.; Bolbach, G.; Tabet, J. C. Simulation of Ion Beam and Optimization of Orthogonal Tandem Ion Trap/Reflector Time-of-Flight Mass Spectrometry. Int. J. Mass Spectrom. 2002, 213, 45–62.CrossRefGoogle Scholar
  4. 4.
    Dawson, P. H.; Whetten, N. R. Ion Storage in Three-Dimensional, Rotationally Symmetric, Quadrupole Fields. I. Theoretical Treatment. J. Vac. Sci. Technol. 1968, 5, 91–107.Google Scholar
  5. 5.
    March, R. E.; Todd, J. F. J., Eds; Practical Aspects of Ion Trap Mass Spectrometry, Vol. I: Fundamentals of Ion Trap Mass Spectrometry; CRC Press: Boca Raton, FL, 1995.Google Scholar
  6. 6.
    Xiang, X.; Guan, S.; Marshall, A. G. Simulated Ion Trajectory and Induced Signal in Ion Cyclotron Resonance Ion Traps. J. Am. Soc. Mass Spectrom. 1994, 5, 238–249.CrossRefGoogle Scholar
  7. 7.
    Mitchell, D. W. Realistic Simulation of the Ion Cyclotron Resonance Mass Spectrometer Using a Distributed Three-Dimensional Particle-in-Cell Code. J. Am. Soc. Mass Spectrom. 1999, 10, 136–152.CrossRefGoogle Scholar
  8. 8.
    Franzen, J. Simulation Study of an Ion Cage with Superimposed Multipole Fields. Int. J. Mass Spectrom. Ion Processes. 1991, 106, 63–78.CrossRefGoogle Scholar
  9. 9.
    Vedel, F.; Andre, J.; Vedel, M.; Brincourt, G. Computed Energy and Spatial Statistical Properties of Stored Ions Cooled by a Buffer Gas. Phys. Rev. A. 1983, 27, 2321–2330.CrossRefGoogle Scholar
  10. 10.
    Vedel, F.; Andre, J. Influence of Space Charge on the Computed Statistical Properties of Stored Ions Cooled by a Buffer Gas in a Quadrupole RF Trap. Phys. Rev. A. 1984, 29, 2098–2101.CrossRefGoogle Scholar
  11. 11.
    Londry, F. A.; Alfred, R. L.; March, R. E. Computer Simulation of Single-Ion Trajectories in Paul-Type Ion Traps. Int. J. Mass Spectrom. 1993, 4, 687–705.CrossRefGoogle Scholar
  12. 12.
    Sevugarajan, S.; Menon, A. G. Frequency Perturbation in Nonlinear Paul Traps: A Simulation Study of the Effect of Geometric Aberration, Space Charge, Dipolar Excitation, and Damping on Ion Axial Secular Frequency. Int. J. Mass Spectrom. 2000, 197, 263–278.CrossRefGoogle Scholar
  13. 13.
    Blain, M. G.; Riter, L. S.; Cruz, D.; Austin, D. E.; Wu, G.; Plass, W. R.; Cooks, R. G. Towards the Hand-Held Mass Spectrometer: Design Considerations, Simulation, and Fabrication of Micrometer-Scaled Cylindrical Ion Traps. Int. J. Mass Spectrom. 2004, 236, 91–104.CrossRefGoogle Scholar
  14. 14.
    Ding, L.; Sudakov, M.; Kumashiro, S. A Simulation Study of the Digital Ion Trap Mass Spectrometer. Int. J. Mass Spectrom. 2002, 221, 117–138.CrossRefGoogle Scholar
  15. 15.
    Lammert, S. A.; Plass, W. R.; Thompson, C. V.; Wise, M. B. Design, Optimization, and Initial Performance of a Toroidal RF Ion Trap Mass Spectrometer. Int. J. Mass Spectrom. 2001, 212, 25–40.CrossRefGoogle Scholar
  16. 16.
    Wu, G.; Cooks, R. G.; Ouyang, Z. Geometry Optimization for the Cylindrical Ion Trap: Field Calculations, Simulations, and Experiments. Int. J. Mass Spectrom. 2005, 241, 119–132.CrossRefGoogle Scholar
  17. 17.
    Dahl, D. A. SIMION for the Personal Computer in Reflection. Int. J. Mass Spectrom. 2000, 200, 3–25.CrossRefGoogle Scholar
  18. 18.
    Veryovkin, I. V.; Calaway, W. F.; Pellin, M. J. A Virtual Reality Instrument: Near-Future Perspective of Computer Simulations of Ion Optics. Nucl. Instrum. Methods A. 2004, 519, 363–372.CrossRefGoogle Scholar
  19. 19.
    Forbes, M. W.; Sharifi, M.; Croley, T.; Lausevic, Z.; March, R. E. Simulation of Ion Trajectories in a Quadrupole Ion Trap: A Comparison of Three Simulation Programs. J. Mass Spectrom. 1999, 34, 1219–1239.CrossRefGoogle Scholar
  20. 20.
    March, R. E.; Londry, F. A.; Alfred, R. L.; Todd, J. F. J.; Penman, A. D.; Vedel, F.; Vedel, M. Resonance Excitation of Ions Stored in a Quadrupole Ion Trap. Part III. Introduction to the Field Interpolation Simulation Method. Int. J. Mass Spectrom. Ion Processes. 1991, 110, 159–178.CrossRefGoogle Scholar
  21. 21.
    March, R. E.; Todd, J. F. J., Eds. Quadrupole Ion Trap Mass Spectrometry; John Wiley and Sons, Inc: Hoboken, NJ, 2005, Chap IV.Google Scholar
  22. 22.
    Bui, H. A.; Cooks, R. G. Windows Version of the Ion Trap Simulation Program ITSIM: A Powerful Heuristic and Predictive Tool in Ion Trap Mass Spectrometry. J. Mass Spectrom. 1998, 33, 297–304.CrossRefGoogle Scholar
  23. 23.
    Plass, W. R. Thesis, Justus Liebig Universität Giessen, Giessen, Germany, 2001.Google Scholar
  24. 24.
    Londry, F. A.; Hager, J. W. Mass Selective Axial Ion Ejection from a Linear Quadrupole Ion Trap. J. Am. Soc. Mass Spectrom. 2003, 14, 1130–1147.CrossRefGoogle Scholar
  25. 25.
    Hieke, A. GEMIOS—a 64-Bit Multi-Physics Gas and Electromagnetic Ion Optical Simulator. Proceedings of the 51st ASMS Conference on Mass Spectrometry and Allied Topics; Montreal, Canada, June 2003.Google Scholar
  26. 26.
    Hieke, A. 3D Electro-Pneumatic Monte-Carlo Simulations of Ion Trajectories and Temperatures during RF quadrupole injection in the presence of gas flow fields. Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics; Nashville, TN, May 2004.Google Scholar
  27. 27.
    Weil, C.; Nappi, M.; Cleven, C. D.; Wollnik, H.; Cooks, R. G. Multiparticle Simulation of Ion Injection into the Quadrupole Ion Trap Under the Influence of Helium Buffer Gas Using Short Injection Times and DC Pulse Potential. Int. J. Mass Spectrom. 1996, 10, 742–750.Google Scholar
  28. 28.
    Julian, R. K.; Reiser, H.-P.; Cooks, R. G. Large Scale Simulation of Mass Spectra Recorded with a Quadrupole Ion Trap Mass Spectrometer. Int. J. Mass Spectrom. 1993, 123, 85–96.CrossRefGoogle Scholar
  29. 29.
    Reiser, H.-P.; Julian, R. K.; Cooks, R. G. A Versatile Method of Simulation of the Operation of Ion Trap Mass Spectrometers. Int. J. Mass Spectrom. 1992, 121, 49–63.CrossRefGoogle Scholar
  30. 30.
    Plass, W. R.; Cooks, R. G. A Model for Energy Transfer in Inelastic Molecular Collisions Applicable at Steady State or Non-Steady State and for an Arbitrary Distribution of Collision Energies. J. Am. Soc. Mass Spectrom. 2003, 14, 1348–1359.CrossRefGoogle Scholar
  31. 31.
    Wells, M. J.; Plass, W. R.; Cooks, R. G. Control of Chemical Mass Shifts in the Quadrupole Ion Trap through Selection of Resonance Ejection Working Point and RF Scan Direction. Anal. Chem. 2000, 72, 2677–2683.CrossRefGoogle Scholar
  32. 32.
    Wells, M. J.; Plass, W. R.; Patterson, G. E.; Ouyang, Z.; Badman, E. R.; Cooks, R. G. Chemical Mass Shifts in Ion Trap Mass Spectrometry: Experiments and Simulations. Anal. Chem. 1999, 71, 3405–3415.CrossRefGoogle Scholar
  33. 33.
    Plass, W. R.; Li, H.; Cooks, R. G. Theory, Simulation, and Measurement of Chemical Mass Shifts in RF Quadrupole Ion Traps. Int. J. Mass Spectrom. 2003, 228, 237–267.CrossRefGoogle Scholar
  34. 34.
    Badman, E. R.; Johnson, R. C.; Plass, W. R.; Cooks, R. G. A Miniature Cylindrical Quadrupole Ion Trap: Simulation and Experiment. Anal. Chem. 1998, 70, 4896–4901.CrossRefGoogle Scholar
  35. 35.
    Wells, J. M.; Badman, E. R.; Cooks, R. G. A Quadrupole Ion Trap with Cylindrical Geometry Operated in the Mass-Selective Instability Mode. Anal. Chem. 1998, 70, 438–444.CrossRefGoogle Scholar
  36. 36.
    Jackson, G. P.; Hyland, J. J.; Laskay, U. A. Energetics and Efficiencies of Collision-Induced Dissociation Achieved During the Mass Acquisition Scan in a Quadrupole Ion Trap. Rapid Commun. Mass Spectrom. 2006, 19, 3555–3563.CrossRefGoogle Scholar
  37. 37.
    Dobson, G.; Murrell, J.; Despeyroux, D.; Wind, F.; Tabet, J. C. Investigation into Factors Affecting Precision in Ion Trap Mass Spectrometry Using Different Scan Directions and Axial Modulation Potential Amplitudes. J. Mass Spectrom. 2004, 39, 1295–1304.CrossRefGoogle Scholar
  38. 38.
    Dobson, G.; Murrell, J.; Despeyroux, D.; Wind, F.; Tabet, J. C. Influence on Mass-Selective Ion Ejection of the Phase Difference Between the Driven RF and the Axial Modulation Potentials. J. Mass Spectrom. 2005, 40, 714–721.CrossRefGoogle Scholar
  39. 39.
    Chaudhary, A.; van Amerom, F. H. W.; Short, R. T.; Bhansali, S. Fabrication and Testing of a Miniature Cylindrical Ion Trap Mass Spectrometer Constructed from Low Temperature Cofired Ceramics. Int. J. Mass Spectrom. 2006, 251, 32–39.CrossRefGoogle Scholar
  40. 40.
    Plass, W. R. Theory of Dipolar DC Excitation and DC Tomography in the RF Quadrupole Ion Trap. Int. J. Mass Spectrom. 2000, 202, 175–197.CrossRefGoogle Scholar
  41. 41.
    Hu, Q.; Noll, R. J.; Wu, G.; Makarov, A.; Plass, W. R.; Cooks, R. G. Ion Motion Control in the Orbitrap Mass Analyzer. Proceedings of the 53rd ASMS Conference on Mass Spectrometry and Allied Topics; San Antonio, TX, June 2005.Google Scholar
  42. 42.
    Schwartz, J. C.; Senko, M. W.; Syka, J. E. P. A Two-Dimensional Quadrupole Ion Trap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2002, 13, 659–669.CrossRefGoogle Scholar
  43. 43.
    Hager, J. M. A New Linear Ion Trap Mass Spectrometer. Rapid Commun. Mass Spectrom. 2002, 16, 512–526.CrossRefGoogle Scholar
  44. 44.
    Ouyang, Z.; Wu, G.; Song, Y.; Li, H.; Plass, W. R.; Cooks, R. G. Rectilinear Ion Trap: Concepts, Calculations, and Analytical Performance of a New Mass Analyzer. Anal. Chem. 2004, 76, 4595–4605.CrossRefGoogle Scholar
  45. 45.
    Steer, M. B.; Bandler, J. W.; Snowden, C. M. Computer-Aided Design of RF and Microwave Circuits and Systems. IEEE Trans. Microwave Theory Tech. 2002, 50, 996–1005.CrossRefGoogle Scholar
  46. 46.
    Billen, J. H.; Young, L. M. Poisson/Superfish on PC Compatibles. Proceedings of the 1993 Particle Accelerator Conference, Washington, D.C., May 1993, pp 790–792.Google Scholar
  47. 47.
    Hagg, C.; Szabo, I. New Ion-Optical Devices Utilizing Oscillatory Electric Fields. IV. Computer Simulations of the Transport of an Ion Beam Through an Ideal Quadrupole, Hexapole, and Octopole Operating in the RF-Only Mode. Int. J. Mass Spectrom. Ion Proc. 1986, 73, 295–312.CrossRefGoogle Scholar
  48. 48.
    Song, Q.; Kothari, S.; Senko, M. A.; Schwartz, J. C.; Amy, R. J. W.; Stafford, G. C.; Cooks, R. G.; Ouyang, Z. Rectilinear Ion Trap Mass Spectrometers with Atmospheric Pressure Interface and Electrospray Ionization Source. Anal. Chem. 2006, 78, 718–725.CrossRefGoogle Scholar
  49. 49.
    Zhang, C.; Chen, H.; Guymon, A. J.; Wu, G.; Cooks, R. G.; Ouyang, Z. Instrumentation and Methods for Ion and Reaction Monitoring Using A Non-Scanning Rectilinear Ion Trap. Int. J. Mass Spectrom., in press.Google Scholar
  50. 50.
    Levine, R. D., Ed. Molecular Reaction Dynamics; Cambridge University Press: New York, NY 2005, 356–393.CrossRefGoogle Scholar
  51. 51.
    Baer, T.; Dutuit, O.; Mestdagh, H.; Rolando, C. Dissociation Dynamics of n-Butylbenzene Ions: The Competitive Production of m/z 91 and 92 Fragment Ions. J. Phys. Chem. 1988, 92, 5674–5679.CrossRefGoogle Scholar
  52. 52.
    Gunawardena, H. P.; He, M.; Chrisman, P. A.; Pitteri, S. J.; Hogan, J. M.; Hodges, B. D. M.; McLuckey, S. A. Electron Transfer versus Proton Transfer in Gas-Phase Ion/Ion Reactions of Polyprotonated Peptides. J. Am. Chem. Soc. 2005, 127, 12627–12639.CrossRefGoogle Scholar
  53. 53.
    Syka, J. E. P.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528–9533.CrossRefGoogle Scholar
  54. 54.
    Xia, Y.; Wu, J.; McLuckey, S. A.; Londry, F. A.; Hager, J. W. Mutual Storage Mode Ion/Ion Reactions in a Hybrid Linear Ion Trap. J. Am. Soc. Mass Spectrom. 2005, 16, 71–81.CrossRefGoogle Scholar
  55. 55.
    Xia, Y.; Liang, X.; McLuckey, S. A. Sonic Spray as a Dual Polarity Ion Source for Ion/Ion Reaction. Anal. Chem. 2005, 77, 3683–3689.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2006

Authors and Affiliations

  • Guangxiang Wu
    • 1
  • R. Graham Cooks
    • 1
  • Zheng Ouyang
    • 1
  • Meng Yu
    • 2
  • William J. Chappell
    • 2
  • Wolfgang R. Plass
    • 3
  1. 1.Department of ChemistryPurdue UniversityWest LafayetteUSA
  2. 2.School of Electrical and Computer EngineeringPurdue UniversityWest LafayetteUSA
  3. 3.II. Physikalisches InstitutJustus Liebig Universität GiessenGiessenGermany

Personalised recommendations