From Gels to Results

Two-dimensional gel electrophoresis is a fundamental technology of proteomics research. Thousands of proteins can be separated on a single gel, representing a large share of the proteins in a sample. By comparing gel images taken from different samples, one can find and later identify proteins that are crucial in fundamental processes of Life and in the progression of disease. However, the position of a protein spot may vary considerably from one gel to another. These variations make gel comparison a very tedious process, consuming a large share of the time to analyse an experiment.

In 2000, Delta2D, Version 1.0 introduced rapid visual comparison of 2D-electrophoresis gels. Delta2D uses advanced image processing technology to eliminate the variation between spot-positions. The result is one dual channel image with clearly highlighted differences in protein expression levels. The dual channel image allows for the rapid visual identification of whole sets of proteins whose expression varies from one sample to the other or is influenced by an experimental condition. Typically, Delta2D's approach speeds up the comparison process by a factor of five.

Spot detection and quantitation can be done in a subsequent step. Since the gels are aligned first, spot matching is extremely reliable and fully automatic. The results of the quantitation and matching step are presented in an easy to use tabular view that allows for a wide variety of analysis procedures.

Delta2D is used by researchers in industry and at academic institutions for a variety of tasks such as comparing diseased vs. control samples, analyzing genetic regulatory networks by controlled mutagenesis, and monitoring how a proteome changes over time.

Delta2D's process for gel comparison

In a nutshell, Delta2D's approach to comparing two gels is:
 

1. Load both images, they are automatically combined into one false color image
2. Mark a few pairs of corresponding spots
3. Globally Warp one gel image such that the initial match pairs are used for a global alignment
4. Mark a some more pairs of corresponding spots to compensate remaining distortions
5. Exactly Warp one gel image such that the match pairs are used for aligning the gel images exactly
6. repeat steps 4 and 5 if there are any unaligned spots left
7. Read the differences directly off the false color image. Red spots are stronger on gel A, green spots are stronger on gel B. Yellow spots have the same intensity on both gels. Shades of these colors correspond to intermediate values.
8. Detect and Quantify spots on both gels. This step is fully automatic, including spot matching.
9. Interpret results using Delta2D's flexible quantitation table. It allows for sorting and filtering on spot parameters and expression ratios as well as highlighting interesting spot sets on the gels.

Delta2D's process is very quick because you have to assign only a small fraction of the spots in order to get a perfectly aligned image - Delta2D's image processing technology does the rest. As a result, you recognize those interesting spots earlier and more accurately.