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DeCyder 2-D Differential Analysis Software v7.2

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DeCyder 2D 7.2 SPN 1 concurrent network license

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.

  • Fully optimized and integrated to the 2-D DIGE platform.
  • DeCyder extended data analysis (EDA), a multivariate statistics module for easier and faster biomarker discovery, included as standard.
  • Automatic Oracle client and server installation, offering easy project handling and data security.
  • No spot matching within gels, eliminating matching errors.
  • Internal standard approach, increasing accuracy and simplifying gel-to-gel matching.
  • Spike Protein Normalization (SPN) is available as an integrated component of the DeCyder package
  • Windows 7 compatible
  • Automated analysis, significantly reducing hands-on time.

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:

  • Differential In-gel Analysis (DIA) co-detection, background subtraction, normalization, and quantitation of spots in images from a single 2-D DIGE gel.

  • Biological Variation Analysis (BVA) matching multiple 2-D DIGE gels for comparison and statistical analysis of protein abundance changes.

  • Extended Data Analysis (EDA) providing advanced statistical analysis for characterization and classification of biological samples based on protein expression data.

  • Batch Processor automated detection, quantitation, matching, and comparison of multiple 2-D DIGE gels.

  • Image Loader importing images into an Oracle database.

  • Administration tools database administration, maintenance, and user access control.

  • XML toolbox exporting spot data from DIA or BVA modules for further downstream analysis

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.

References

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, 3644 (2003).
2. Yan, J. X. et al. Fluorescence 2-D Difference Gel Electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2, 16821698 (2002).
3. Unlu, M. et al. Difference gel electrophoresis: a single method for detecting changes in protein extracts. Electrophoresis 18, 20712077 (1997).
4. Tonge, R. P. et al. Validation and development of fluorescence two-dimensional difference gel electrophoresis proteomics technology. Proteomics 1, 377396 (2001).

DeCyder 2D 7.2 SPN 1 concurrent network license

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