An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

  • Jimmy K. Eng
  • Ashley L. McCormack
  • John R. Yates


A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (10–50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of ±1 u of the precursor ion molecular weight A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions of the first- and second-ranked search results indicates a successful match between sequence and spectrum. Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matching of the spectra to amino acid sequences within proteins of these organisms. The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.


High Performance Liquid Chromatography Mass Tolerance Tandem Mass Spectrum Searching Protein Database High Performance Liquid Chromatography Fraction 
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.


  1. 1.
    Edman, P.; Begg, G., Eur. J. Biochem. 1967, 1, 80–91.CrossRefGoogle Scholar
  2. 2.
    Hewick, R. M.; Hunkapiller, M. W.; Hood, L. E.; Dryer, W. J. J. BioI. Chem, 1981, 256, 7990–7997.Google Scholar
  3. 3.
    Pearson, W. R. In Methods in Enzymology, Vol. 183; Doolittle, R. F., Ed.; Academic: San Diego, 1990; pp 63–98.Google Scholar
  4. 4.
    Doolittle, R. F. In Methods in Enzymology, Vol. 183; Doolittle.. R. F., Ed.; Academic San Diego, 1990; pp 99–110.Google Scholar
  5. 5.
    Cox, A. L.; Skipper, J.; Chen, Y.; Henderson, R. A.; Darrow, T. L.; Shabanowitz, J.; Engelhard, V.; Hunt, D. F.; Slinghuff, C. L., Jr. Science 1994, 216, 716–719.CrossRefGoogle Scholar
  6. 6.
    Henzel, W.; Billeci,. T.; Stults, J.; Wond, S.; Grimley, C.; Watanabe, C. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5011–5015.CrossRefGoogle Scholar
  7. 7.
    Yates, J. R.; Speicher, S.; Griffin, P. R.; Hunkapiller, T. Anal. Biochem. 1993, 214, 397–408.CrossRefGoogle Scholar
  8. 8.
    Pappin, D.; Hojrup, P.; Bleasby, A. Curro Biol. 1993, 3, 327–332.CrossRefGoogle Scholar
  9. 9.
    James. P.; Qaudroni, M.; Carafoli, E.; Gonnet, G. Biochem. Biophys. Res. Commun. 1993, 195, 58–64.CrossRefGoogle Scholar
  10. 10.
    Mann, M.; Hojrup, P.; Roepstorff, P. Biol. Mass Spectrom. 1993, 22, 338–345.CrossRefGoogle Scholar
  11. 11.
    Penn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F; Whitehouse, C. M. Science 1989, 246, 64–71.CrossRefGoogle Scholar
  12. 12.
    Amott, D.; Shabanowitz, J.; Hunt, D. F. Clin. Chem. 1993, 39, 2005–2010.Google Scholar
  13. 13.
    Biernann, K. Ann. Rev. Biochem. 1992, 61, 977–1010.CrossRefGoogle Scholar
  14. 14.
    Hunt, D. E.; Yates, J. R., III; Shabanowitz, J.; Winston, S.; Hauer, C. R. Proc. Natl. Acad. Sci. U.S.A. 1986, 84, 620–623.CrossRefGoogle Scholar
  15. 15.
    Hunt, D. F.; Griffin, P. R.; Yates, J. R., III; Shabanowitz, J.; Pox, J.W.; Beggerly, L. K. In Techniques in Protein Chemistry; Hugli, T. E., Ed.; Academic: San Diego, 1989; pp 580–588.Google Scholar
  16. 16.
    Hunt, D. F.; Alexander J. E.; McCormack, A. L.; Martino, P. A.; Michel, H.; Shabanowitz, J. In Techniques in Protein Chemistry II; Villafranca, J. T., Ed.; Academic: San Diego, 1991; pp 455–465.Google Scholar
  17. 17.
    Hunt, D. F.; Henderson, R. A.; Shabanowitz, J.; Sakaguchi, K.; Michet H.; Sevilir, N.; Cox, A. L.; Apella, E.; Engelhard, V. N. Science 1992, 255, 1261–1263.CrossRefGoogle Scholar
  18. 18.
    Henderson, R. A.; Michel, H.; Sakaguchi, K.; Shabanowitz, J.; Appella, E.; Hunt, D. F.; Engelhard, V. H. Science 1992, 255. 1264–1266.CrossRefGoogle Scholar
  19. 19.
    Johnson, R.S.; Biemann, K. Biomed. Env. Mass Spectrom. 1989, 18, 945–957.CrossRefGoogle Scholar
  20. 20.
    Hines, W. M.; Falick, A. M.; Burlingame, A. L.; Gibson, B. W., J. Am. Soc. Mass Spectrum. 1992, 3, 326–336.CrossRefGoogle Scholar
  21. 21.
    Yates, J. R., III; Zhou, J.; Griffin, P. R.; Hood, L. E. In Techniques in Protein Chemistry II; Villafranca, J. J., Ed.; Academic: San Diego, 1990; pp 477–485.Google Scholar
  22. 22.
    Martinsen, D. P.; Song, B-H. Mass Spectrom. Rev. 1985, 4, 461–490.CrossRefGoogle Scholar
  23. 23.
    Lee, T. D.; Vemuri, S. Biomed. Environ. Mass Specitom. 1990, 19, 639–645.CrossRefGoogle Scholar
  24. 24.
    Papayannopoulos, I. A.; Biernann, K. J. Am. Soc. Mass Spectram. 1991, 2, 174–177.CrossRefGoogle Scholar
  25. 25.
    Watkins, P. J.; Jardine, L; Zhou, J. X. Biochem. Soc. Trans. 1991, 19, 957–962.Google Scholar
  26. 26.
    Demotz, S.; Grey, H.; Appella, E.; Sette, A. Nature (London) 1989, 342, 682–684.CrossRefGoogle Scholar
  27. 27.
    Kaartinen. V.; Williams, J. C.; Tomich, J.; Yates, J. R., III; Hood, L. E.; Mononen, I. J. Biol. Chem. 1991, 266, 5860–5869.Google Scholar
  28. 28.
    Kolodziej, P.; Young, R. In Guideto Yeast Genetics and Molecular Biology; Guthrie, C.; Fink, G., Eds.; Academic: San Diego, 1991; pp 508–519.CrossRefGoogle Scholar
  29. 29.
    Griffin, P. R.; Coffman, J. A.; Hood, L. K; Yates, J. R., III. Int. J. Mass Specirom. Ion Processes 1991, 111, 131–149.CrossRefGoogle Scholar
  30. 30.
    Powell, L. A.; Heiftje, G. M. Anal. Chim. Acta 1978, 100, 313–327.CrossRefGoogle Scholar
  31. 31.
    Owens, K. Appl. Spectrosc. Rev. 1992, 27, 1–49.CrossRefGoogle Scholar
  32. 32.
    Chicz, R. M.; Urban, R. G.; Gorga, J. C.; Vignali, A. A.; Lane, W. S.; Strominger, J. L. J. Exp. Med. 1993, 178, 27–47.CrossRefGoogle Scholar
  33. 33.
    Rudensky, A. Y.; Preston-Hurlburt, P.; Hong, S-C.; Barlow, A.; Janeway, C. A., Jr. Nature 1991, 353, 622–627.CrossRefGoogle Scholar
  34. 34.
    Daniels, D. L.; Plunkett, G., III; Burland, V.; Blattner, F. R. Science 1992, 257, 771–778.CrossRefGoogle Scholar
  35. 35.
    Mononen, L; Heisterkamp, N.; Kaartinen, V.; Williams, J. C.; Yates, J. R., III; Griffin, P. R.; Hood, L. E.; Groffen, J. Proc. Natl. Acad. Sci. U.S.A 1991, 88, 2941–2945.CrossRefGoogle Scholar
  36. 36.
    Stahl, D. C.; Martino, P. A.; Swiderek, K. M.; Davis, M. T.; Lee, T. D. Proceedings of the 40th ASMS Conference on Mass Spectrometry and Allied Topics; Washington OC, 1992; pp 180l–1802.Google Scholar
  37. 37.
    Johnson, R. S.; Biemann, K. Biochemistry 1987, 26, 1209–1214.CrossRefGoogle Scholar
  38. 38.
    Hunt, D. F.; Shabanowitz, J.; Yates, J. R. J. Chem. Soc, Chem, Commun. 1987, 8, 548–550.CrossRefGoogle Scholar
  39. 39.
    Kasler, R. E., Jr.; Cooks, R. G.; Syka, J. E. P.; Stafford, G. C., Jr. Rapid Mass Spectrom. 1990, 4, 30–33.CrossRefGoogle Scholar
  40. 40.
    Kaufmann, R.; Spengler, B.; Lutzenkirchen, F. Rapid Commun. Mass Specirom. 1993, 7, 902–910.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 1994

Authors and Affiliations

  • Jimmy K. Eng
    • 1
  • Ashley L. McCormack
    • 1
  • John R. Yates
    • 1
  1. 1.Department of Molecular BiotechnologyUniversity of WashingtonSeattleUSA

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