Multispectra CWT-Based Algorithm (MCWT) in Mass Spectra for Peak Extraction

REFERENCES

• Adam , B. L. , Qu , Y. , Davis , J. W. , Ward , M. D. , Clements , M. A. , Cazares , L. H. , Semmes , O. J. , Schellhammer , P. F. , Yasui , Y. , Feng , Z. , Wright , G. L. , Jr . ( 2002 ). Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men . Cancer Res. 62 : 3609 – 3614 .
   PubMed Web of Science ®Google Scholar
• Baggerly , K. A. , Morris , J. S. , Edmonson , S. R. , Coombes , K. R. ( 2005 ). Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer . J. Natl. Cancer Inst. 97 : 307 – 309 .
   PubMed Web of Science ®Google Scholar
• CAMDA ( 2006 ). CAMDA 2006 Competition Data Set. http://camda.duke.edu://camda.duke.edu
   Google Scholar
• Clarke , C. H. , Buckley , J. A. , Fung , E. T. ( 2005 ). SELDI-TOF-MS proteomics of breast cancer . Clin. Chem. Lab. Med. 43 : 1314 – 1320 .
   PubMed Web of Science ®Google Scholar
• Coombes , K. R. , Tsavachidis , S. , Morris , J. S. , Baggerly , K. A. , Hung , M.-C. , Kuerer , H. M. ( 2005 ). 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 5 : 4107 – 4117 .
   PubMed Web of Science ®Google Scholar
• Diamandis , E. P. ( 2004 ). Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems . J. Natl. Cancer Inst. 96 : 353 – 356 .
   PubMed Web of Science ®Google Scholar
• Du , P. , Kibbe , W. A. , Lin , S. M. ( 2006 ). Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching . Bioinformatics 22 : 2059 – 2065 .
   PubMed Web of Science ®Google Scholar
• Gentleman , R. , Vandal , A. C. ( 2001 ). Computational algorithms for censored data problems using intersection graphs . J. Comput. Graph. Stat. 10 : 403 – 421 .
   Web of Science ®Google Scholar
• Li , J. , Zhang , Z. , Rosenzweig , J. , Wang , Y. Y. , Chan , D. W. ( 2002 ). Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer . Clin. Chem. 48 : 1296 – 1304 .
   PubMed Web of Science ®Google Scholar
• Malik , G. , Ward , M. D. , Gupta , S. K. , Trosset , M. W. , Grizzle , W. E. , Adam , B. L. , Diaz , J. I. , Semmes , O. J. ( 2005 ). Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer . Clin. Cancer Res. 11 : 1073 – 1085 .
   PubMed Web of Science ®Google Scholar
• Morris , J. S. , Coombes , K. R. , Koomen , J. , Baggerly , K. A. , Kobayashi , R. ( 2005 ). Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum . Bioinformatics 21 : 1764 – 1775 .
   PubMed Web of Science ®Google Scholar
• Petricoin , E. F. , Liotta , L. A. ( 2004 ). SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer . Curr. Opin. Biotechnol. 15 : 24 – 30 .
   PubMed Web of Science ®Google Scholar
• Petricoin , E. F. , Fishman , D. A. , Conrads , T. P. , Veenstra , T. D. , Liotta , L. A. ( 2004 ). Lessons from Kitty Hawk: from feasibility to routine clinical use for the field of proteomic pattern diagnostics . Proteomics 4 : 2357 – 2360 .
   PubMed Web of Science ®Google Scholar
• Semmes , O. J. , Feng , Z. , Adam , B. L. , Banez , L. L. , Bigbee , W. L. , et al. . ( 2005 ). Evaluation of serum protein profiling by surface-enhanced laser desorptionionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility . Clin. Chem. 51 : 102 – 112 .
   PubMed Web of Science ®Google Scholar
• Tibshirani , R. , Hastie , T. , Narasimhan , B. , Soltys , S. , Shi , G. , Koong , A. , Le , Q.-T . (2004). Sample classification from protein mass spectrometry, by ‘peak probability contrast’. Bioinformatics 20:3034–3044.
   PubMedGoogle Scholar
• Wong , J. W. H. , Cagney , G. , Cartwright , H. M. ( 2005 ). SpecAlign-processing and alignment of mass spectra datasets . Bioinformatics 21 : 2088 – 2090 .
   PubMed Web of Science ®Google Scholar
• Yasui , Y. , Pepe , M. , Thompson , M. L. , Adam , B.-L. , Wright , G. L. , Jr. , Qu , Y. , Potter , J. D. , Winget , M. , Thornquist , M. , Feng , Z. ( 2003 ). A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection . Biostatistics 4 : 449 – 463 .
   PubMed Web of Science ®Google Scholar