Advertisement

An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum

  • Bin Ma
  • Kaizhong Zhang
  • Chengzhi Liang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2676)

Abstract

The determination of the amino acid sequence of a peptide from its MS/MS spectrum is an important task in proteomics. The determination without the help of a protein database is called the de novo sequencing, which is especially useful in the identification of unknown proteins. Many studies on the de novo sequencing problem have been done but none proves to be practical. In this paper, we define a new model for this problem, and provide a sophisticated dynamic programming algorithm to solve it. Experiments on real MS/MS data demonstrated that the algorithm works very well on QTof MS/MS data.

Keywords

Peptide Sequencing Score Function Tandem Mass Spectrum Sequencing Problem Fast Atom Bombardment Mass Spectrometry 
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.
    Bartels, C. 1990. Fast algorithm for peptide sequencing by mass spectroscopy. Biomed. Environ. Mass Spectrom 19, 363–368.CrossRefGoogle Scholar
  2. 2.
    Chen, T., Kao, M-Y., Tepel, M., Rush J., and Church, G. 2001. A Dynamic Programming Approach to de novo Peptide Sequencing via Tandem Mass Spectrometry. J. Comp. Biology 8(3), 325–337.CrossRefGoogle Scholar
  3. 3.
    Dančík, V., Addona, T., Clauser, K., Vath, J., and Pevzner, P. 1999. De novo protein sequencing via tandem mass-spectrometry. J. Comp. Biology 6, 327–341.CrossRefGoogle Scholar
  4. 4.
    Eng, J.K., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data pf peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom 5, 976–989.CrossRefGoogle Scholar
  5. 5.
    Fernández de Cossío, J., Gonzales, J., and Besada, V. 1995. A computer program to aid the sequencing of peptides in collision-activated decomposition experiments. CABIOS 11(4), 427–434.Google Scholar
  6. 6.
    Hamm, C.W., Wilson, W.E., and Harvan, D.J. 1986. Peptide sequencing program. CABIOS 2, 365.Google Scholar
  7. 7.
    Hines, W.M., Falick, A.M., Burlingame, A.L., and Gibson, B.W. 1992. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra. J. Am. Sco. Mass. Spectrom. 3, 326–336.CrossRefGoogle Scholar
  8. 8.
    Ishikawa K., and Niva, Y. 1986. Computer-aided peptide sequencing by fast atom bombardment mass spectrometry. Biomed. Environ. Mass Spectrom. 13, 373–380.CrossRefGoogle Scholar
  9. 9.
    Johnson, R.J., and Biemann, K. 1989. Computer program (seqpep) to aid the interpretation of high-energy collision tandem mass spectra of peptides. Biomed. Environ. Mass. Spectrom. 18, 945–957.CrossRefGoogle Scholar
  10. 10.
    Johnson, R.S., Martin, S.A., Biemann, K., Stults, J.T., and Watson, J.T. 1987. Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal. Chem. 59(21), 2621–5.CrossRefGoogle Scholar
  11. 11.
    Ma, B., Zhang, K., Lajoie, G., Doherty-Kirby, A., Liang, C., and Li, M. 2002. A powerful software tool for the de novo sequencing of peptides from MS/MS data. 50th ASMS Conference on Mass Spectrometry and Allied Topics.Google Scholar
  12. 12.
    Mann, M., and Wilm, M. 1994. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390–4399.CrossRefGoogle Scholar
  13. 13.
    Perkins, D.N., Pappin, D.J.C., Creasy, D.M., and Cottrell, J.S. 1999. Probability-based protein identification by searching sequence database using mass spectrometry data. Electrophoresis 20, 3551–3567.CrossRefGoogle Scholar
  14. 14.
    Pevzner, P.A., Dančík, V., and Tang, C. 2000. Mutation Tolerant Protein Identification by Mass Spectrometry. Journal of Computational Biology 6, 777–787.CrossRefGoogle Scholar
  15. 15.
    Roepstorff, P., and Fohlman J. 1984. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11(11), 601.CrossRefGoogle Scholar
  16. 16.
    Sakurai, T., Matsuo, T., Matsuda, H., and Katakuse, I. 1984. Paas3: A computer program to determine probable sequence of peptides from mass spectrometric data. Biomed. Mass spectrum 11(8), 396–399.CrossRefGoogle Scholar
  17. 17.
    Siegel, M.M., and Bauman, N. 1988. An efficient algorithm for sequencing peptides using fast atom bombardment mass spectral data. Biomed. Environ. Mass Spectrom 15, 333–343.CrossRefGoogle Scholar
  18. 18.
    Snyder, A.P. 2000. Interpreting Protein Mass Spectra: A Comprehensive Resource. Oxford University Press.Google Scholar
  19. 19.
    Taylor, J.A., and Johnson, R.S. 1997. Sequence Database Searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Communications in Mass Spectrometry 11, 1067–1075.CrossRefGoogle Scholar
  20. 20.
    Yates, J.R.I., Eng, J.K., McCormack, A.L., and Schieltz, D. 1995. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Analytical Chemistry 67, 1426–36.CrossRefGoogle Scholar
  21. 21.
    Yates, J.R., Griffin, P.R., Hood, L.E., and Zhou, J.X. 1991. Computer aided interpretation of low energy MS/MS mass spectra of peptides, 477–485. in J.J. Villafranca ed., Techniques in Protein Chmistry II, Academic Press, San Diego.Google Scholar
  22. 22.
    Zidarov, D., Thibault, P., Evans, M.J., and Bertrand, M.J. 1990. Determination of the primary structure of peptidesusing fast atom bombardment mass spectrometry. Biomed. Environ. Mass Spectrom 19, 13–16.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Bin Ma
    • 1
  • Kaizhong Zhang
    • 1
  • Chengzhi Liang
    • 2
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondonCanada
  2. 2.Bioinformatics Solutions Inc.WaterlooCanada

Personalised recommendations