Rephasing ion packets in the orbitrap mass analyzer to improve resolution and peak shape

  • Richard H. Perry
  • Qizhi Hu
  • Gary A. Salazar
  • R. Graham Cooks
  • Robert J. Noll
Focus: The Orbitrap


A method is described to improve resolution and peak shape in the Orbitrap under certain experimental conditions. In these experiments, an asymmetric anharmonic axial potential was first produced in the Orbitrap by detuning the voltage on the compensator electrode, which results in broad and multiply split mass spectral peaks. An AC waveform applied to the outer electrode, 180° out of phase with ion axial motion and resonant with the frequency of ion axial motion, caused ions of a given m/z to be de-excited to the equator (z=0) and then immediately re-excited. This process, termed “rephasing,” leaves the ion packet with a narrower axial spatial extent and frequency distribution. For example, when the Orbitrap axial potential is thus anharmonically de-tuned, a resolution of 124,000 to 171,000 is obtained, a 2- to 3-fold improvement over the resolution of 40,000 to 60,000 without rephasing, at 10 ng/µL reserpine concentration. Such a rephasing capability may ultimately prove useful in implementing tandem mass spectrometry (MS/MS) in the Orbitrap, bringing the Orbitrap’s high mass accuracy and resolution to bear on both the precursor and product ions in the same MS/MS scan and making available the collision energy regime of the Orbitrap, ∼1500 eV.


  1. 1.
    Makarov, A.; Denisov, E.; Kholomeev, A.; Balschun, W.; Lange, O.; Strupat, K.; Horning, S. Performance evaluation of a hybrid linear ion trap/Orbitrap mass spectrometer. Anal. Chem. 2006, 78, 2113–2120.CrossRefGoogle Scholar
  2. 2.
    Olsen, J. V.; de Godoy, L. M. F.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A. A.; Lange, O.; Horning, S.; Mann, M. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteom. 2005, 4, 2010–2021.CrossRefGoogle Scholar
  3. 3.
    Olsen, J. V.; Macek, B.; Lange, O.; Makarov, A. A.; Horning, S.; Mann, M. Higher-energy C-trap dissociation for peptide modification analysis. Nature Methods. 2007, 4, 709–712.CrossRefGoogle Scholar
  4. 4.
    Perry, R. H.; Cooks, R. G.; Noll, R. J. Orbitrap mass spectrometry: Instrumentation, ion motion, and applications. Mass Spectrom. Rev. 2008, 27, 661–699.CrossRefGoogle Scholar
  5. 5.
    Makarov, A. A.; Denisov, E.; Lange, O.; Horning, S. Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer. J. Am. Soc. Mass Spectrom. 2006, 17, 977–982.CrossRefGoogle Scholar
  6. 6.
    Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature. 2003, 422, 198–207.CrossRefGoogle Scholar
  7. 7.
    Henzel, W. J.; Billeci, T. M.; Stults, J. T.; Wong, S. C.; Grimley, C.; Watanabe, C. Identifying proteins from two dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 5011–5015.CrossRefGoogle Scholar
  8. 8.
    Wilm, M.; Shevchenko, A.; Houthaeve, T.; Breit, S.; Schweigerer, L.; Fotsis, T.; Mann, M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature. 1996, 379, 466–469.CrossRefGoogle Scholar
  9. 9.
    Li, X.; Gerber, S. A.; Rudner, A. D.; Beausoleil, S. A.; Haas, W.; Villén, J.; Elias, J. E.; Gygi, S. P. Large-scale phosphorylation analysis of alpha-factor-arrested. Saccharomyces cerevisiae. J. Proteome. Res. 2007, 6, 1190–1197.CrossRefGoogle Scholar
  10. 10.
    Yates, J. R.; Cociorva, D.; Liao, L.; Zabrouskov, V. Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Anal. Chem. 2006, 78, 493–500.CrossRefGoogle Scholar
  11. 11.
    Aebersold, R.; Goodlett, D. R. Mass spectrometry in proteomics. Chem. Rev. 2001, 101, 269–295.CrossRefGoogle Scholar
  12. 12.
    Hunt, D. F.; Yates, J. R.; Shabanowitz, J.; Winston, S.; Hauer, C. R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 1986, 83, 6233–6237.CrossRefGoogle Scholar
  13. 13.
    Frank, A. M.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A.; Pevzner, P. A. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6, 114–123.CrossRefGoogle Scholar
  14. 14.
    Scigelova, M.; Makarov, A. Orbitrap mass analyzer — Overview and applications in proteomics. Proteomics. 2006, 6, 16–21.CrossRefGoogle Scholar
  15. 15.
    Macek, B.; Waanders, L. F.; Olsen, J. V.; Mann, M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-Orbitrap mass spectrometer. Mol. Cell. Proteom. 2006, 5, 949–958.CrossRefGoogle Scholar
  16. 16.
    Thevis, M.; Bredehöft, M.; Geyer, H.; Kamber, M.; Delahaut, P.; Schänzer, W. Determination of Synacthen in human plasma using immunoaffinity purification and liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2006, 20, 3551–3556.CrossRefGoogle Scholar
  17. 17.
    Zhang, Z.; Shah, B. Characterization of variable regions of monoclonal antibodies by top-down mass spectrometry. Anal. Chem. 2007, 79, 5723–5729.CrossRefGoogle Scholar
  18. 18.
    Ge, Y.; Lawhorn, B. G.; El Naggar, M.; Strauss, E.; Park, J.-H.; Begley, T. P.; McLafferty, F. W. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc. 2002, 124, 672–678.CrossRefGoogle Scholar
  19. 19.
    Kelleher, N. L.; Lin, H. Y.; Valaskovic, G. A.; Aaserud, D. J.; Fridriksson, E. K.; McLafferty, F. W. Top-down versus bottom-up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc. 1999, 121, 806–812.CrossRefGoogle Scholar
  20. 20.
    Sze, A. K.; Ge, Y.; Oh, H.; McLafferty, F. W. Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 1774–1779.CrossRefGoogle Scholar
  21. 21.
    Peterman, A. M.; Duczak, N.; Kalgutkar, A. S.; Lame, M. E.; Soglia, J. R. Application of a linear ion trap/Orbitrap mass spectrometer in metabolite characterization studies: Examination of the human liver microsomal metabolism of the non-tricyclic anti-depressant nefazodone using data-dependent accurate mass measurements. J. Am. Soc. Mass Spectrom. 2006, 17, 363–375.CrossRefGoogle Scholar
  22. 22.
    Ejsing, C. S.; Moehring, T.; Bahr, U.; Duchoslav, E.; Karas, M.; Simons, K.; Shevchenko, A. Collision-induced dissociation pathways of yeast sphingolipids and their molecular profiling in total lipid extracts: A study by quadrupole TOF and linear ion trap-Orbitrap mass spectrometry. J. Mass Spectrom. 2006, 41, 372–389.CrossRefGoogle Scholar
  23. 23.
    Barceló, D.; Petrovic, M. Challenges and achievements of LC-MS in environmental analysis: 25 years on. Trends Anal. Chem. 2007, 26, 2–11.CrossRefGoogle Scholar
  24. 24.
    Hardman, M.; Makarov, A. A. Interfacing the Orbitrap mass analyzer to an electrospray ion source. Anal. Chem. 2003, 75, 1699–1705.CrossRefGoogle Scholar
  25. 25.
    Hu, Q.; Noll, R. J.; Li, H. Y.; Makarov, A.; Hardman, M.; Cooks, R. G. The Orbitrap: A new mass spectrometer. J. Mass Spectrom. 2005, 40, 430–443.CrossRefGoogle Scholar
  26. 26.
    Makarov, A. Electrostatic axially harmonic orbital trapping: A high-performance technique of mass analysis. Anal. Chem. 2000, 72, 1156–1162.CrossRefGoogle Scholar
  27. 27.
    Brigham, E. O. The Fast Fourier Transform; Prentice-Hall: Englewood Cliffs, NJ, 1974.Google Scholar
  28. 28.
    Champeney, D. C. Fourier Transforms and their Physical Applications; Academic Press: New York, NY, 1973.Google Scholar
  29. 29.
    Bracewell, R. The Fourier Transform and Its Applications 3rd ed.; McGraw Hill: Boston, MA, 2000.Google Scholar
  30. 30.
    Senko, M. W.; Canterbury, J. D.; Guan, S.; Marshall, A. G. A high-performance modular data system for Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10, 1839–1844.CrossRefGoogle Scholar
  31. 31.
    Hu, Q.; Cooks, R. G.; Noll, R. J. Phase-enhanced selective ion ejection in an Orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom. 2007, 18, 980–983.CrossRefGoogle Scholar
  32. 32.
    Hu, Q.; Makarov, A. A.; Cooks, R. G.; Noll, R. J. Resonant AC dipolar excitation for ion motion control in the Orbitrap mass analyzer. J. Phys. Chem. A 2006, 110, 2682–2689.CrossRefGoogle Scholar
  33. 33.
    Wu, G.; Noll, R. J.; Plass, W. R.; Hu, Q.; Perry, R. H.; Cooks, R. G. Ion trajectory simulations of axial AC dipolar excitation in the Orbitrap. Int. J. Mass Spectrom. 2006, 254, 53–62.CrossRefGoogle Scholar
  34. 34.
    Chen, L.; Marshall, A. G. Stored waveform simultaneous mass-selective ejection/excitation for Fourier transform ion cyclotron resonance mass spectrometry. Int. J. Mass Spectrom. Ion Processes. 1987, 79, 115–125.CrossRefGoogle Scholar
  35. 35.
    Marshall, A. G.; Wang, T.-C. L.; Ricca, T. L. Ion cyclotron resonance excitation/de-excitation: A basis for stochastic Fourier transform ion cyclotron mass spectrometry. Chem. Phys. Lett. 1984, 105, 233–236.CrossRefGoogle Scholar
  36. 36.
    Kaiser, N. K.; Bruce, J. E. Observation of increased ion cyclotron resonance signal duration through electric field perturbations. Anal. Chem. 2005, 77, 5973–5981.CrossRefGoogle Scholar
  37. 37.
    Gough, W. The graphical analysis of a Lorentzian function and a differentiated Lorentzian function. J. Phys. A. 1968, 1, 704–709.CrossRefGoogle Scholar
  38. 38.
    Schwartz, J. C.; Zhou, X. G.; Bier, M. E. Method and apparatus of increasing dynamic range and sensitivity of a mass spectrometer, U. S. Patent 5,572,022, 1995.Google Scholar
  39. 39.
    Landau, L. D.; Lifshitz, E. M. Mechanics; Pergamon Press: Oxford, NY, 1976.Google Scholar
  40. 40.
    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
  41. 41.
    Mitchell, D. W.; Rockwood, A. L.; Smith, R. D. Frequency shifts and modulation effects due to solenoidal magnetic field inhomogeneities in ion cyclotron mass spectrometry. Int. J. Mass Spectrom. Ion Processes. 1995, 141, 101–116.CrossRefGoogle Scholar
  42. 42.
    Jeffries, J. B.; Barlow, S. E.; Dunn, G. H. Theory of space-charge shift of ion cyclotron resonance frequencies. Int. J. Mass Spectrom. Ion Processes. 1983, 54, 167–187.CrossRefGoogle Scholar
  43. 43.
    Huang, J.; Tiedemann, P. W.; Land, D. P.; McIver, R. T.; Hemminger, J. C. Dynamics of ion coupling in a FTMS ion trap and resulting effects on mass spectra, including isotope ratios. Int. J. Mass Spectrom. Ion Processes. 1994, 134, 11–21.CrossRefGoogle Scholar
  44. 44.
    Jungmann, K.; Hoffnagle, J.; DeVoe, R. G.; Brewer, R. G. Collective oscillations of stored ions. Phys. Rev. A At. Mol. Opt. Phys. 1987, 36, 3451–3454.CrossRefGoogle Scholar
  45. 45.
    Mo, W.; Todd, J. F. J. Investigation of the mass shifts caused by the coupling of ion motions in the ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 1996, 10, 424–428.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2009

Authors and Affiliations

  • Richard H. Perry
    • 1
  • Qizhi Hu
    • 2
  • Gary A. Salazar
    • 1
  • R. Graham Cooks
    • 1
  • Robert J. Noll
    • 1
  1. 1.Department of ChemistryPurdue UniversityWest LafayetteUSA
  2. 2.Amgen Inc.Thousand OaksUSA

Personalised recommendations