DeCyder

Eight significantly regulated proteins are indicated by arrows and respective spot number. In the zoomed sections two differentially regulated proteins white box) are displayed in 3D view obtained with the DeCyder software. 

Erom the DeCyder software it is possible to find the background-subtracted spot volumes, i.e., for a single spot the lowest lOfh percentile pixel values on the spot boundary have been excluded. Several features of this raw data require calibration and normalization prior to statistical analysis. The volume values are affected by dye-specific system gains and constant additive biases. In figure 3.10 the Cy5 and Cy3 spot volumes of one gel are plotted against each other. It can clearly be seen that the difference between Cy5 and Cy3 spot volumes increases when the spot volumes increase. 

Determining a significant change in protein expression with DeCyder during a pairwise comparison using two-dimensional difference gel electrophoresis. Proteomics 4, 1421-1432. 

Key Words Difference Gel Electrophoresis multiplexing fluorescent labeling two-dimensional gel electrophoresis DeCyder DIGE. 

A key feature of DeCyder 2-D is the ability to compare not just two samples (e.g., control and treated) but an unlimited number of samples (e.g., time 0, time 1, time 2,...) within the same experiment. This increases the ability to design a complex experiment on the least number of gels and allow intra-sample comparisons between any groups within the same experiment. An example of an experiment containing multiple samples can be seen in Fig. 3. On the basis of the analysis, spots of interest can be assigned for spot picking and a pick list can be exported. 

Fig. 3. Data from a 2-D difference gel electrophoresis (DICE) experiment can be viewed in a number of ways in DeCyder 2-D, including 2-D spot maps, 3-D images visualizing specific spot intensities, and graphical depiction comparing the abundance of each matched spot across the samples in the experiment. This experiment compared lung tissue (universal control, UC) against tissue exposed to smoke (Smoke) and tissue exposed to smoke in the presence of an inhibitor (Ini or In2). All possible t-test and average ratio values can be calculated very easily as shown for this spot. Unpublished data from samples kindly provided by Dr. Koustubh Panda, Cleveland Clinic Foundation.

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