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


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.


  1. 1.

    Edman, P.; Begg, G., Eur. J. Biochem. 1967, 1, 80–91.

    CAS  Article  Google Scholar 

  2. 2.

    Hewick, R. M.; Hunkapiller, M. W.; Hood, L. E.; Dryer, W. J. J. BioI. Chem, 1981, 256, 7990–7997.

    CAS  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.

    Article  Google 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.

    CAS  Article  Google Scholar 

  7. 7.

    Yates, J. R.; Speicher, S.; Griffin, P. R.; Hunkapiller, T. Anal. Biochem. 1993, 214, 397–408.

    CAS  Article  Google Scholar 

  8. 8.

    Pappin, D.; Hojrup, P.; Bleasby, A. Curro Biol. 1993, 3, 327–332.

    CAS  Article  Google Scholar 

  9. 9.

    James. P.; Qaudroni, M.; Carafoli, E.; Gonnet, G. Biochem. Biophys. Res. Commun. 1993, 195, 58–64.

    CAS  Article  Google Scholar 

  10. 10.

    Mann, M.; Hojrup, P.; Roepstorff, P. Biol. Mass Spectrom. 1993, 22, 338–345.

    CAS  Article  Google Scholar 

  11. 11.

    Penn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F; Whitehouse, C. M. Science 1989, 246, 64–71.

    Article  Google 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.

    Article  Google 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.

    Article  Google 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.

    CAS  Article  Google 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.

    CAS  Article  Google Scholar 

  19. 19.

    Johnson, R.S.; Biemann, K. Biomed. Env. Mass Spectrom. 1989, 18, 945–957.

    CAS  Article  Google Scholar 

  20. 20.

    Hines, W. M.; Falick, A. M.; Burlingame, A. L.; Gibson, B. W., J. Am. Soc. Mass Spectrum. 1992, 3, 326–336.

    CAS  Article  Google 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.

    CAS  Article  Google Scholar 

  23. 23.

    Lee, T. D.; Vemuri, S. Biomed. Environ. Mass Specitom. 1990, 19, 639–645.

    CAS  Article  Google Scholar 

  24. 24.

    Papayannopoulos, I. A.; Biernann, K. J. Am. Soc. Mass Spectram. 1991, 2, 174–177.

    CAS  Article  Google Scholar 

  25. 25.

    Watkins, P. J.; Jardine, L; Zhou, J. X. Biochem. Soc. Trans. 1991, 19, 957–962.

    CAS  Google Scholar 

  26. 26.

    Demotz, S.; Grey, H.; Appella, E.; Sette, A. Nature (London) 1989, 342, 682–684.

    CAS  Article  Google 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.

    CAS  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.

    Chapter  Google 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.

    CAS  Article  Google Scholar 

  30. 30.

    Powell, L. A.; Heiftje, G. M. Anal. Chim. Acta 1978, 100, 313–327.

    CAS  Article  Google Scholar 

  31. 31.

    Owens, K. Appl. Spectrosc. Rev. 1992, 27, 1–49.

    Article  Google 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.

    CAS  Article  Google Scholar 

  33. 33.

    Rudensky, A. Y.; Preston-Hurlburt, P.; Hong, S-C.; Barlow, A.; Janeway, C. A., Jr. Nature 1991, 353, 622–627.

    CAS  Article  Google Scholar 

  34. 34.

    Daniels, D. L.; Plunkett, G., III; Burland, V.; Blattner, F. R. Science 1992, 257, 771–778.

    CAS  Article  Google 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.

    CAS  Article  Google 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.

  37. 37.

    Johnson, R. S.; Biemann, K. Biochemistry 1987, 26, 1209–1214.

    CAS  Article  Google Scholar 

  38. 38.

    Hunt, D. F.; Shabanowitz, J.; Yates, J. R. J. Chem. Soc, Chem, Commun. 1987, 8, 548–550.

    Article  Google 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.

    Article  Google Scholar 

  40. 40.

    Kaufmann, R.; Spengler, B.; Lutzenkirchen, F. Rapid Commun. Mass Specirom. 1993, 7, 902–910.

    CAS  Article  Google Scholar 

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Correspondence to John R. Yates.

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Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5, 976–989 (1994).

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