Automated reduction and interpretation of

  • David M. Horn
  • Roman A. Zubarev
  • Fred W. McLafferty
Article

Abstract

Here a fully automated computer algorithm is applied to complex mass spectra of peptides and proteins. This method uses a subtractive peak finding routine to locate possible isotopic clusters in the spectrum, subjecting these to a combination of the previous Fourier transform/ Patterson method for primary charge determination and the method for least-squares fitting to a theoretically derived isotopic abundance distribution for m/z determination of the most abundant isotopic peak, and the statistical reliability of this determination. If a predicted protein sequence is available, each such m/z value is checked for assignment as a sequence fragment. A new signal-to-noise calculation procedure has been devised for accurate determination of baseline and noise width for spectra with high peak density. In 2 h, the program identified 824 isotopic clusters representing 581 mass values in the spectrum of a GluC digest of a 191 kDa protein; this is \s>50% more than the number of mass values found by the extremely tedious operator-applied methodology used previously. The program should be generally applicable to classes of large molecules, including DNA and polymers. Thorough high resolution analysis of spectra by Horn (THRASH) is proposed as the program’s verb.

Keywords

Charge State Electron Capture Dissociation Abundance Distribution Isotopic Peak Isotopic Cluster 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray ionization-principles and practice. Mass Spectrom. Rev. 1990, 9, 37–70.CrossRefGoogle Scholar
  2. 2.
    Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 1988, 60, 2299–2301.CrossRefGoogle Scholar
  3. 3.
    Burlingame, A. L.; Boyd, R. K.; Gaskell, S. J. Mass spectrometry. Anal. Chem. 1998, 70, 647R-716R.CrossRefGoogle Scholar
  4. 4.
    Senko, M. W.; McLafferty, F. W. Mass spectrometry of macromolecules: has its time now come? Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 763–785.CrossRefGoogle Scholar
  5. 5.
    Little, D. P.; Aaserud, D. J.; Valaskovic, G. A.; McLafferty, F. W. Sequence information from 42–108-mer DNAs (complete for a 50-mer) by tandem mass spectrometry. J. Am. Chem. Soc. 1996, 118, 9352–9359.CrossRefGoogle Scholar
  6. 6.
    Nordhoff, E.; Kirpekar, F.; Roepstorff, P. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 1996, 15, 67–138.CrossRefGoogle Scholar
  7. 7.
    O’Connor, P. B.; McLafferty, F. W. Oligomer characterization of 4–23 kDa polymers by electrospray Fourier transform mass spectrometry. J. Am. Chem. Soc. 1995, 117, 12826–12831.CrossRefGoogle Scholar
  8. 8.
    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
  9. 9.
    McLafferty, F. W.; Kelleher, N. L.; Begley, T. P.; Fridriksson, E. K.; Zubarev, R. A.; Horn, D. M. Two-dimensional mass spectrometry of biomolecules at the subfemtomole level. Curr. Opin. Chem. Biol. 1998, 2, 571–578.CrossRefGoogle Scholar
  10. 10.
    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
  11. 11.
    McLafferty, F. W.; Fridriksson, E. K.; Horn, D. M.; Lewis, M. A.; Zubarev, R. A. Biomolecule mass spectrometry. Science 1999, 284, 1289–1290.CrossRefGoogle Scholar
  12. 12.
    Zubarev, R A.; Horn, D. M.; Fridriksson, 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., to be published.Google Scholar
  13. 13.
    McLafferty, F. W.; Aaserud, D. J.; Guan, Z.; Little, D. P.; Kelleher, N. L. Double stranded DNA sequencing by tandem mass spectrometry. Int. J. Mass Spectrom. Ion Processes 1997, 165/166, 457–466.CrossRefGoogle Scholar
  14. 14.
    Kelleher, N. L.; Nicewonger, R. B.; Begley, T. P.; McLafferty, F. W. Identification of modification sites in large biomolecules by stable isotope labeling and tandem high resolution mass spectrometry. The active site nucleophile of thiaminase I. J. Biol. Chem. 1997, 272, 32215–32220.CrossRefGoogle Scholar
  15. 15.
    Wood, T. D.; Guan, Z.; Borders, C. L., Jr., Chen, L. H.; Kenyon, G. L.; McLafferty, F. W. Creatine kinase: essential arginine residues at the nucleotide binding site identified by chemical modification and high-resolution tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 1998, 95, 3362–3365.CrossRefGoogle Scholar
  16. 16.
    Kelleher, N. L.; Taylor, S. V.; Grannis, D.; Kinsland, C.; Chiu, H.; Begley, T. P.; McLafferty, F. W. Efficient sequence analysis of the six gene products (7–74 kDa) from the Escherichia coli thiamin biosynthetic operon by tandem high-resolution mass spectrometry. Protein Sci. 1998, 7, 1796–1801.CrossRefGoogle Scholar
  17. 17.
    Mortz, E.; O’Connor, P. B.; Roepstorff, P.; Kelleher, N. L.; Wood, T. D.; McLafferty, F. W.; Mann, M. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. USA 1996, 93, 8264–8267.CrossRefGoogle Scholar
  18. 18.
    Shevchenko, A.; Jensen, O. N.; Podtelejnikov, A. V.; Sagliocco, F.; Wilm, M.; Vorm, O.; Mortensen, P.; Boucherie, H.; Mann, M. Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 1996, 93, 14440–14445.CrossRefGoogle Scholar
  19. 19.
    Jensen, P. K.; Pasa-Tolic, L.; Anderson, G. A.; Horner, J. A.; Lipton, M. S.; Bruce, J. E.; Smith, R. D. Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 1999, 71, 2076–2084.CrossRefGoogle Scholar
  20. 20.
    Williams, E. R. Tandem FTMS of large biomolecules. Anal. Chem. 1998, 70, 179A-185A.CrossRefGoogle Scholar
  21. 21.
    Marshall, A.; Hendrickson, C.; Jackson, G. Fourier transform ion cyclotron resonance mass spectrometry: A primer. Mass Spectrom. Rev. 1998, 17, 1–35.CrossRefGoogle Scholar
  22. 22.
    Speir, J. P.; Senko, M. W.; Little, D. P.; Loo, J. A.; McLafferty, F. W. High-resolution tandem mass spectra of 37–67 kDa proteins. J. Mass Spectrom. 1995, 30, 39–42.CrossRefGoogle Scholar
  23. 23.
    Mann, M.; Meng, C. K.; Fenn, J. B. Interpreting mass spectra of multiply charged ions. Anal. Chem. 1989, 61, 1702–1708.CrossRefGoogle Scholar
  24. 24.
    Senko, M. W.; Beu, S. C.; McLafferty, F. W. Automated assignment of charge states from resolved isotopic peaks for multiply-charged ions. J. Am. Soc. Mass Spectrom. 1995, 6, 52–56.CrossRefGoogle Scholar
  25. 25.
    Senko, M. W.; Beu, S. C.; McLafferty, F. W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 1995, 6, 229–233.CrossRefGoogle Scholar
  26. 26.
    Zhang, Z. Q.; Guan, S. H.; Marshall, A. G. Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J. Am. Soc. Mass Spectrom. 1997, 8, 659–670.CrossRefGoogle Scholar
  27. 27.
    Zhang, Z. Q.; Marshall, A. G. A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom. 1998, 9, 225–233.CrossRefGoogle Scholar
  28. 28.
    Henry, K. D.; McLafferty, F. W. Electrospray ionization with Fourier-transform mass spectrometry. Charge state assignment from resolved isotopic peaks. Org. Mass Spectrom. 1990, 25, 490–492.CrossRefGoogle Scholar
  29. 29.
    McLafferty, F. W. High-resolution tandem FT mass spectrometry above 10 kDa. Acc. Chem. Res. 1994, 27, 379–386.CrossRefGoogle Scholar
  30. 30.
    Fenyo, D.; Zhang, W.; Chait, B. T.; Beavis, R. C. Internet-based analytical chemistry resource: A model project. Anal. Chem. 1996, 68, A721-A726.Google Scholar
  31. 31.
    Rockwood, A. L.; Van Orden, S. L.; Smith, R. D. Ultrahigh resolution isotope distribution calculations. Rapid Commun. Mass Spectrom. 1996, 10, 54–59.CrossRefGoogle Scholar
  32. 32.
    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
  33. 33.
    Fridriksson, E. K.; Beavil, A.; Baird, B. A.; Holowka, D. A.; Gould, H. J.; McLafferty, F. W. Heterogeneous Glycosylation of Immunoglobulin E Constructs Characterized by Top Down High-Resolution 2-D Mass Spectrometry. Biochemistry, to be published.Google Scholar
  34. 34.
    Beu, S. C.; Senko, M. W.; Quinn, J. P.; Wampler, F. M.; McLafferty, F. W. Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules. J. Am. Soc. Mass Spectrom. 1993, 4, 557–565.CrossRefGoogle Scholar
  35. 35.
    Kelleher, N. L.; Weinreb, P. H.; Konz, D.; Marahiel, M. A.; Walsh, C. T., unpublished results.Google Scholar
  36. 36.
    Senko, M. W.; Hendrickson, C. L.; PasaTolic, L.; Marto, J. A.; White, F. M.; Guan, S. H.; Marshall, A. G. Electrospray ionization Fourier transform ion cyclotron resonance at 9.4 T. Rapid Commun. Mass Spectrom. 1996, 10, 1824–1828.CrossRefGoogle Scholar
  37. 37.
    Shi, S. D.-H.; Hendrickson, C. L.; Marshall, A. G. Counting individual sulfur atoms in a protein by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry: Experimental resolution of isotopic fine structure in proteins. Proc. Natl. Acad. Sci. USA 1998, 95, 11532–11537.CrossRefGoogle Scholar
  38. 38.
    Marshall, A. G.; Want, T.-C. L.; Ricca, T. L. Tailored excitation for Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Chem. Soc. 1985, 107, 7893–7897.CrossRefGoogle Scholar
  39. 39.
    Yergey, J. A. A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337–349.CrossRefGoogle Scholar
  40. 40.
    Marshall, A. G.; Senko, M. W.; Li, W. Q.; Li, M.; Dillon, S.; Guan, S. H.; Logan, T. M. Protein molecular mass to 1 Da by C-13, N-15 double-depletion and FT-ICR mass spectrometry. J. Am. Chem. Soc. 1997, 119, 433–434.CrossRefGoogle Scholar
  41. 41.
    Zubarev, R. A.; Demirev, P. A. Isotope depletion of large biomolecules: Implications for molecular mass measurements. J. Am. Soc. Mass Spectrom. 1998, 9, 149–156.CrossRefGoogle Scholar
  42. 42.
    Bruce, J. E.; Anderson, G. A.; Wen, J.; Harkewicz, R.; Smith, R. D. High-mass-measurement accuracy and 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum. Anal. Chem. 1999, 71, 2595–2599.CrossRefGoogle Scholar
  43. 43. (a)
    Dictionary of the English Language; Random House: New York, 1966.Google Scholar
  44. 43. (b)
    Webster’s Third New International Dictionary; Merriam-Webster: Springfield, MA, 1981.Google Scholar
  45. 44. (a)
    Venkataraghavan, R.; McLafferty, F. W.; Amy, J. W. Anal. Chem. 1967, 39, 178–185.CrossRefGoogle Scholar
  46. 44. (b)
    Deconvolution, with Applications to Spectroscopy; Jansson, P. A., Ed., Academic: New York, 1984.Google Scholar
  47. 45.
    Blattner, F. R.; Plunkett, G. III; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D.; Rode, C. K.; Mayhew, G. F.; Grego, J.; Davis, N. W.; Kirkpatrick, H. A.; Goeden, M. A.; Rose, D. J.; Mau, B.; Shao, Y. The complete genome sequence of Escherichia coli K-12. Science 1997, 277, 1453–1462.CrossRefGoogle Scholar
  48. 46.
    Anderson, G. A.; Bruce, J. E.; Pacific Northwest National Laboratory, Richland, WA. To obtain a copy, e-mail: Gordon. Anderson@pnl.govGoogle Scholar
  49. 47.
    Drader, J. J.; Shi, S. D.-H.; Freitas, M. A.; Hendrickson, C. L.; Marshall, A. G. Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics; Orlando, FL, 31 May–4 June 1998; p. 499, http://magnet.fsu.edu/~midas.Google Scholar

Copyright information

© American Society for Mass Spectrometry 2000

Authors and Affiliations

  • David M. Horn
    • 1
  • Roman A. Zubarev
    • 1
  • Fred W. McLafferty
    • 1
  1. 1.Department of Chemistry, Baker LaboratoryCornell UniversityIthacaUSA

Personalised recommendations