Improved mass accuracy for tandem mass spectrometry

  • Nathan K. Kaiser
  • Gordon A. Anderson
  • James E. Bruce


With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.

Supplementary material

13361_2011_160400463_MOESM1_ESM.doc (294 kb)
Supplementary material, approximately 301 KB.


  1. 1.
    Marshall, A. G.; Hendrickson, C. L.; Jackson, G. S. Fourier transform ion cyclotron resonance mass spectrometry: A primer. Mass Spectrom. Rev. 1998, 17(1), 1–35.CrossRefGoogle Scholar
  2. 2.
    Ledford E. B., Jr.; Rempel, D. L.; Gross, M. L. Space charge effects in Fourier transform mass spectrometry: I. Electrons. Int. J. Mass Spectrom. Ion Processes 1984, 55(2), 143–154.CrossRefGoogle Scholar
  3. 3.
    Ledford E. B., Jr.; Rempel, D. L.; Gross, M. L. Space charge effects in Fourier transform mass spectrometry. Mass calibration. Anal. Chem. 1984, 56(14), 2744–2748.CrossRefGoogle Scholar
  4. 4.
    Easterling, M. L.; Mize, T. H.; Amster, I. J. Routine part-per-million mass accuracy for high-mass ions: Space-charge effects in MALDI FT-ICR. Anal. Chem. 1999, 71(3), 624–632.CrossRefGoogle Scholar
  5. 5.
    Francl, T. J.; Hunter, R. L.; McIver R. T., Jr. Zoom transform for mass measurement accuracy in Fourier transform mass spectrometry. Anal. Chem. 1983, 55(13), 2094–2096.CrossRefGoogle Scholar
  6. 6.
    Belov, M. E.; Zhang, R.; Strittmatter, E. F.; Prior, D. C.; Tang, K.; Smith, R. D. Automated gain control and internal calibration with external ion accumulation capillary liquid chromatography-electrospray ionization Fourier transform ion cyclotron resonance. Anal. Chem. 2003, 75(16), 4195–4205.CrossRefGoogle Scholar
  7. 7.
    Belov, M. E.; Rakov, V. S.; Nikolaev, E. N.; Goshe, M. B.; Anderson, G. A.; Smith, R. D. Initial implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control. Rapid Commun. Mass Spectrom. 2003, 17(7), 627–636.CrossRefGoogle Scholar
  8. 8.
    Burton, R. D.; Matuszak, K. P.; Watson, C. H.; Eyler, J. R. Exact mass measurements using a 7 tesla Fourier transform ion cyclotron resonance mass spectrometer in a good laboratory practices-regulated environment. J. Am. Soc. Mass Spectrom. 1999, 10(12), 1291–1297.CrossRefGoogle Scholar
  9. 9.
    Bruce, J. E.; Anderson, M. D.; Brands, G. A.; Pasa-Tolic, L.; Smith, R. D. Obtaining more accurate Fourier transform ion cyclotron resonance mass measurements without internal standards using multiply charged ions. J. Am. Soc. Mass Spectrom. 2000, 11(5), 416–421.CrossRefGoogle Scholar
  10. 10.
    Ge, Y.; Lawhorn, B. G.; ElNaggar, 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(4), 672–678.CrossRefGoogle Scholar
  11. 11.
    Reid, G. E.; McLuckey, S. A. “Top down” protein characterization via tandem mass spectrometry. J. Mass Spectrom. 2002, 37(7), 663–675.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. Proc. Natl. Acad. Sci. U. S. A. 2002, 99(4), 1774–1779.CrossRefGoogle Scholar
  13. 13.
    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(13), 3265–3266.CrossRefGoogle Scholar
  14. 14.
    McLafferty, F. W.; Horn, D. M.; Breuker, K.; Ge, Y.; Lewis, M. A.; Cerda, B.; Zubarev, R. A.; Carpenter, B. K. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J. Am. Soc. Mass Spectrom. 2001, 12(3), 245–249.CrossRefGoogle Scholar
  15. 15.
    Kelleher, N. L.; Zubarev, R. A.; Bush, K.; Furie, B.; Furie, B. C.; McLafferty, F. W.; Walsh, C. T. Localization of labile posttranslational modifications by electron capture dissociation: The case of g-carboxyglutamic acid. Anal. Chem. 1999, 71(19), 4250–4253.CrossRefGoogle Scholar
  16. 16.
    Hakansson, K.; Cooper, H. J.; Emmett, M. R.; Costello, C. E.; Marshall, A. G.; Nilsson, C. L. Electron capture dissociation and infrared multiphoton dissociation MS/MS of an N-glycosylated tryptic peptide to yield complementary sequence information. Anal. Chem. 2001, 73(18), 4530–4536.CrossRefGoogle Scholar
  17. 17.
    Mirgorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal. Chem. 1999, 71(20), 4431–4436.CrossRefGoogle Scholar
  18. 18.
    Shi, S. D. H.; Hemling, M. E.; Carr, S. A.; Horn, D. M.; Lindh, I.; McLafferty, F. W. Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal. Chem. 2001, 73(1), 19–22.CrossRefGoogle Scholar
  19. 19.
    Zubarev, R. A. Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 2003, 22(1), 57–77.CrossRefGoogle Scholar
  20. 20.
    Syka, J. E.; 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(26), 9528–9533.CrossRefGoogle Scholar
  21. 21.
    Takach, E. J.; Hines, W. M.; Patterson, D. H.; Juhasz, P.; Falick, A. M.; Vestal, M. L.; Martin, S. A. Accurate mass measurements using MALDI-TOF with delayed extraction. J. Prot. Chem. 1997, 16(5), 363–369.CrossRefGoogle Scholar
  22. 22.
    Clauser, K. R.; Baker, P.; Burlingame, A. L. Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 1999, 71(14), 2871–2882.CrossRefGoogle Scholar
  23. 23.
    Goodlett, D. R.; Bruce, J. E.; Anderson, G. A.; Rist, B.; Pasa-Tolic, L.; Fiehn, O.; Smith, R. D.; Aebersold, R. Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal. Chem. 2000, 72(6), 1112–1118.CrossRefGoogle Scholar
  24. 24.
    Masselon, C.; Anderson, G. A.; Harkewicz, R.; Bruce, J. E.; Pasa-Tolic, L.; Smith, R. D. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal. Chem. 2000, 72(8), 1918–1924.CrossRefGoogle Scholar
  25. 25.
    Kruppa, G.; Schnier, P. D.; Tabei, K.; Van Orden, S.; Siegel, M. M. Multiple ion isolation applications in FT-ICR MS: Exact-mass MSn internal calibration and purification/interrogation of protein-drug complexes. Anal. Chem. 2002, 74(15), 3877–3886.CrossRefGoogle Scholar
  26. 26.
    Hannis, J. C.; Muddiman, D. C. A dual electrospray ionization source combined with hexapole accumulation to achieve high mass accuracy of biopolymers in Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 2000, 11(10), 876–883.CrossRefGoogle Scholar
  27. 27.
    Brock, A.; Horn, D. M.; Peters, E. C.; Shaw, C. M.; Ericson, C.; Phung, Q. T.; Salomon, A. R. An automated matrix-assisted laser desorption/ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometer for “bottom-up” proteomics. Anal. Chem. 2003, 75(14), 3419–3428.CrossRefGoogle Scholar
  28. 28.
    Chan, T. W. D.; Duan, L.; Sze, T. P. E. Accurate mass measurements for peptide and protein mixtures by using matrix-assisted laser desorption/ionization Fourier transform mass spectrometry. Anal. Chem. 2002, 74(20), 5282–5289.CrossRefGoogle Scholar
  29. 29.
    Senko, M.; Zabrouskov, V.; Lange, O.; Wieghaus, A.; Horning, S. LC/MS with external calibration mass accuracies approaching 100 ppb. Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics; Nashville, TN, May, 2004.Google Scholar
  30. 30.
    Easterling, M. L.; Amster, I. J.; van Rooij, G. J.; Heeren, R. M. A. Isotope beating effects in the analysis of polymer distributions by Fourier transform mass spectrometry. J. Am. Soc. Mass Spectrom. 1999, 10(11), 1074–1082.CrossRefGoogle Scholar
  31. 31.
    Hofstadler, S. A.; Bruce, J. E.; Rockwood, A. L.; Anderson, G. A.; Winger, B. E.; Smith, R. D. Isotopic beat patterns in Fourier transform ion cyclotron resonance mass spectrometry: Implications for high resolution mass measurements of large biopolymers. Int. J. Mass Spectrom. Ion Processes 1994, 132(1/2), 109–127.CrossRefGoogle Scholar
  32. 32.
    Taylor, P. K.; Amster, I. J. Space charge effects on mass accuracy for multiply charged ions in ESI-FTICR. Int. J. Mass Spectrom 2003, 222(1/3), 351–361.CrossRefGoogle Scholar
  33. 33.
    Anderson, G. A.; Bruce, J. E.; Smith, R. D. ICR-2LS. 1996: Pacific Northwest National Laboratory: Richland, WA.Google Scholar
  34. 34.
    Taylor, G. K.; Kim, Y.-B.; Forbes, A. J.; Meng, F.; McCarthy, R.; Kelleher, N. L. Web and database software for identification of intact proteins using “top down” mass spectrometry. Anal. Chem. 2003, 75(16), 4081–4086.CrossRefGoogle Scholar
  35. 35.
    Meng, F.; Cargile, B. J.; Miller, L. M.; Forbes, A. J.; Johnson, J. R.; Kelleher, N. L. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat. Biotechnol. 2001, 19(10), 952–957.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2004

Authors and Affiliations

  • Nathan K. Kaiser
    • 1
  • Gordon A. Anderson
    • 2
  • James E. Bruce
    • 3
  1. 1.Department of ChemistryWashington State UniversityPullmanUSA
  2. 2.Biological Sciences Division and Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandUSA
  3. 3.Department of ChemistryWashington State UniversityPullmanUSA

Personalised recommendations