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Searching sequence databases via De novo peptide sequencing by tandem mass spectrometry

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Abstract

There are many computer programs that can match tandem mass spectra of peptides to database-derived sequences; however, situations can arise where mass spectral data cannot be correlated with any database sequence. In such cases, sequences can be automatically deduced de novo, without recourse to sequence databases, and the resulting peptide sequences can be used to perform homologous nonexact searches of sequence databases. This article describes details on how to implement both a de novo sequencing program called “Lutefisk,” and a version of FASTA that has been modified to account for sequence ambiguities inherent in tandem mass spectrometry data.

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5. References

  1. Humphery-Smith, I., Cordwell, S. J., and Blackstock, W. P. (1997) Electrophoresis 18, 1217–1242.

    Article  PubMed  CAS  Google Scholar 

  2. Aebersold, R. and Goodlett, D. R. (2001) Chem. Rev. 101, 269–295.

    Article  PubMed  CAS  Google Scholar 

  3. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Annu. Rev. Biochem. 70, 437–473.

    Article  PubMed  CAS  Google Scholar 

  4. Eng, J. K., McCormack, A. L., and Yates, J. R., III (1994) J. Am. Soc. Mass Spectrom. 5, 976–989.

    Article  CAS  Google Scholar 

  5. Mann, M. and Wilm, M. (1994) Anal. Chem. 66, 4390–4399.

    Article  PubMed  CAS  Google Scholar 

  6. Clauser, K., Baker, P., and Burlingame, A. (1999) Anal. Chem. 71, 2871–2882.

    Article  PubMed  CAS  Google Scholar 

  7. Fenyo, D., Qin, J., and Chait, B. T. (1998) Electrophoresis 19, 998–1005.

    Article  PubMed  CAS  Google Scholar 

  8. Perkins, D., Pappin, D., Creasy, D., and Cottrell, J. (1999) Electrophoresis 20, 3551–3567.

    Article  PubMed  CAS  Google Scholar 

  9. Johnson, R. (2000) in Proteome Research: Mass Spectrometry (P, J., ed.), Springer-Verlag, Berlin.

    Google Scholar 

  10. Taylor, J. A. and Johnson, R. S. (1997) Rapid Commun. Mass Spectrom. 11, 1067–1075.

    Article  PubMed  CAS  Google Scholar 

  11. Taylor, J. A. and Johnson, R. S. (2001) Anal. Chem. 73, 2594–2604.

    Article  PubMed  CAS  Google Scholar 

  12. Johnson, R. and Taylor, J. (2000) in Methods in Molecular Biology: Mass Spectrometry of Proteins and Peptides (Chapman, J., ed) Vol. 146, pp. 41–62, Humana Press, Totowa, New Jersey.

    Chapter  Google Scholar 

  13. Bartels, C. (1990) Biomedical and Environmental Mass Spectrom. 19, 363–368.

    Article  CAS  Google Scholar 

  14. Fernandez-de-Cossio, J., Gonzalez, J., and Besada, V. (1995) Comput. Appl. Biosci. 11, 427–434.

    PubMed  CAS  Google Scholar 

  15. Fernandez-de-Cossio, J., Gonzalez, J., Satomi, Y., Shima, T., Okumura, N., Besada, V., Betancourt, L., Padron, G., Shimonishi, Y., and Takao, T. (2000) Electrophoresis 21, 1694–1699.

    Article  PubMed  CAS  Google Scholar 

  16. Pearson, W. R. (1990) Meth. Enzymol. 183, 63–98.

    Article  PubMed  CAS  Google Scholar 

  17. Pearson, W. R. and Lipman, D. J. (1988) Proc..Nat. Acad. Sci. USA 85, 2444–2448.

    Article  PubMed  CAS  Google Scholar 

  18. Wilm, M. and Mann, M. (1996) Anal. Chem. 68, 1–8

    Article  PubMed  CAS  Google Scholar 

  19. Papayannopoulos, I. A. (1995) Mass Spectrom. Rev. 14, 49–73.

    Article  CAS  Google Scholar 

  20. Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Proc. Natl. Acad. Sci. USA 83, 6233–6237.

    Article  PubMed  CAS  Google Scholar 

  21. Tang, X., and Boyd, R. K. (1992) Rapid Commun. Mass Spectrom. 6, 651–657.

    Article  PubMed  CAS  Google Scholar 

  22. Korner, R., Wilm, M., Morand, K., Schubert, M., and Mann, M. (1996) J. Am. Soc. Mass. Spectrom. 7, 150–156.

    Article  Google Scholar 

  23. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) J. Mol. Biol. 215, 403–410.

    PubMed  CAS  Google Scholar 

  24. Henikoff, S., and Henikoff, J. G. (1992) Proc. Natl. Acad. Sci. USA 89, 10915–10919.

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Richard S. Johnson.

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Johnson, R.S., Taylor, J.A. Searching sequence databases via De novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol 22, 301–315 (2002). https://doi.org/10.1385/MB:22:3:301

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