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.
- Aebersold, R., & Mann, M. (2003), 'Mass spectrometry-based proteomics', Nature 422, 198--207.Google ScholarCross Ref
- Anatassiou, D. (2001), 'Genomic signal processing', IEEE Signal Processing Magazine 18, 8--20.Google ScholarCross Ref
- 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 ScholarDigital Library
- 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 ScholarCross Ref
- 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 ScholarCross Ref
- 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 ScholarCross Ref
- Deutsch, C. V. (2002), Geostatistical Reservoir Modeling. Oxford University Press, New York.Google ScholarCross Ref
- de Trad, C. H., Fang, Q. & Cosic, I. (2002), 'Protein sequence comparison based on the wavelet transform approach', Protein Engineering 15, 193--203.Google ScholarCross Ref
- Gray, R. M. (1984), 'Vector quantization', IEEE ASSP Mag. 1, 4--29.Google ScholarCross Ref
- Griffin, T., Goodlett, T. & Aebersold, R. (2001), 'Advances in proteomic analysis by mass spectrometry', Curr. Opin. Biotechnol. 12, 607--612.Google ScholarCross Ref
- Isaaks, E. H. & Srivastava, R. M. (1989), An Introduction to Applied Geostatistics. Oxford University Press, New York, 1989.Google Scholar
- 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 Scholar
- Lazovic, J. (1996), 'Selection of amino acid parameters for Fourier transform-based analysis of proteins', CABIOS 12, 553--562.Google Scholar
- 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 ScholarCross Ref
- 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 ScholarCross Ref
- Linde, Y., Buzo, A., and Gray, R. M. (1980), 'An Algorithm for Vector Quantization', IEEE Trans. Communications 28, 84--95.Google ScholarCross Ref
- Makhoul, J. (1975), 'Linear prediction: a tutorial review', Proc. IEEE 63, 561--580.Google ScholarCross Ref
- 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 ScholarDigital Library
- Petricoin, E. F., et al. (2002), 'Use of proteomic patterns in serum to identify ovarian cancer', Lancet 359, 572--577.Google ScholarCross Ref
- Petricoin, E. F. & Liotta, L. A. (2003), 'Mass spectrometry-based diagnostics: The upcoming revolution in disease detection', Clinical Chemistry 49, 533--534.Google ScholarCross Ref
- Pham, T. D. & Wagner, M. (1998), 'A geostatistical model for linear prediction analysis of speech', Pattern Recognition 31, 1981--1991.Google ScholarCross Ref
- Pham, T. D. (2006), 'LPC cepstral distortion measure for protein sequence comparison', IEEE Trans. Nano Bioscience 5, 83--88.Google ScholarCross Ref
- 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 ScholarCross Ref
- Rabiner, L. & Juang, B. H. (1993), Fundamentals of Speech Recognition. New Jersey, Prentice Hall. Google ScholarDigital Library
- 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 ScholarDigital Library
- 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 ScholarCross Ref
- 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 ScholarDigital Library
- 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 Scholar
- 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 ScholarDigital Library
- Vaidyanathan, P. P. (2004), 'Genomics and proteomics: A signal processor's tour', IEEE Circuits and Systems Magazine, Fourth Quarter pp. 6--28.Google Scholar
- Xiong, J. (2006), Essential Bioinformatics, Cambridge University Press, New York.Google ScholarCross Ref
- 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 ScholarDigital Library
- 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 ScholarCross Ref
- 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 ScholarDigital Library
- 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 ScholarCross Ref
- Wulfkuhle, J. D., Liotta, L. A. & Petricoin, E. F. (2003), 'Proteomic applications for the early detection of cancer', Nature 3, 267--275.Google Scholar
- 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 ScholarCross Ref
Index Terms
- Linear predictive coding and its decision logic for early prediction of major adverse cardiac events using mass spectrometry data
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