A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Genomics, Proteomics and Bioinformatics

Volumn 10, Issue 6, 2012, Pages 336-344

  Natale, Massimo ^a,b   Caiazzo, Alfonso ^c   Bucci, Enrico M ^b,d   Ficarra, Elisa ^a  

^a POLITECNICO DI TORINO   (Italy)

^b BioDigitalValley Srl   (Italy)

^c WIAS Berlin   (Germany)

^d CNR   (Italy)

Author keywords

Image analysis; Proteomics; Software tools; Two dimensional gel electrophoresis

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; IMAGE ANALYSIS; NORMAL DISTRIBUTION; PROTEIN ANALYSIS; RELIABILITY; TWO DIMENSIONAL ELECTROPHORESIS; VALIDATION PROCESS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; IMAGE PROCESSING, COMPUTER-ASSISTED; NORMAL DISTRIBUTION; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 84872399436     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2012.06.005     Document Type: Article

References (21)

1. O'Farrel P.H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975, 250:4007-4021.
2. Görg A., Weiss W., Dunn M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4:3665-3685.
3. Miller I., Crawford J., Gianazza E. Protein stains for proteomic applications: which, when, why?. Proteomics 2006, 6:5385-5408.
4. Hortin G.L., Sviridov D. The dynamic range problem in the analysis of the plasma proteome. J Proteomics 2010, 73:629-636.
5. Millioni R., Puricelli L., Sbrignadello S., Iori E., Murphy E., Tessari P. Operator- and software-related post-experimental variability and source of error in 2-DE analysis. Amino Acids 2012, 42:1583-1590.
6. Clark B.N., Gutstein H.B. The myth of automated, high-throughput two-dimensional gel analysis. Proteomics 2008, 8:1197-1203.
7. Wheelock ÅM, Buckpitt A.R. Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 2005, 26:4508-4520.
8. dos Anjos A., Møller A.L., Ersbøll B.K., Finnie C., Shahbazkia H.R. New approach for segmentation and quantification of two-dimensional gel electrophoresis images. Bioinformatics 2011, 27:368-375.
9. Srinark T., Kambhamettu C. An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels. Electrophoresis 2008, 29:706-715.
10. Rashwan S, Faheem T, Sarhan A, Youssef BAB. A fuzzy-watershed based algorithm for protein spot detection in 2DGE images. In: Proceedings of the 9th WSEAS international conference on signal processing, computational geometry and artificial vision (ISCGAV'09), Stevens Point, Wisconsin, USA: World Scientific and Engineering Academy and Society (WSEAS); 2009 p. 35-40.
11. Daszykowski M., Bierczynska-Krzysik A., Silberring J., Walczak B. Avoiding spots detection in analysis of electrophoretic gel images. Chemometr Intell Lab Syst 2010, 104:2-7.
12. Berth M., Moser F.M., 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.
13. Maurer M.H. Software analysis of two-dimensional electrophoretic gels in proteomic experiments. Curr Bioinform 2006, 1:255-262.
14. Kim MA, Yoon YW. Spot detection of complex regions by accumulated gradient in two dimensional electrophoresis images. In: Proceedings of the 11th International Conference on Advanced Communication Technology (ICACT'09) 2009;3:1982-5, Piscataway, NJ, USA: IEEE Press.
15. Serackis A., Navakauskas D. Treatment of over-saturated protein spots in two-dimensional electrophoresis gel images. Informatica 2010, 21:409-424.
16. Matuzevičius D., Serackis A., Navakauskas D. Mathematical models of oversaturated protein spots. Electron Electr Eng 2007, 1:63-68.
17. Natale M., Maresca B., Abrescia P., Bucci E.M. Image analysis workflow for 2-D electrophoresis gels based on ImageJ. Proteomics Insights 2011, 4:37-49.
18. Maresca B., Cigliano L., Corsaro M.M., Pieretti G., Natale M., Bucci E.M., et al. Quantitative determination of haptoglobin glycoform variants in psoriasis. Biol Chem 2010, 391:1429-1439.
19. Kaczmarek K., Walczak B., de Jong S., Vandeginste B.G.M. Preprocessing of two-dimensional gel electrophoresis images. Proteomics 2004, 4:2377-2389.
20. Cannistraci C.V., Montevecchi F.M., Alessio M. Median-modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing. Proteomics 2009, 9:4908-4919.
21. Sternberg S. Biomedical image processing. IEEE Computer 1983, 16:22-34.