Journal of the American Society for Mass Spectrometry

, Volume 15, Issue 12, pp 1869–1873

Electron capture dissociation at low temperatures reveals selective dissociations

  • Romulus Mihalca
  • Anne J. Kleinnijenhuis
  • Liam A. McDonnell
  • Albert J. R. Heck
  • Ron M. A. Heeren


Electron capture dissociation at 86 K of the linear peptide Substance P produced just two backbone fragments, whereas at room temperature eight backbone fragments were formed. Similarly, with the cyclic peptide gramicidin S, just one backbone fragment was formed at 86 K but five at room temperature. The observation that some backbone scissions are active and others inactive, when all involve N-Cα cleavages and have a high rate constant, indicates that the more specific fragments at low temperatures reflects the reduced conformation heterogeneity at low temperatures. This is supported by reduced or inactive hydrogen loss, a channel that has previously been shown to be affected by conformation. The conclusion that the ECD fragments are a snapshot of the conformational (intramolecular solvation shell) heterogeneity helps explain how the relative intensities of ECD fragments can be different on different instrument and highlights the common theme in methodologies used to increase sequence coverage, namely an increase in the conformational heterogeneity of the precursor ion population.


  1. 1.
    Zubarev, R. A.; Kruger, N. A.; Fridriksson, E. K.; Lewis, M. A.; Horn, D. M.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation of Gaseous Multiply-Charged Proteins is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity. J. Am. Chem. Soc. 1999, 121, 2857–2862.CrossRefGoogle Scholar
  2. 2.
    Zubarev, R. A. Reactions of Polypetide Ions with Electrons in the Gas Phase. Mass Spectrom. Rev. 2003, 22, 57–77.CrossRefGoogle Scholar
  3. 3.
    Zubarev, R. A.; Horn, D. M.; Fredricksson, E. K.; Kelleher, N. L.; Kruger, N. A.; Lewis, M. A.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations. Anal. Chem. 2000, 72, 563–573.CrossRefGoogle Scholar
  4. 4.
    Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process. J. Am. Chem. Soc. 1998, 120, 3265–3266.CrossRefGoogle Scholar
  5. 5.
    Ge, Y.; ElNaggar, M.; Sze, S. K.; Oh, H. B.; Begley, T. P.; McLafferty, F. W.; Boshoff, H.; Barry, C. E. I. I. I. Top Down Characterization of Secreted Proteins from Mycobacterium tuberculosis by Electron Capture Dissociation Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2003, 14, 253–261.CrossRefGoogle Scholar
  6. 6.
    Hanash, S. Disease Proteomics. Nature 2003, 422, 226–232.CrossRefGoogle Scholar
  7. 7.
    Pierson, J.; Norris, J. I.; Aerni, H.-R.; Svenningsson, P.; Caprioli, R. M.; Andrén, P. E. Molecular Profiling of Experimental Parkinson’s Disease: Direct Analysis of Peptides and Proteins on Brain Tissue Sections by MALDI Mass Spectrometry. J. Proteome Res. 2004, 3, 289–295.CrossRefGoogle Scholar
  8. 8.
    Connors, L. H.; Richardson, A. M.; Théberge, R.; Costello, C. E. Tabulation of Transthyretin (TTR) Variants as of 1/1/2000. Amyloid-Journal Protein Folding Disorder 2000, 7, 54–69.CrossRefGoogle Scholar
  9. 9.
    Breuker, K.; Oh, H.; Horn, D. M.; Cerda, B. A.; McLafferty, F. W. Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation. J. Am. Chem. Soc. 2002, 124, 6407–6420.CrossRefGoogle Scholar
  10. 10.
    Håkansson, K.; Chalmers, M. J.; Quinn, J. P.; McFarland, M. A.; Hendrickson, C. L.; Marshall, A. G. Combined Electron Capture and Infrared Multiphoton Dissociation for Multistage MS/MS in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Anal. Chem. 2003, 75, 3256–3262.CrossRefGoogle Scholar
  11. 11.
    Tsybin, Y. O.; Witt, M.; Baykut, G.; Kjeldsen, F.; Håkansson, P. Combined Infrared Multiphoton Dissociation and Electron Capture Dissociation with a Hollow Electron Beam in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Comm. Mass Spectrom. 2003, 17, 1759–1768.CrossRefGoogle Scholar
  12. 12.
    Sze, S. 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. PNAS 2002, 99, 1774–1779.CrossRefGoogle Scholar
  13. 13.
    Jarrold, M. F. Peptides and Proteins in the Vapor Phase. Annu. Rev. Phys. Chem. 2000, 51, 179–207.CrossRefGoogle Scholar
  14. 14.
    Oh, H.-B.; Breuker, K.; Sze, S. K.; Ge, Y.; Carpenter, B. K.; McLafferty, F. W. Secondary and Tertiary Structures of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry and Photofragment Spectroscopy. PNAS 2002, 99, 15863–15868.CrossRefGoogle Scholar
  15. 15.
    Fung, Y. M. E.; Duan, L.; Chan, T.-W. D. Top-Down Characterization of Secreted Proteins from Mycobacterium Tuberculosis by Electron Capture Dissociation Mass Spectrometry. Eur. J. Mass Spectrom. 2004, in press.Google Scholar
  16. 16.
    Adams, C. M.; Kjeldsen, F.; Zubarev, R. A.; Budnik, B. A.; Haselmann, K. F. Electron Capture Dissociation Distinguishes a Single D-Amino Acid in a Protein and Probes Tertiary Structure. J. Am. Soc. Mass Spectrom. 2004, 15, 1087–1098.CrossRefGoogle Scholar
  17. 17.
    Haselmann, K. F.; Budnik, B. A.; Kjeldsen, F.; Polfer, N. C.; Zubarev, R. A. Can the (M·-X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides. Eur. J. Mass Spectrom 2002, 8, 461–469.CrossRefGoogle Scholar
  18. 18.
    Turecek, F.; Syrstad, E. A.; Seymour, J. L.; Chen, X.; Yao, C. Peptide cation-radicals. A Computational Study of the Competition Between Peptide N-Ca Bond Cleavage and Loss of the Side Chain in the [GlyPhe-NH2 + 2H]+· Cation-Radical. J. Mass Spectrom. 2003, 38, 1093–1104.CrossRefGoogle Scholar
  19. 19.
    Guo, X.; Duursma, M.; Al-Khalili, A.; McDonnell, L. A.; Heeren, R. M. A. Design and Performance of a New FT-ICR Cell Operating at a Temperature Range of 77–438 K. Int. J. Mass Spectrom. 2004, 231, 37–45.CrossRefGoogle Scholar
  20. 20.
    Marshall, A. G.; Wang, T. C. L.; Ricca, T. L. Tailored Excitation for Fourier Transform Ion Cyclotron Mass Spectrometry. J. Am. Chem. Soc. 1985, 107, 7893–7897.CrossRefGoogle Scholar
  21. 21.
    Axelsson, J.; Palmblad, M.; Håkansson, K.; Håkansson, P. Electron Capture Dissociation of Substance P Using a Commercially Available Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Rapid Commun. Mass Spectrom. 1999, 13, 474–477.CrossRefGoogle Scholar
  22. 22.
    Syrstad, E. A.; Turecek, F. Computational Evidence for Direct Electron Attachment to the Peptide Backbone in ECD. Proceedings of the 52nd ASMS Conference on Mass Spectrometry; Nashville, TN, 2004.Google Scholar
  23. 23.
    Chan, T.-W. D.; Ip, W. H. H. Optimization of Experimental Parameters for Electron Capture Dissociation of Peptides in a Fourier Transform Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2002, 13, 1396–1406.CrossRefGoogle Scholar
  24. 24.
    McFarland, M. A.; Hudgins, R. R.; Håakansson, K.; Hendrickson, C. L.; Marshall, A. G. ECD of peptides following gas-phase H/D exchange, Proceedings of the 50th ASMS Conference on Mass Spectrometry and Allied Topics; Orlando, FL, 2002.Google Scholar
  25. 25.
    Breuker, K.; Oh, H.; Cerda, B. A.; Horn, D. M.; McLafferty, F. W. Hydrogen Atom Loss in Electron-Capture Dissociation: A Fourier Transform-Ion Cyclotron Resonance Study with Single Isotopomeric Ubiquitin Ions. Eur. J. Mass Spectrom. 2002, 8, 177–180.CrossRefGoogle Scholar
  26. 26.
    Gill, A. C.; Jennings, K. R.; Wyttenbach, T.; Bowers, M. T. Conformations of Biopolymers in the Gas Phase: A New Mass Spectrometric Method. Int. J. Mass Spectrom. 2000, 195/196, 685–697.CrossRefGoogle Scholar
  27. 27.
    Turecek, F. N-Cα Bond Dissociation Energies and Kinetics in Amide and Peptide Radicals. Is the Dissociation a Non-Ergodic Process?. J. Am. Chem. Soc. 2003, 125, 5954–5963.CrossRefGoogle Scholar
  28. 28.
    Leymarie, N.; Costello, C. E.; O’Connor, P. B. Electron Capture Dissociation Initiates a Free Radical Reaction Cascade. J. Am. Chem. Soc. 2003, 125, 8949–8958.CrossRefGoogle Scholar
  29. 29.
    Iavarone, A. T.; Paech, K.; Williams, E. R. Effects of Charge State and Cationizing Agent on the Electron Capture Dissociation of a Peptide. Anal. Chem. 2004, 76, 2231–2238.CrossRefGoogle Scholar
  30. 30.
    Horn, D. M.; Ge, Y.; McLafferty, F. W. Activated Ion Electron Capture Dissociation for Mass Spectral Sequencing of Larger (42 kDa) Proteins. Anal. Chem. 2000, 72, 4778–4784.CrossRefGoogle Scholar
  31. 31.
    Marqusee, S.; Robbins, V. H.; Baldwin, R. L. Unusually Stable Helix Formation in Short-Alanine Based Peptides. PNAS 1989, 86, 5286–5290.CrossRefGoogle Scholar
  32. 32.
    Chalmers, M. J.; Håkansson, K.; Johnson, R.; Smith, R.; Shen, J.; Emmett, M. R.; Marshall, A. G. Protein Kinase A Phosphorylation Characterized by Tandem Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics 2004, 4, 970–981.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2004

Authors and Affiliations

  • Romulus Mihalca
    • 1
  • Anne J. Kleinnijenhuis
    • 1
  • Liam A. McDonnell
    • 1
  • Albert J. R. Heck
    • 2
  • Ron M. A. Heeren
    • 2
    • 3
  1. 1.FOM Institute for Atomic and Molecular Physics (AMOLF)AmsterdamThe Netherlands
  2. 2.Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
  3. 3.FOM Institute for Atomic and Molecular PhysicsAmsterdamThe Netherlands

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