The role of bioinformatics in two‐dimensional gel electrophoresis

Abstract

Over the last two decades, two-dimensional electrophoresis (2-DE) gel has established itself as the de facto approach to separating proteins from cell and tissue samples. Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research topic. The results of these analyses include accurate protein quantification, isoelectric point and relative molecular mass estimation, and the detection of differential expression between samples run on different gels. Systematic errors such as current leakage and regional expression inhomogeneities are corrected for, followed by each protein spot in the gel being segmented and modelled for quantification. To assess differential expression of protein spots in different samples run on a series of two-dimensional gels, a number of image registration techniques for correcting geometric distortion have been proposed. This paper provides a comprehensive review of the computation techniques used in the analysis of 2-DE gels, together with a discussion of current and future trends in large scale analysis. We examine the pitfalls of existing techniques and highlight some of the key areas that need to be developed in the coming years, especially those related to statistical approaches based on multiple gel runs and image mining techniques through the use of parallel processing based on cluster computing and the grid technology.

Development and application of proteomics technologies in Saccharomyces cerevisiae

“…In this way, changes in individual protein spots can be detected and quantified. Several commercially available software packages have been developed to perform the image analysis of 2D gels (for a review, see [42]). …”

MAQ – A Bioinformatics Tool for Automatic Macroarray Analysis

“…For instance, the field Area is the result of the multiplication of the number of pixels of the spot by the area of each pixel. The area of each pixel is calculated from the resolution of the image and that is done automatically without the (3,5) need to input the resolution of the image or the size of a pixel. The column Integrated Intensity, also called Optical Density in other publications [5], is calculated by x,y I(x, y), with I(x, y) representing the graylevel intensity at the coordinates x and y.…”

The Use of Proteomics in Assisted Reproduction

“…In typical 2-D electrophoresis, proteins are separated according to their electric charge (isoelectric point-IP) through isoelectric focusing (IEF) and according to their molecular mass on a polyacrylamide gel containing sodium dodecyl sulfate (SDS-PAGE) and are subsequently visualized through staining (19). Acquired gel images are digitalized and further analyzed through computers for protein volume or intensity quantification (20). Other techniques, such as highperformance liquid chromatography (HPLC) or affinity chromatography, or capillary electrophoresis can be useful tools in analytical proteomics, especially when integrating different protein and peptide separations, as multidimensional techniques (MudPIT) (21).…”