Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies - COPD biomarker discovery study

Proteomics

Volumn 8, Issue 15, 2008, Pages 3030-3041

  Bandow, Julia E ^a,e   Baker, John D ^a   Berth, Matthias ^b   Painter, Cory ^a   Sepulveda, Osvaldo J ^c   Clark, Kelly A ^a   Kilty, Iain ^d   VanBogelen, Ruth A ^a  

^a PFIZER INC   (United States)

^b DECODON GmbH   (Germany)

^c UNIVERSITY OF TOLEDO   (United States)

^d PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^e RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

2 D gel image analysis; Biomarker; Chronic obstructive pulmonary disease

Indexed keywords

APOLIPOPROTEIN E; BIOLOGICAL MARKER; COMPLEMENT COMPONENT C3; COMPLEMENT COMPONENT C4B; FIBRINOGEN; GLUTATHIONE PEROXIDASE; INTER ALPHA TRYPSIN INHIBITOR; RETINOID BINDING PROTEIN; THIOREDOXIN PEROXIDASE;

AMINO ACID SEQUENCE; ARTICLE; BLOOD SAMPLING; CHRONIC OBSTRUCTIVE LUNG DISEASE; CIGARETTE SMOKING; CONSENSUS; CONTROLLED STUDY; HUMAN; IMAGE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BIOLOGICAL MARKERS; BLOOD PROTEINS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; IMAGE PROCESSING, COMPUTER-ASSISTED; PRINCIPAL COMPONENT ANALYSIS; PROTEOMICS; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; SMOKING;

EID: 49749123013     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200701184     Document Type: Article

References (39)

1. O'Farrell, P. H., High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021.
2. Görg, A., Postel, W., Günther, S., The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 1988, 9, 531-546.
3. Tonge, R., Shaw, J., Middleton, B., Rowlinson, R. et al., Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1, 377-396.
4. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C. et al., Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 1993, 90, 5011-5015.
5. Garrels, J. I., Two-dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. J. Biol. Chem. 1979, 254. 7961-7977.
6. Lemkin, P. F., Lipkin, L. E., GELLAB: A computer system for two-dimensional gel electrophoresis analysis. III. Multiple two-dimensional gel analysis. Comput. Biomed. Res. 1981, 14, 407-446.
7. Gosset, W. S. (under pseudonym "Student"), The probable error of a mean. Biometrika 1908, 6, 1-25.
8. Fisher, R. A., Applications of Student's distribution. Metron 1925, 5, 90-104.
9. Benjamini, Y., Hochberg, Y., Controlling the False Discovery Rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 1995, 57, 289-300.
10. Berth, M., Moser, F., Kolbe, M., Bernhardt, J., The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl. Microbiol. Biotechnol. 2007, 76, 1223-1243.
11. Takacs, L., Szende, B., Monostori, E., Rot, A. et al., Expression of HLA-DR antigens on bileduct cells of rejected liver transplant. Lancet 1983, 2, 1500.
12. Luhn, S., Berth, M., Hecker, M., Bernhardt, J., Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics 2003, 3, 1117-1127.
13. Wold, S., Esbensen, K., Geladi, P., Principal component analysis. Chemom. Intell. Lab. Syst. 1987, 2, 37-52.
14. Wheelock, Å. M., Buckpitt, A. R., Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 2005, 26, 4508-4520.
15. Eravci, M., Fuxius, S., Broedel, O., Weist, S. et al., Improved comparative proteome analysis based on two-dimensional gel electrophoresis. Proteomics 2007, 7, 513-523.
16. Molloy, M. P., Brzezinski, E. E., Hang, J., McDowell, M. T., VanBogelen, R. A., Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003, 3, 1912-1919.
17. Karp, N. A., Kreil, D. P., Lilley, K. S., Determining a significant change in protein expression with DeCyder™ during a pairwise comparison using two-dimensional difference gel electrophoresis. Proteomics 2004, 4, 1421-1432.
18. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., Gygi, S. P., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 2003, 100, 6940-6945.
19. Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B. et al., Mass spectrometry quantitation of peptides and proteins using stable isotope standards and capture by antipeptide antibodies (SISCAPA). J. Proteome Res. 2004, 3, 235-244.
20. Winkler, M. F., Gerrior, S. A., Pomp, A., Albina, J. E., Use of retinol-binding protein and prealbumin as indicators of the response to nutrition therapy. J. Am. Diet Assoc. 1989, 89, 684-687.
21. Paiva, S. A., Godoy, I., Vannucchi, H., Favaro, R. M. et al., Assessment of vitamin A status in chronic obstructive pulmonary disease patients and healthy smokers. Am. J. Clin. Nutr. 1996, 64, 928-934.
22. Piitulainen, E., Areberg, J., Linden, M., Eriksson, S. et al., Nutritional status and muscle strength in patients with emphysema and severe alpha(1)-antitrypsin deficiency. Chest 2002, 122, 1240-1246.
23. Sergi, G., Coin, A., Marin, S., Vianello, A. et al., Body composition and resting energy expenditure in elderly male patients with chronic obstructive pulmonary disease. Respir. Med. 2006, 100, 1918-1924.
24. Rahman, I., Biswas, S. K., Kode, A., Oxidant and antioxidant balance in the airways and airway diseases. Eur. J. Pharmacol. 2006, 533, 222-239.
25. Jornot, L., Junod, A. F., Response of human endothelial cell antioxidant enzymes to hyperoxia. Am. J. Respir. Cell Mol. Biol. 1992, 6, 107-115.
26. Roum, J. H., Aledia, A. S., Carungcong, L. A., Kim, K. J., Borok, Z., Extracellular glutathione inhibits oxygen-induced permeability changes in alveolar epithelial monolayers. J. Appl. Physiol. 2001, 91, 748-754.
27. Liao, M. F., Chen, C. C., Hsu, M. H., Evaluation of the serum antioxidant status in asthmatic children. Acta Paediatr. Taiwan 2004, 45, 213-217.
28. Dauletbaev, N., Rickmann, J., Viel, K., Diegel, H. et al., Antioxidant properties of cystic fibrosis sputum. Am. J. Physiol. Lung Cell. Mol. Physiol. 2005, 288, 903-909.
29. Lehtonen, S. T., Svensk, A. M., Soini, Y., Paakko, P. et al., Peroxiredoxins, a novel protein family in lung cancer. Int. J. Cancer 2004, 111, 514-521.
30. Donaldson, G. C., Seemungal, T. A., Patel, I. S., Bhowmik, A. et al., Airway and systemic inflammation and decline in lung function in patients with COPD. Chest 2005, 128, 1995-2004.
31. Weitz, J. I., Leslie, B., Ginsberg, J., Soluble fibrin degradation products potentiate tissue plasminogen activator-induced fibrinogen proteolysis. J. Clin. Invest. 1991, 87, 1082-1090.
32. Kunter, E., Ilvan, A., Ozmen, N., Demirer, E. et al., Effect of corticosteroids on hemostasis and pulmonary arterial pressure during chronic obstructive pulmonary disease exacerbation. Respiration 2008, 75, 145-154.
33. Miller, R. D., Kueppers, F., Offord, K. P., Serum concentrations of C3 and C4 of the complement system in patients with chronic obstructive pulmonary disease. J. Lab. Clin. Med. 1980, 95, 266-271.
34. Kosmas, E. N., Zorpidou, D., Vassilareas, V., Roussou, T., Michaelides, S., Decreased C4 complement component serum levels correlate with the degree of emphysema in patients with chronic bronchitis. Chest 1997, 112, 341-347.
35. Martins, I. J., Hone, E., Foster, J. K., Sunram-Lea, S. I. et al., Apolipoprotein E, cholesterol metabolism, diabetes, and the convergence of risk factors for Alzheimer's disease and cardiovascular disease. Mol. Psychiatry 2006, 11, 721-736.
36. Curkendall, S. M., DeLuise, C., Jones, J. K., Lanes, S. et al., Cardiovascular disease in patients with chronic obstructive pulmonary disease, Saskatchewan Canada cardiovascular disease in COPD patients. Ann. Epidemiol. 2006, 16, 63-70.
37. Basili, S., Ferroni, P., Vieri, M., Cardelli, P. et al., Lipoprotein(a) serum levels in patients affected by chronic obstructive pulmonary disease. Atherosclerosis 1999, 147, 249-252.
38. Pineiro, M., Alava, M. A., Gonzales-Ramon, N., Osada, J. et al., ITIH4 serum concentration increases during acute-phase processes in human patients and is up-regulated by interleukin-6 in hepatocarcinoma HepG2 cells. Biochem. Biophys. Res. Commun. 1999, 263, 224-229.
39. Fujita, Y., Ezura, Y., Emi, M., Sato, K. et al., Hypercholesterolemia associated with splice-junction variation of inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) gene. J. Hum. Genet. 2004, 49, 24-28.