2D DIGE data analysis for differential protein spot identification

Differential in-gel electrophoresis (DIGE) technique has been used for differential protein analysis to improve the reproducibility of comparative 2D gel experiments. Because the sample size in 2D DIGE experiments is usually very small, the traditional statistical methods such as student t-test could not provide an accurate and reliable detection/identification of differentially expressed protein spots. This paper proposed a ranking based approach for DE protein spot identification, in which the information of comparative ranks of the protein spot volume ratio rather than their distribution were used in selection. Two methods were designed to integrate the ranking information from a set of pair-wise comparisons. The evaluation results demonstrated that the proposed methods are effective in DE protein spot identification when sample size is small.