Fast elastic peak detection for mass spectrometry data mining

IEEE Transactions on Knowledge and Data Engineering

Volumn 24, Issue 4, 2012, Pages 634-648

  Zhang, Xin ^a   Shasha, Dennis E ^a   Song, Yang ^b   Wang, Jason T L ^b  

^a POLYTECHNIC UNIVERSITY   (United States)

^b University Heights   (United States)

Author keywords

algorithms and data structures; bioinformatics; computational proteomics; Knowledge discovery from LC MS data; time series data mining

Indexed keywords

ALGORITHMS AND DATA STRUCTURES; BOTTOM-UP MANNER; COMPUTATIONAL PROTEOMICS; DATA MINING PROBLEMS; DATA SETS; ELASTIC PEAK; FALSE NEGATIVES; FALSE POSITIVE; INTENSITY VALUES; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; MASS SPECTROMETRY DATA; MULTIPLE WINDOWS; REAL WORLD DATA; SLIDING TIME WINDOWS; STATE-SPACE; TIME POINTS; TIME SERIES DATA MINING; TOP-DOWN MANNER;

ALGORITHMS; BIOINFORMATICS; DATA STRUCTURES; MASS SPECTROMETRY; MOLECULAR BIOLOGY; TIME SERIES;

DATA MINING;

EID: 84863259465     PISSN: 10414347     EISSN: None     Source Type: Journal    
DOI: 10.1109/TKDE.2010.238     Document Type: Article

References (40)

1. R.E. Ardrey, Liquid Chromatography-Mass Spectrometry: An Introduction. John Wiley & Sons, 2003.
2. A.E. Ashcroft, "An Introduction to Mass Spectrometry," http:// www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm, 2011.
3. K.A. Baggerly, J.S. Morris, J. Wang, D. Gold, L.C. Xiao, and K.R. Coombes, "A Comprehensive Approach to the Analysis of Matrix-Assisted Laser Desorption/Ionization-Time of Flight Proteomics Spectra from Serum Samples," Proteomics, vol. 3, no. 9, pp. 1667-1672, 2003. (Pubitemid 37129810)
4. Analysis of Biological Data: A Soft Computing Approach, S. Bandyopadhyay, U. Maulik, and J.T.L. Wang, eds. World Scientific, 2007.
5. F.K.-P. Chan, A.W.-C. Fu, and C. Yu, "Haar Wavelets for Efficient Similarity Search of Time-Series: With and without Time Warping," IEEE Trans. Knowledge and Data Eng., vol. 15, no. 3, pp. 686-705, May/June 2003.
6. S. Chen, D. Hong, and Y. Shyr, "Wavelet-Based Procedures for Proteomic Mass Spectrometry Data Processing," Computational Statistics & Data Analysis, vol. 52, pp. 211-220, 2007. (Pubitemid 47331725)
7. Y. Chen, G. Dong, J. Han, ".W. Wah, and J. Wang, "Multi-Dimensional Regression Analysis of Time-Series Data Streams," Proc. 28th Int'l Conf. Very Large Data Bases, pp. 323-334, 2002.
8. C. Christin, A.K. Smilde, H.C.J. Hoefsloot, F. Suits, R. Bischoff, and P.L. Horvatovich, "Optimized Time Alignment Algorithm for LC-MS Data: Correlation Optimized Warping Using Component Detection Algorithm-Selected Mass Chromatograms," Analytical Chemistry, vol. 80, no. 18, pp. 7012-7021, 2008.
9. M.C. Codrea, C.R. Jimenez, S. Piersma, J. Heringa, and E. Marchiori, "Robust Peak Detection and Alignment of nanoLCFT Mass Spectrometry Data," Proc. Fifth European Conf. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, pp. 35-46, 2007.
10. K.R. Coombes, S. Tsavachidis, J.S. Morris, K.A. Baggerly, M.C. Hung, and H.M. Kuerer, "Improved Peak Detection and Quantification of Mass Spectrometry Data Acquired from Surface-Enhanced Laser Desorption and Ionization by Denoising Spectra with the Undecimated Discrete Wavelet Transform," Proteomics, vol. 5, no. 16, pp. 4107-4117, 2005. (Pubitemid 41626078)
11. I. Eidhammer, K. Flikka, L. Martens, and S.-O. Mikalsen, Computational Methods for Mass Spectrometry Proteomics, first ed. Wiley-Interscience, 2008.
12. M.G. Elfeky, W.G. Aref, and A.K. Elmagarmid, "Periodicity Detection in Time Series Databases," IEEE Trans. Knowledge and Data Eng., vol. 17, no. 7, pp. 875-887, July 2005. (Pubitemid 41049862)
13. A. Felinger, Data Analysis and Signal Processing in Chromatography. Elsevier Science, 1998.
14. T. Fushiki, H. Fujisawa, and S. Eguchi, "Identification of Biomarkers from Mass Spectrometry Data Using a Common Peak Approach," BMC Bioinformatics, vol. 7, article 358, 2006.
15. T. Hankemeier, J. Rozenbrand, M. Abhadur, J.J. Vreuls, and U.A.T. Brinkman, "Data Correlation in On-Line Solid-Phase Extraction-Gas Chromatography-Atomic Emission/Mass Spectrometric Detection of Unknown Microcontaminants," Chromatographia, vol. 48, pp. 273-283, 1998. (Pubitemid 28383471)
16. M. Karnstedt, D. Klan, C. Politz, K.U. Sattler, and C. Franke, "Adaptive Burst Detection in a Stream Engine," Proc. ACM Symp. Applied Computing, pp. 1511-1515, 2009.
17. M. Katajamaa and M. Oresic, "Processing Methods for Differential Analysis of LC/MS Profile Data," BMC Bioinformatics, vol. 6, no. 1, article 179, 2005.
18. E. Keogh, S. Lonardi, and W. Chiu, "Finding Surprising Patterns in a Time Series Database in Linear Time and Space," Proc. Eighth ACM SIGKDD Int'l Conf. Knowledge Discovery and Data Mining, 2002.
19. J. Kleinberg, "Bursty and Hierarchical Structure in Streams," Proc. Eighth ACM SIGKDD Int'l Conf. Knowledge Discovery and Data Mining, pp. 91-101, 2002.
20. J. Listgarten, R.M. Neal, S.T. Roweis, P. Wong, and A. Emili, "Difference Detection in LC-MS Data for Protein Biomarker Discovery," Bioinformatics, vol. 23, no. 2, pp. 198-204, 2007.
21. Z. Michalewicz and D.B. Fogel, How to Solve It: Modern Heuristics. Springer, 2002.
22. B.Y. Renard, M. Kirchner, H. Steen, J.A.J. Steen, and F.A. Hamprecht, "NITPICK: Peak Identification for Mass Spectrometry Data," BMC Bioinformatics, vol. 9, article 355, 2008.
23. D. Shasha and Y. Zhu, High Performance Discovery in Time Series: Techniques and Case Studies. Springer, 2004.
24. L. Singh and M. Sayal, "Privacy Preserving Burst Detection of Distributed Time Series Data Using Linear Transforms," Proc. IEEE Symp. Computational Intelligence and Data Mining, pp. 646-653, 2007. (Pubitemid 47431501)
25. R. Stolt, R.J.O. Torgrip, J. Lindberg, L. Csenki, J. Kolmert, I. Schuppe-Koistinen, and S.P. Jacobsson, "Second-Order Peak Detection for Multicomponent High-Resolution LC/MS Data," Analytical Chemistry, vol. 78, pp. 975-983, 2006. (Pubitemid 43271825)
26. M.H.M. van de Meent and G.J. de Jong, "Improvement of the Liquid-Chromatographic Analysis of Protein Tryptic Digests by the Use of Long-Capillary Monolithic Columns with UV and MS Detection," Analytical and Bioanalytical Chemistry, vol. 388, pp. 195-200, 2007. (Pubitemid 46712507)
27. M. Vlachos, C. Meek, Z. Vagena, and D. Gunopulos, "Identifying Similarities, Periodicities and Bursts for Online Search Queries," Proc. ACM SIGMOD Int'l Conf. Management of Data, pp. 131-142, 2004.
28. Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications, J.T.L. Wang, ".A. Shapiro, and D. Shasha, eds. Oxford Univ. Press, 1999.
29. Data Mining in Bioinformatics, J.T.L. Wang, M.J. Zaki, H.T.T. Toivonen, and D. Shasha, eds. Springer, 2005.
30. M. Wang, T. Madhyastha, N.H. Chan, S. Papadimitriou, and C. Faloutsos, "Data Mining Meets Performance Evaluation: Fast Algorithms for Modeling Bursty Traffic," Proc. 18th Int'l Conf. Data Eng., pp. 507-516, 2002. (Pubitemid 34278766)
31. J. Wong, G. Cagney, and H.M. Cartwright, "SpecAlign-Processing and Alignment of Mass Spectra Data Sets," Bioinformatics, vol. 21, pp. 2088-2090, 2005. (Pubitemid 40668050)
32. C. Yang, Z. He, and W. Yu, "Comparison of Public Peak Detection Algorithms for MALDI Mass Spectrometry Data Analysis," BMC Bioinformatics, vol. 10, article 4, 2009.
33. J. Yang, W. Wang, and P.S. Yu, "Mining Asynchronous Periodic Patterns in Time Series Data," IEEE Trans. Knowledge and Data Eng., vol. 15, no. 3, pp. 613-628, May/June 2003.
34. W. Yu, ". Wu, N. Lin, K. Stone, K. Williams, and H. Zhao, "Detecting and Aligning Peaks in Mass Spectrometry Data with Applications to MALDI," Computational Biology and Chemistry, vol. 30, pp. 27-38, 2006. (Pubitemid 43144429)
35. Z. Yuan, K. Du, Y. Jia, and J. Miao, "Stream Event Detection: A Unified Framework for Mining Outlier, Change and Burst Simultaneously over Data Stream," Proc. Seventh IEEE Int'l Conf. Data Mining-Workshops, pp. 575-580, 2007.
36. X. Zhang and D. Shasha, "Better Burst Detection," Proc. 22 Int'l Conf. Data Eng., p. 146, 2006. (Pubitemid 44539938)
37. A. Zhou, S. Qin, and W. Qian, "Adaptively Detecting Aggregation Bursts in Data Streams," Proc. 10th Int'l Conf. Database Systems for Advanced Applications, pp. 435-446, 2005. (Pubitemid 41274136)
38. Y. Zhu and D. Shasha, "StatStream: Statistical Monitoring of Thousands of Data Streams in Real Time," Proc. 28th Int'l Conf. Very Large Data Bases, pp. 358-369, 2002.
39. Y. Zhu and D. Shasha, "Warping Indexes with Envelope Transforms for Query by Humming," Proc. ACM SIGMOD Int'l Conf. Management of Data, pp. 181-192, 2003.
40. Y. Zhu and D. Shasha, "Efficient Elastic Burst Detection in Data Streams," Proc. Ninth ACM SIGKDD Int'l Conf. Knowledge Discovery and Data Mining, pp. 336-345, 2003.