- Research Article
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MALDI-TOF Baseline Drift Removal Using Stochastic Bernstein Approximation
EURASIP Journal on Advances in Signal Processing volume 2006, Article number: 063582 (2006)
Stochastic Bernstein (SB) approximation can tackle the problem of baseline drift correction of instrumentation data. This is demonstrated for spectral data: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) data. Two SB schemes for removing the baseline drift are presented: iterative and direct. Following an explanation of the origin of the MALDI-TOF baseline drift that sheds light on the inherent difficulty of its removal by chemical means, SB baseline drift removal is illustrated for both proteomics and genomics MALDI-TOF data sets. SB is an elegant signal processing method to obtain a numerically straightforward baseline shift removal method as it includes a free parameter that can be optimized for different baseline drift removal applications. Therefore, research that determines putative biomarkers from the spectral data might benefit from a sensitivity analysis to the underlying spectral measurement that is made possible by varying the SB free parameter. This can be manually tuned (for constant) or tuned with evolutionary computation (for).
Kolibal J, Saltiel C: Data regularization using stochastic methods. 2005.
Karas M, Hillenkamp F: Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Analytical Chemistry 1988, 60(20):2299–2301. 10.1021/ac00171a028
Ryan MA, Buehler MG, Horner ML, et al.: Results from the space shuttle STS-95 electronic nose experiment. JPL Publication 99-0780, 1999
Lorentz GG: Bernstein Polynomials. Chelsea, New Yourk, NY, USA; 1986.
Williams B, Cornett S, Crecelius A, Caprioli R, Dawant B, Bodenheimer B: An algorithm for baseline correction of MALDI mass spectra. Proceedings of the 43rd ACM Southeast Conference (ACMSE '05), March 2005, Kennesaw, Ga, USA
Krutchinsky AN, Chait BT: On the nature of the chemical noise in MALDI mass spectra. Journal of American Society of Mass Spectrometry 2002, 13: 129–134. 10.1016/S1044-0305(01)00336-1
Koza JR: Genetic Programming. MIT Press, Cambridge, Mass, USA; 1992.
Ressom HW, Varghese RS, Orvisky E, et al.: Analysis of MALDI-TOF serum profiles for biomarker selection and sample classification. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '05), November 2005, San Diego, Calif, USA
Howard D, Kolibal J: Solution of Differential Equations with Genetic Programming and the Stochastic Bernstein Interpolation. In Tech. Rep. BDS-TR-2005-001. Biocomputing Developmental Systems Group, University of Limerick, Limerick, Ireland; June 2005.
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Kolibal, J., Howard, D. MALDI-TOF Baseline Drift Removal Using Stochastic Bernstein Approximation. EURASIP J. Adv. Signal Process. 2006, 063582 (2006) doi:10.1155/ASP/2006/63582
- Spectral Data
- Free Parameter
- Spectral Measurement
- Evolutionary Computation
- Inherent Difficulty