Analysis of mass spectral serum profiles for biomarker selection

Bioinformatics

Volumn 21, Issue 21, 2005, Pages 4039-4045

  Ressom, Habtom W ^a   Varghese, Rency S ^a   Abdel Hamid, Mohamed ^b   Eissa, Sohair Abdel Latif ^c   Saha, Daniel ^a   Goldman, Lenka ^a   Petricoin, Emanuel F ^d   Conrads, Thomas P ^e   Veenstra, Timothy D ^e   Loffredo, Christopher A ^a   Goldman, Radoslav ^a  

^a GEORGETOWN UNIVERSITY   (United States)

^b NHTMRI   (Egypt)

^c NATIONAL CANCER INSTITUTE   (Egypt)

^d NATIONAL CANCER INSTITUTE   (United States)

^e SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ACCURACY; ALGORITHM; ARTICLE; BLOOD ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DISEASE ASSOCIATION; HEPATITIS C; HUMAN; INFORMATION PROCESSING; LIVER CELL CARCINOMA; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PREDICTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN DATABASE; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

HEPATITIS C VIRUS;

EID: 27744595524     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti670     Document Type: Article

References (26)

1. Baggerly,K.A. et al. (2004) Reproducibility of SELDI-TOF protein patterns in serum: Comparing datasets from different experiments. Bioinformatics, 20, 777-785.
2. Baggerly,K.A. et al. (2003) A comprehensive approach to the analysis of MALDI-TOF proteomics spectra from serum samples. Proteomics, 3, 1667-1672.
3. Conrads,T.P. et al. (2004) High-resolution serum proteomic features for ovarian cancer detection. Endocr. Relat. Cancer, 11, 163-178.
4. Coombes,K.R., Tsavachidis,S., Morris,J.S., Baggerly,K.A., Hung,M.C. and Kuerer,H.M. (2004) 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. Technical Report UTMDABTR-001-04; The University of Texas MD Anderson Cancer Center, http://www.mdanderson.org/pdf/ biostats_utmdabtr-001-04.pdf.
5. Diamandis,E.P. (2004) Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: Opportunities and potential limitations. Mol. Cell Proteomics, 3, 367-378.
6. Eilers,P.H.C. and Marx,B.D. (1996) Flexible smoothing with B-splines and penalties, Stat. Sci., 11, 89-121.
7. Ezzat,S. et al. (2005) Associations of pesticides, HCV, HBV, and hepatocellular carcinoma in Egypt. Int. J. Hygiene Env. Health (in press).
8. Fung,E.T. and Enderwick,C. (2002) ProteinChip clinical proteomics: computational challenges and solutions. Biotechniques, 32(suppl.), 34-41.
9. Koomen,J.M. et al. (2005) Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin. Cancer Res., 11, 1110-1118.
10. Koopmann,J. et al. (2004) Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry. Clin. Cancer Res., 10, 860-868.
11. Li,J. et al. (2002) Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 48, 1296-1304.
12. Malyarenko,D.I. 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, 65-74.
13. Paradis,V. et al. (2005) Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology, 41, 40-47.
14. Petricoin,E.F. et al. (2002a) Use of proteomic patterns in serum to identify ovarian cancer. Lancet, 359, 572-577.
15. Petricoin,E.F. et al. (2002b) Serum proteomic patterns for detection of prostate cancer. J. Natl Cancer Inst., 94, 1576-1578.
16. Petricoin,E.F. et al. (2004) Proteomic pattern diagnostics: Producers and consumers in the era of correlative science. BMC Bioinformatics, 4, http://www.biomedcentral.com/1471-2105/4/24/comments.
17. Pusztai,L. et al. (2004) Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer, 100, 1814-1822.
18. Ransohoff,D.F. (2005) Bias as a threat to the validity of cancer molecular-marker research. Nat. Rev. Cancer, 5, 142-149.
19. Ressom,H., Varghese,R.S., Saha,D., Orvisky,E., Goldman,L., Petricoin,E.F., Conrads,T.P., Veenstra,T.D., Abdel-Hamid,M., Loffredo,C.A. and Goldman,R. (2005) Particle swarm optimization for analysis of mass spectral serumprofiles. In Beyer,H.G. et al. (eds), Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005, ACM Press, NY, Vol. 1, pp. 431-438.
20. Sauve,A.C. and Speed,T.P. (2004) Normalization, baseline correction and alignment of high-throughput mass spectrometry data. Proceedings of the Genomic Signal Processing and Statistics workshop, Baltimore, MO, USA, May 26-27, 2004. http://stat-www.berkeley.edu/users/terry/Group/ publications/Final2Gensips2004Sauve.pdf.
21. Semmes,O.J. et al. (2005) Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin. Chem., 51, 102-112.
22. Sorace,J.M. and Zhan,M. (2003) A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC. Bioinformatics, 4, 24.
23. Villanueva,J. et al. (2004) Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem., 76, 1560-1570.
24. Yasui,Y. et al. (2003) A data-analytic strategy for protein biomarker discovery: Profiling of high-dimensional proteomic data for cancer detection. Biostatistics, 4, 449-463.
25. Zhang,Z. et al. (2004) Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res., 64, 5882-5890.
26. Zhu,W. et al. (2003) Detection of cancer-specific markers amid massive mass spectral data. Proc. Natl Acad. Sci. USA, 100, 14666-1467.