Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model
1Center for Biotechnology and Informatics (CBI), The Methodist Hospital Research Institute, and Department of Radiology, The Methodist Hospital, Weill Cornell Medical College, Houston, TX 77030, USA, 2School of Electronics, Information and Electrical Engineering, Shanghai Jiao Tong University, China and 3Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
*To whom correspondence should be addressed.
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Abstract |
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Mass spectrometry (MS) has shown great potential in detecting disease-related biomarkers for early diagnosis of stroke. To discover potential biomarkers from large volume of noisy MS data, peak detection must be performed first. This article proposes a novel automatic peak detection method for the stroke MS data. In this method, a mixture model is proposed to model the spectrum. Bayesian approach is used to estimate parameters of the mixture model, and Markov chain Monte Carlo method is employed to perform Bayesian inference. By introducing a reversible jump method, we can automatically estimate the number of peaks in the model. Instead of separating peak detection into substeps, the proposed peak detection method can do baseline correction, denoising and peak identification simultaneously. Therefore, it minimizes the risk of introducing irrecoverable bias and errors from each substep. In addition, this peak detection method does not require a manually selected denoising threshold. Experimental results on both simulated dataset and stroke MS dataset show that the proposed peak detection method not only has the ability to detect small signal-to-noise ratio peaks, but also greatly reduces false detection rate while maintaining the same sensitivity.
Contact: XZhou{at}tmhs.org
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