PDQuest 3 2-D Analysis Software From Bio-Rad

PDQuest 3 2-D Analysis Software From Bio-Rad
PDQuest has been on the market for at least 6 years. To use the program, users first upload images to the software, and then PDQuest automatically detects the spots for each image according to parameters set by the user. After detection, automated matching of spots between gels is performed. Then, the user will need to manually ensure the matching was done correctly. After matching, users can perform data analysis using the analysis manger (i.e. t-test, fold change, etc). Users can also export data for more advanced statistical analysis using Excel or other software packages.

I have been using PDQuest since version 7.3 (more than 6 years). I used it to do analysis every 2 weeks or so after gel images were acquired. It is a great program that greatly reduces the time for spot matching and spot detection. The detection and matching is only possible through a computer program, and PDQuest fits this need more than adequately. However, PDQuest is not very user friendly. It takes about 2-3 weeks to learn the software, and it can be months before users are able fully utilize all the functions. However, once the users are familiar with the program, PDQuest will enable users to analyze many images and perform data analysis with magnified efficiency. The automatic matching has been improved dramatically in version 8.0, which requires little manual matching. This improvement significantly reduces the time that is required for manual matching. On the downside, PDQuest 8.0 does not support the FX imager from Bio-Rad.

The network license is a red USB key (or other key in earlier models) that allows other computers to communicate with the main computer where the red USB key is plugged-in. Once the PDQuest software has been installed and communication established, PDQuest can be used on other computers where the password has been entered. However, the set up of the network licenses is pretty complicated. It requires some computer networking experience. Sometimes, the network license could ask for a new password if the main computer has been switched off. However, this problem can be quickly resolved with the help of Bio-Rad’s technical support.

Another glitch occurs when you select “open file” from the tool bar. The window to locate the files is not visible (possibly due to a bug). You have to click on the screen in order for the window to show up. In my opinion, though, this is a very small issue that that doesn’t cause any real problem.

Overall, PDQuest –multiple network licenses is a great program for 2D gel image analysis. There are some bugs with the software, but they can be worked around. PDQuest has great technical support that usually resolves the issues. Also, the software can be coupled with other instruments such as FX imager, ExQuest spot cutter, etc. These features make PDQuest a great program for 2D gel image analysis software.

Sr R&D Scientist
SAFC Bioscience
Sigma-Aldrich
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PDQuest 3 2-D Analysis Software From Bio-Rad
The Good

PDQuest Software is a great program that saves a lot of time with its image analysis in proteomics.

The Bad

It is expensive and setting up the multiple licenses is complicated for users who are not familiar with computer networking.

The Bottom Line

An expensive program that allows users to quantitatively analyze 2D gel images. It can take a long training period, but the efficiency in 2D gel image analysis is worth the training time that’s put in.

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