Proteomics: 2D DIGE & Mass Spectrometry

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Data Analysis

The data analysis of a typical 2-D DIGE experiment consists of two main parts:

A. ImageQuant analysis: Gel images of individual samples and overlay of two sample images will be generated. In the overlay image, spots with green, red and yellow color indicate decreased, increased and similar expression, respectively.

Mutant

Overlay: WT / Mutant

Decreased

Increased

Similar

B. DeCyder DIA Analysis: Quantitative analysis and comparison of all spots between different samples. The differential protein expression is assessed by Differential In-gel Analysis (DIA), giving the high accuracy and reproducibility. The data will provide: 1) General statistic data (2 S.D. value, total spot number detected, number of decreased and increased spots etc.); 2) protein expression ratio (fold of change); 2) 3-D image view of the corresponding spot.

Upper left: Gel spot view (left: control, right: treated). Red: increased; Blue: decreased Orange: selected spot	Upper right: Spot distribution. threshold level, the number of spots that are increased, decreased and within the threshold.
		Threshold 2 S.D. value
		The height of a spot indicates the volume of the spot, the curves indicate the number of spots
		Selected spot
Lower left: 3D view. Characteristics of the selected spot	Lower right: Table view. All spots of interest. The fold change (increase of decrease) of each spot is indicated. The spot that shows at the 3D view is highlighted.

Examples: In-gel Image Analysis Using DeCyder Software

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