Improving mass spectrometry peak detection using multiple peak alignment results

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 123-129

  Yu, Weichaun ^a   He, Zengyou ^a   Liu, Junfeng ^b   Zhao, Hongyu ^c  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^b WEST VIRGINIA UNIVERSITY   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

Biomarker discovery; Mass spectrometry data analysis; Peak alignment; Peak detection

Indexed keywords

ARTICLE; DISEASE MARKER; FALSE POSITIVE RESULT; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION;

BIOLOGICAL MARKERS; MASS SPECTROMETRY; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 38649091017     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070370n     Document Type: Article

References (16)

1. Baggerly, K. A.; Morris, J. S.; Wang, J.; Gold, D.; Xiao, L. C.; Coombes, K. R. A comprehensive approach to the analysis of matrix-assisted laser desorpuon/ionization-time of flight proteomics spectra from serum samples. Proteomics 2003, 3, 1667-1672.
2. Coombes, K. R.; Fritsche, H. A., Jr.; Clarke, C.; Chen, J.; Baggerly, K. A.; Morris, J. S.; Xiao, L.; Hung, M.; Kuerer, H. M. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin. Chem. 2003, 49 (10), 1615-1623.
3. Coombes, K. R.; Tsavachidis, S.; Morris, J. S.; Baggerly, K. A.; Hung, M.; Kuerer, H. M. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising sepctra with the undecimated discrete wavelet transform. Proteomics 2005, 5, 107-4117.
4. Kononenko, I. Estimating attributes: Analysis and extensions of relief. In ECML, Lecture Notes in Computer Science; Francesco, B., Luc De, R., Eds.; Springer: New York, 1994; Vol. 784, pp. 171-182.
5. Morris, J. S.; Coombes, K. R.; Kooman, J.; Baggerly, K. A.; Kobayashi, R. Feature extraction and quantification for mass spectrometry data in biomedical applications using the mean spectrum. Bioinformatics 2005, 21 (9), 1764-1775.
6. Petricoin, E. F., III; M Ardekani, A.; A Hitt, B.; Levine, P. J.; Fusaro, V. A.; Steinberg, S. M.; Mills, G. B.; Simone, C.; Fishman, D. A.; C Kohnb, E.; Liottab, L. A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359 (9306), 572-577.
7. Satten, G. A.; Datta, S.; Moura, H.; Woolfitt, A. R.; Carvalho, G.; Facklam, R.; Barr, J. R. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics 2004, 20 (17), 3128-3136.
8. Tibshirani, R.; Hastie, T.; Narasimhan, B.; Soltys, S.; Shi, G.; Koong, A.; Le, Q. Sample classification from protein mass spectrometry, by "peak probability contrasts". Bioinformatics 2004, 20 (17), 3034-3044.
9. Wadsworth, J. T.; Somers, K. D.; Cazares, L. H.; Malik, G.; Adam, B. L.; Stack, B. C., Jr.; Wright, G. L., Jr.; Semmes, O. J. Serum protein profiles to identify head and neck cancer. Clin. Cancer Res. 2004, 10 (5), 1625-1632.
10. Wagner, M.; Naik, D.; Pothen, A. Protocols for disease classification from mass spectrometry data. Proteomics 2003, 3 (9), 1692-1698.
11. Witten, I. H.; Frank, E. Data Mining-Practical Machine Learning Tooh and Techniques with JAVA Implementations, 2nd ed.; Morgan Kaufmann Publishers; San Francisco, CA, 2005.
12. Wu, B.; Abbott, T.; Fishman, D.; McMurray, W.; Mor, G.; Stone, K.; Ward, D.; Williams, K.; Zhao, H. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 2003, 19, 1636-1643.
13. Yasui, Y.; Pepe, M.; Thompson, M. L.; Adam, B.; Wright, G. L., Jr.; Qu, Y.; Potter, J. D.; Winget, M.; Thornquist, M.; Feng, Z. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics 2003, 4 (3), 449-463.
14. Yu, W.; Li, X.; Liu, J.; Wu, B.; Williams, K.; Zhao, H. Multiple peak alignment in sequential data analysis: A scale-space based approach. IEEE/ACM Trans. Comput. Biol. Bioinf. 2006, 3 (3), 208-219.
15. Yu, W.; Wu, B.; Lin, N.; Stone, K.; Williams, K.; Zhao, H. Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Computat. Biol Chem. 2006, 30, 27-38.
16. Yu, W.; Wu, B.; Liu, J.; Li, X.; Williams, K.; Zhao, H. MALDI-MS data analysis for disease biomarker discovery. In New and Emerging Proteomics Techniques; Humana Press, Inc.: Tolowa, NJ, 2006; Chapter 14, 199-216