An improved pixel‐based approach for analyzing images in two‐dimensional gel electrophoresis

An improved pixel‐based approach for analyzing 2‐DE images is presented. The key feature of the method is to create a mask based on all gels in the experiment using image morphology, followed by multivariate analysis on the pixel level. The method reduces the impact of noise and background by identifying regions in the image where protein spots are present, but make no assumption on individual spot boundaries for isolated spots. This makes it possible to detect significant changes in complex regions, and visualize these changes over multiple gels in an easy way. False missing values and spot volumes caused by imposing erroneous spot boundaries are thus circumvented. The approach presented gives improved pixel‐based information from the gels, and is also an alternative to existing methods for data‐reduction, significance testing and visualization of 2‐DE data. Results are compared with software using a common spot boundary approach on an experiment consisting of 35 full size gel images. Gel alignment is required before analysis.

[1]  D. Baunsgaard,et al.  Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis , 2004, Proteomics.

[2]  Bo Jørgensen,et al.  Extractin information from two‐dimensional electrophoresis gels by partial least squares regression , 2002 .

[3]  Fabio Pastorino,et al.  Spot overlapping in two‐dimensional maps: A serious problem ignored for much too long , 2005, Proteomics.

[4]  Emilio Marengo,et al.  New approach based on fuzzy logic and principal component analysis for the classification of two-dimensional maps in health and disease. Application to lymphomas. , 2003, Journal of chromatography. A.

[5]  Michael M Skolnick Application of morphological transformations to the analysis of two-dimensional electrophoretic gels of biological materials , 1986 .

[6]  J. Bernhardt,et al.  Using standard positions and image fusion to create proteome maps from collections of two‐dimensional gel electrophoresis images , 2003, Proteomics.

[7]  A. Mahadevan-Jansen,et al.  Automated Method for Subtraction of Fluorescence from Biological Raman Spectra , 2003, Applied spectroscopy.

[8]  Beata Walczak,et al.  Pixel‐based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2‐D electrophoresis gel images , 2007 .

[9]  Susanne Jacobsen,et al.  Explorative data analysis of two‐dimensional electrophoresis gels , 2004, Electrophoresis.

[10]  Stanley R Sternberg,et al.  Grayscale morphology , 1986 .

[11]  Emilio Marengo,et al.  Identification of the regulatory proteins in human pancreatic cancers treated with Trichostatin A by 2D-PAGE maps and multivariate statistical analysis , 2004, Analytical and bioanalytical chemistry.

[12]  Francesca Antonucci,et al.  Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems , 2005, Proteomics.

[13]  Harald Martens,et al.  Challenges related to analysis of protein spot volumes from two-dimensional gel electrophoresis as revealed by replicate gels. , 2006, Journal of proteome research.