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DeCyder 2-D Differential Analysis Software 7.2 is specifically designed for 2-D fluorescence difference gel electrophoresis (DIGE) analysis and is a key element in the Ettan DIGE system. Fully optimized and integrated to the 2-D DIGE platform.
DeCyder 2-D Differential Analysis Software (DeCyder 2D) v7.2 is specifically designed for 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE)analysis and is a key element in the EttanTM DIGE system. Unlike other 2-D electrophoresis methods, DIGE allows the option of reference to an internal standard for each spot, effectively eliminating gel-to-gel variation and delivering highly accurate, reproducible, and dependable quantitation. DeCyder 2D applies a gel comparison method that introduces zero statistical error, offering reliable data and analysis for 2-D DIGE experiments.
DeCyder 2-D v7.2 consists of several modules:
DeCyder 2D v7.2 includes functionalities not present in previous versions. An integrated image editor enables preparation of raw images (cropping, rotating, etc.) prior to analysis and also allows high-resolution images to be exported. The warping function improves matching accuracy and simplifies the evaluation of matching results. Improved gel image functionality includes gel overlay for match editing and additional spot editing functions. The "save as" feature allows data to be saved at any stage of the process
The DeCyder EDA module, standard in DeCyder 2D v7.2, offers support throughout the statistical analyses of 2-D DIGE data, with no requirement for statistical expertise. DeCyder EDA provides multivariate statistics tools for easy and fast data mining of 2-D DIGE data. The software enables the combined analysis of different datasets, aiding the biological interpretation of results by matching with data retrieved from public and local databases
DeCyder 7.2 includes a new functionality, available as an option, to normalize abundance values using proteins added as spikes (Spike Protein Normalization, SPN). This function complements the present model-based normalization. SPN is suitable for applications with samples that have few protein spots or samples where the majority of the proteins differ in abundance (or expression level) between sample groups. Prerequisite for the function is that one or several spike proteins are added to samples prior to CyDye labeling.
1. Alban, A. et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 3644 (2003).
2. Yan, J. X. et al. Fluorescence 2-D Difference Gel Electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2, 16821698 (2002).
3. Unlu, M. et al. Difference gel electrophoresis: a single method for detecting changes in protein extracts. Electrophoresis 18, 20712077 (1997).
4. Tonge, R. P. et al. Validation and development of fluorescence two-dimensional difference gel electrophoresis proteomics technology. Proteomics 1, 377396 (2001).
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