P15-T SameSpots: Validating a Novel Approach to 2D Electrophoresis Image Analysis.

2D-PAGE experiments can provide a powerful means of investigating protein expression behavior in a cell or tissue across different disease states or other experimental conditions. Traditional analysis of 2D experiments typically requires a large amount of post-detection editing in order to prepare the data for statistical research. With the application of SameSpots, all protein spots are fully matched and thus no missing values exist. This enables a more robust statistical exploration of the data with a reduction in subjective editing. The SameSpots workflow has a semi-automatic gel alignment step and uses the arcsinh transform introduced by Huber et al.1 for inter-gel calibration and variance stabilization (VSN). To validate these techniques we repeated the work of Nishihara and Champion2 and Karp and Lilley.3 The results of this study demonstrate that gel alignment has no adverse affect on spot volume quantitation, and we also show that VSN outperforms traditional normalization and variance stabilizing methods used in 2D gel analysis.