skip to main content
10.5555/1274172.1274182dlproceedingsArticle/Chapter ViewAbstractPublication PageswisbConference Proceedingsconference-collections
Article
Free Access

Linear predictive coding and its decision logic for early prediction of major adverse cardiac events using mass spectrometry data

Published:01 December 2006Publication History

ABSTRACT

Proteomics is an emerging field of modern biotechnology and an attractive research area in bioinformatics. Protein annotation by mass spectrometry has recently been utilized for the classification and prediction of diseases. In this paper we apply the theory of linear predictive coding and its decision logic for the prediction of major adverse cardiac risk using mass spectra. The new method was tested with a small set of mass spectrometry data. The initial experimental results are found promising for the prediction and show the implication of the potential use of the data for biomarker discovery.

References

  1. Aebersold, R., & Mann, M. (2003), 'Mass spectrometry-based proteomics', Nature 422, 198--207.Google ScholarGoogle ScholarCross RefCross Ref
  2. Anatassiou, D. (2001), 'Genomic signal processing', IEEE Signal Processing Magazine 18, 8--20.Google ScholarGoogle ScholarCross RefCross Ref
  3. Anderle, M., Roy, S., Lin, H., Becker, C., & Joho, K. (2004), 'Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum', Bioinformatics 20, 3575--3582. Google ScholarGoogle ScholarDigital LibraryDigital Library
  4. Ball, G., Mian, S., Holding, F., Allibone, R. O., Lowe, J., Ali, S., Li, G., McCardle, S., Ellis, I. O., Creaser, C., & Rees, R. C. (2002), 'An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers', Bioinformatics 18, 395--404.Google ScholarGoogle ScholarCross RefCross Ref
  5. Brennan, M.-L., Penn, M. S., Van Lente, Nambi, V., Shishehbor, M. H., Aviles, R. J., Goormastic, M., Pepoy, M. L., McErlean, E. S., Topol, E. J., Nissen, S. E., & Hazen, S. L. (2003), 'Prognostic value of myeloperoxidase in patients with chest pain', The New England Journal of Medicine 13, 1595--1604.Google ScholarGoogle ScholarCross RefCross Ref
  6. Conrads, T. P., Zhou, M., Petricoin III, E. F., Liotta, L. & Veenstra, T. D. (2003), 'Cancer diagnosis using proteomic patterns', Expert Rev. Mol. Diagn. 3, 411--420.Google ScholarGoogle ScholarCross RefCross Ref
  7. Deutsch, C. V. (2002), Geostatistical Reservoir Modeling. Oxford University Press, New York.Google ScholarGoogle ScholarCross RefCross Ref
  8. de Trad, C. H., Fang, Q. & Cosic, I. (2002), 'Protein sequence comparison based on the wavelet transform approach', Protein Engineering 15, 193--203.Google ScholarGoogle ScholarCross RefCross Ref
  9. Gray, R. M. (1984), 'Vector quantization', IEEE ASSP Mag. 1, 4--29.Google ScholarGoogle ScholarCross RefCross Ref
  10. Griffin, T., Goodlett, T. & Aebersold, R. (2001), 'Advances in proteomic analysis by mass spectrometry', Curr. Opin. Biotechnol. 12, 607--612.Google ScholarGoogle ScholarCross RefCross Ref
  11. Isaaks, E. H. & Srivastava, R. M. (1989), An Introduction to Applied Geostatistics. Oxford University Press, New York, 1989.Google ScholarGoogle Scholar
  12. Itakura, F. & Saito, S. (1970), A statistical method for estimation of speech spectral density and formant frequencies', Electronics and Communications in Japan 53A, 36--43.Google ScholarGoogle Scholar
  13. Lazovic, J. (1996), 'Selection of amino acid parameters for Fourier transform-based analysis of proteins', CABIOS 12, 553--562.Google ScholarGoogle Scholar
  14. Levner, I. (2005), 'Feature selection and nearest centroid classification for protein mass spectrometry', BMC Bioinformatics 6:68, (http://www.biomedcentral.com/1471-2105/6/68).Google ScholarGoogle ScholarCross RefCross Ref
  15. Lilien, R. H., Farid, H., & Donald, B. R. (2003), 'Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum', J. Computational Biology 10, 925--946.Google ScholarGoogle ScholarCross RefCross Ref
  16. Linde, Y., Buzo, A., and Gray, R. M. (1980), 'An Algorithm for Vector Quantization', IEEE Trans. Communications 28, 84--95.Google ScholarGoogle ScholarCross RefCross Ref
  17. Makhoul, J. (1975), 'Linear prediction: a tutorial review', Proc. IEEE 63, 561--580.Google ScholarGoogle ScholarCross RefCross Ref
  18. Morris, J. S., Coombes, K. R., Koomen, J., Baggerly, K. A., & Kobayashi, R. (2005), 'Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum', Bioinformatics 21, 1764--1775. Google ScholarGoogle ScholarDigital LibraryDigital Library
  19. Petricoin, E. F., et al. (2002), 'Use of proteomic patterns in serum to identify ovarian cancer', Lancet 359, 572--577.Google ScholarGoogle ScholarCross RefCross Ref
  20. Petricoin, E. F. & Liotta, L. A. (2003), 'Mass spectrometry-based diagnostics: The upcoming revolution in disease detection', Clinical Chemistry 49, 533--534.Google ScholarGoogle ScholarCross RefCross Ref
  21. Pham, T. D. & Wagner, M. (1998), 'A geostatistical model for linear prediction analysis of speech', Pattern Recognition 31, 1981--1991.Google ScholarGoogle ScholarCross RefCross Ref
  22. Pham, T. D. (2006), 'LPC cepstral distortion measure for protein sequence comparison', IEEE Trans. Nano Bioscience 5, 83--88.Google ScholarGoogle ScholarCross RefCross Ref
  23. Rabiner, L. R., Sondhi M. M., and Levinson, S. E. (1984), 'A vector quantizer incorporating both LPC shape and energy', Proc. Int. Conf. Acoustics, Speech, and Signal Processing, pp. 17.1.1--17.1.4,.Google ScholarGoogle ScholarCross RefCross Ref
  24. Rabiner, L. & Juang, B. H. (1993), Fundamentals of Speech Recognition. New Jersey, Prentice Hall. Google ScholarGoogle ScholarDigital LibraryDigital Library
  25. Salmi, J., Moulder, R., Filen, J.-J., Nevalainen, O. S., Nyman, T. A., Lahesmaa, R. & Aittokallio, T. (2006), 'Quality classification of tandem mass spectrometry data', Bioinformatics 22, 400--406. Google ScholarGoogle ScholarDigital LibraryDigital Library
  26. Sauter, E., et al. (2002), 'Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer', Br. J. Cancer 86, 1440--1443.Google ScholarGoogle ScholarCross RefCross Ref
  27. Shin, H. & Markey, M. K. (2006), 'A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples', J. Biomedical Informatics 39, 227--248. Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. Sorace, J. M. & Zhan, M. (2003), 'A data review and re-assessment of ovarian cencer serum proteomic profiling', BMC Bioinformatics 4:24, (http://www.biomedcentral.com/1471--2105/4/24).Google ScholarGoogle Scholar
  29. Tibshirani, R., Hastie, T., Narasimhan, B., Soltys, S., Shi, G., Koong, A. & Le, Q.-T. (2004), 'Sample classification from protein mass spectrometry, by 'peak probability contrasts", Bioinformatics 20, 3034--3044. Google ScholarGoogle ScholarDigital LibraryDigital Library
  30. Vaidyanathan, P. P. (2004), 'Genomics and proteomics: A signal processor's tour', IEEE Circuits and Systems Magazine, Fourth Quarter pp. 6--28.Google ScholarGoogle Scholar
  31. Xiong, J. (2006), Essential Bioinformatics, Cambridge University Press, New York.Google ScholarGoogle ScholarCross RefCross Ref
  32. Yu, J. S., Ongarello, S., Fiedler, R., Chen, X. W., Toffolo, G., Cobelli, C. & Trajanoski, Z. (2005), 'Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data', Bioinformatics 21, 2200--2209. Google ScholarGoogle ScholarDigital LibraryDigital Library
  33. Weir, M. P., Blackstock, W. P., & Twyman, M. (2003), Proteomics, in C. A. Orengo, D. T. Jones, and J. M. Thornton, eds, 'Bioinformatics: Genes, Proteins & Computers', BIOS Scientific Publishers, pp. 245--257.Google ScholarGoogle ScholarCross RefCross Ref
  34. Wu, Q., & Castleman, K. R. (2000), 'Automated chromosome classification using wavelet-based band pattern descriptors', Proc. 13th IEEE Symp. Computer-Based Medical Systems, pp. 189--194. Google ScholarGoogle ScholarDigital LibraryDigital Library
  35. Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K. & Zhao, H. (2003), 'Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data', Bioinformatics 19, 1636--1643.Google ScholarGoogle ScholarCross RefCross Ref
  36. Wulfkuhle, J. D., Liotta, L. A. & Petricoin, E. F. (2003), 'Proteomic applications for the early detection of cancer', Nature 3, 267--275.Google ScholarGoogle Scholar
  37. Zhou, X., Wang, H., Wang, J., Hoehn, G., Azok. J., Brennan, M. L., Hazen, S. L., Li, K., & Wong, S. T. C., (2006), 'Biomarker discovery for risk stratification of cardiovascular events using an improved genetic algorithm', Proc. IEEE/NLM Int. Symposium on Life Science and Multimodality, July 13--14, Washington, DC.Google ScholarGoogle ScholarCross RefCross Ref

Index Terms

  1. Linear predictive coding and its decision logic for early prediction of major adverse cardiac events using mass spectrometry data
            Index terms have been assigned to the content through auto-classification.

            Recommendations

            Comments

            Login options

            Check if you have access through your login credentials or your institution to get full access on this article.

            Sign in

            PDF Format

            View or Download as a PDF file.

            PDF

            eReader

            View online with eReader.

            eReader