博碩士論文 962211006 詳細資訊




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姓名 陳欣皓(Hsin-Hao Chen)  查詢紙本館藏   畢業系所 系統生物與生物資訊研究所
論文名稱 利用赫伯特-黃轉換法做為在質譜儀分析技術的前處理方法
(A novel preprocessing method using Hilbert Huang transform for MALDI-TOF and SELDI-TOF mass spectrometry data)
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摘要(中) 自人類基因體計畫開始以來,基因序列分析已蓬勃發展。蛋白質體學的研究在近代引起了生物學家的注目,蛋白質體學本身扮演著基因體學與細胞表觀行為溝通的橋樑。在此,我們致力於高通量、更有效率與提高準確的質譜儀分析。表面強化雷射解析電離飛行質譜(SELDI-TOF)與基質輔助雷射脫附游離法飛行質譜(MALDI-TOF)技術是質譜儀技術裡面兩種常用的技術。利用質譜圖所偵測到的波峰,我們可以用來當作正常人與病患間的生物標定物來區分。然而,一個質譜圖裡夾雜許多複雜的訊號,特別是雜訊。因此,對於質譜圖資料的前處理分析就顯得更為重要。
我們以赫伯特-黃轉換法(Hilbert-Huang Transformation)為主要概念,發展一個新的質譜圖前處理方法。並進而與目前較為熱門的幾個錢處理方法做比較,包含PROcess、SpecAlign以及MassSpecWavelet。我們著重於在質譜圖中較為顯著且重要的波峰,並觀察這些波峰在上述幾個方法的表現;同時,為了更顯客觀性,我們另外做了一次實驗,分別為未加入樣本所得到的質譜圖、與加入樣本得到的質譜圖,由此來驗證我們確實能有效去除雜訊,特別是去除部分化學物質所產生的雜訊。
摘要(英) Motivation: There are a lot of gene sequence analyses, especially the time after human genome project. The proteomics becomes more and more attractive for biologists. It can bridge the gap between the genome sequence and the cellular behavior. We are concerned about the Mass spectrometry which is high throughput, fast, and accurate. Matrix assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) time of flight (TOF) are two popular technologies in the field of spectrometry. With the peaks detected in spectra, we can compare the normal group with disease. However, the spectrum is complicated and full of noise. Consequently, the preprocessing of the mass data plays an important role during our analysis.
Results: We provide a novel algorithm of preprocessing dealing with the MALDI and SELDI spectrum. The algorithm uses the Hilbert-Huang Transform mainly. We compare the performance of several famous algorithms including PROcess, SpecAlign, and MassSpecWavelet with ours called HHT. The main thought of performance is chiefly visual comparison. We pick the significant peaks and observe the results which the algorithm shows in figure. The results show that HHT for preprocessing is more fitness than others. Not only detecting the peaks, but HHT has the advantage of denoising the spectra, especially for the complex data.
關鍵字(中) ★ 質譜儀
★ 赫伯特-黃
關鍵字(英) ★ mass spectrum
★ HHT
論文目次 Chapter 1 INTRODUCTION 1
Chapter 2 MATERIAL AND ALGORITHMS 4
2-1 Hilbert Huang transform 4
2-2 Modification 5
2-3 Peak detection 5
Chapter 3 DATA SOURCE 7
Chapter 4 METHODS OF COMPARISON 10
Chapter 5 RESULTS 15
5-1 Results after Hilbert Huang transform and modification 15
5-2 Results of comparison between our methods 17
5-3 Results of comparison between our method and other methods 20
Chapter 6 THE VALIDATION OF EXPERIMENTS 25
Chapter 7 DISCUSSION 27
REFERENCES 29
參考文獻 1. Beyer, S., Y. Walter, et al. (2006). "Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra." J Proteome Res 5(2): 254-61.
2. Coombes, K. R., J. S. Morris, et al. (2005). "Serum proteomics profiling--a young technology begins to mature." Nat Biotechnol 23(3): 291-2.
3. Cruz-Marcelo, A., R. Guerra, et al. (2008). "Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data." Bioinformatics 24(19): 2129-36.
4. DiMagno, E. P., D. Corle, et al. (1989). "Effect of long-term freezer storage, thawing, and refreezing on selected constituents of serum." Mayo Clin Proc 64(10): 1226-34.
5. Du, P., W. A. Kibbe, et al. (2006). "Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching." Bioinformatics 22(17): 2059-65.
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8. Hilario, M., A. Kalousis, et al. (2006). "Processing and classification of protein mass spectra." Mass Spectrom Rev 25(3): 409-49.
9. Kwon, D., M. Vannucci, et al. (2008). "A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise." Proteomics 8(15): 3019-29.
10. Li, X. e. a. (2005). Seldi-tof mass spectrometry protein data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. R. e. a. In Gentleman. New York, Springer: 99-109.
11. Malyarenko, D. I., W. E. Cooke, et al. (2005). "Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques." Clin Chem 51(1): 65-74.
12. Meuleman, W., J. Y. Engwegen, et al. (2008). "Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data." BMC Bioinformatics 9: 88.
13. Morris, J. S., K. R. Coombes, et al. (2005). "Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum." Bioinformatics 21(9): 1764-75.
14. Qu, Y., B. L. Adam, et al. (2003). "Data reduction using a discrete wavelet transform in discriminant analysis of very high dimensionality data." Biometrics 59(1): 143-51.
15. Randolph, T. W. and Y. Yasui (2006). "Multiscale processing of mass spectrometry data." Biometrics 62(2): 589-97.
16. Shin, H. and M. K. Markey (2006). "A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples." J Biomed Inform 39(2): 227-48.
17. Wong, J. W., G. Cagney, et al. (2005). "SpecAlign--processing and alignment of mass spectra datasets." Bioinformatics 21(9): 2088-90.
指導教授 吳立青(Li-Ching Wu) 審核日期 2009-7-22
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