Two-dimensional electrophoresis has nurtured the birth of proteomics. It is however no longer the exclusive setup used in proteomics, with the development of shotgun proteomics techniques that appear more fancy and fashionable nowadays.Nevertheless, 2D gel-based proteomics still has valuable features, and sometimes unique ones, which make it often an attractive choice when a proteomics strategy...

One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in the organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear acids. Several experimental procedures have been tested to increase, in the nuclear extract, the ratio of nuclear proteins compared to contaminant proteins, ...

background and objectives: making stacking gels for polyacrylamide gels in the laboratory by conventional methods is laborious and time consuming. considering the role of temperature in polyacrylamide gels with respect to electrical resistance and viscosity, we assumed that decreasing the temperature would cause an increase in electrical resistance and viscosity.  ultimately, a downward tempera...

Various antibacterial factors in saliva have been demonstrated 2,1"2 la but none seem to have been isolated. A "lytic" agent in saliva and a purified lysozyme from eggwhite seem similar in their effect on Micrococcus Iysodeikticus,"9"' although the two have been shown to be immunologically distinct.10 Inasmuch as separation of protein elements in saliva, by means of paper electrophoresis, has b...

The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. In this paper, we will discuss a new concept of interpreting the 2D images and overcoming the aforementioned technical difficulties using mathematical transformation. T...

Two-dimensional gel electrophoresis (2-DE) technique is used as a performing technique to assess the variability of protein expression in crops, and especially soybean endogenous food allergens, which are a subset of proteins of interest for assessing whether genetically modified (GM) soybean has a different allergenic profile compared to its non-GM counterpart. On top of the biological variabi...

The recent trend in science is to assay as many biological molecules as possible within a single experiment. This trend is evident in proteomics where the aim is to characterize thousands of proteins within cells, tissues, and organisms. While advances in mass spectrometry have been critical, developments made in two-dimensional PAGE (2D-PAGE) have also played a major role in enabling proteomic...

This document briefly describes how to use the prot2D package. An R package designed to analyze (i.e. Normalize and select significant spots) data issued from 2D SDS PAGE experiments. prot2D provides a simple interface for analysing data from 2D gel experiments. Functions for normalization as well as selecting significant spots are provided. Furthermore, a function to simulates realistic 2D Gel...

The electrophoresis chromatography, a popular analysis tool, is able to separate different kinds of protein pro£les. In this paper, we present a robust comparative algorithm Maximum Relation Spanning Tree (MRST) for matching large scale and large sets of two dimensional protein gel electrophoresis (2DGE) chromatography images without the need of a priori landmark. The algorithm not only can han...

The goal of the two-dimensional (2D) electrophoresis protocol described here is to show how to analyse the phenotype of human cultured macrophages. The key role of macrophages has been shown in various pathological disorders such as inflammatory, immunological, and infectious diseases. In this protocol, we use primary cultures of human monocyte-derived macrophages that can be differentiated int...