One of the critical steps in two-dimensional electrophoresis (2-DE) image pre-processing is the denoising, that might aggressively affect either spot detection or pixel-based methods. The Median Modified Wiener Filter (MMWF), a new nonlinear adaptive spatial filter, resulted to be a good denoising approach to use in practice with 2-DE. MMWF is suitable for global denoising, and contemporary for the removal of spikes and Gaussian noise, being its best setting invariant on the type of noise. The second critical step rises because of the fact that 2-DE gel images may contain high levels of background, generated by the laboratory experimental procedures, that must be subtracted for accurate measurements of the proteomic optical density signals. Here we discuss an efficient mathematical method for background estimation, that is suitable to work even before the 2-DE image spot detection, and it is based on the 3D mathematical morphology (3DMM) theory.
This is a preview of subscription content, log in to check access.
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
M.A. is supported by AIRC Special Program Molecular Clinical Oncology 5 per mille n.9965. C.V.C. is supported by the independent group leader starting grant of the Technische Universität Dresden (TUD).
Dowsey AW, Dunn MJ, Yang GZ (2003) The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3:1567–1596CrossRefPubMedGoogle Scholar
Tsakanikas P, Manolakos I (2007) Effective denoising of 2D gel proteomics images using contourlets. Image Processing, 2007, ICIP 2007. IEEE International Conference on 2, 1–22Google Scholar
Marengo E, Robotti E, Antonucci F et al. (2005) Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems. Proteomics 5:654–666CrossRefPubMedGoogle Scholar
Kaczmarek K, Walczak B, de Jong S et al. (2005) Baseline reduction in two dimensional gel electrophoresis images. Acta Chromatogr 15:82–96Google Scholar
Morris JS, Clark BN, Gutstein HB (2008) Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics 24:529–536PubMedCentralCrossRefPubMedGoogle Scholar
Rogers M, Graham J, Tonge PR (2003) Using statistical image models for objective evaluation of spot detection in two-dimensional gels. Proteomics 3:879–886CrossRefPubMedGoogle Scholar
Appel RD, Palagi PM, Walther D et al. (1997) Melanie II–a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface. Electrophoresis 18:2724–2734CrossRefPubMedGoogle Scholar
Skolnick MM (1986) Application of morphological transformations to the analysis of two-dimensional electrophoretic gels of biological materials. Comput Vision Graphics Image Process 35:306–332CrossRefGoogle Scholar
Skolnick MM (1986) Special section on mathematical morphology: introduction. Comput Vision Graphics Image Process 35:281–282CrossRefGoogle Scholar
Cannistraci CV, Ravasi T, Montevecchi F et al. (2010) Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics 26:i1–i9CrossRefGoogle Scholar