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J Biomol Tech. 2007 February; 18(1): 6.
PMCID: PMC2291895

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.


Key to Abstract Numbering
Prefixes: P, Poster; RG, Research Group; SP, Scientific Session Presenter; EP, Educational Session Presenter.
Following the hyphen is the designated presentation day: S, Sunday; M, Monday; T, Tuesday.


1. Huber W, Von Heydebreck A, Sültmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002;18 suppl. 1:S96–S104 [PubMed]
2. Nishihara JC, Champion KM. Quantitative evaluation of proteins in one- and two-dimensional polyacrylamide gels using a fluorescent stain. Electrophoresis 2002;23:2203–2215 [PubMed]
3. Karp NA, Lilley KS. Maximising sensitivity for detecting changes in protein expression: Experimental design using Minimal CyDyes. Proteomics 2005;5 (12):3105. [PubMed]

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