Proteomics can be used in any lab to help answer questions about protein expression and function that cannot be answered using any other method. One method currently employed to obtain information on complex mixtures of proteins (ranging from whole cell lysates to organelle preparations) is two-dimensional (2-D) gel electrophoresis.
Running two-dimensional gels is a time consuming process and variation between gels can make it difficult to obtain good data. Bio-Rad has developed a complete 2-D gel electrophoresis system that allows you to run multiple gels at the same time using their pre-made buffers and solutions to get you off the ground and going with little preparation time. Most 2-D gel electrophoresis experiments require multiple gels to account for the experimental variations inherit to this complex procedure. When we started our trek into proteomics, we found that comparing gels visually was time consuming and difficult, although still possible when we had only a few gels. But we knew that visual comparisons were not a long-term solution and we soon began looking for software to analyze our gels. Bio-Rad’s PDQuest 2-D Analysis Software steps in to organize your gels and unearth the data buried under the polyacrylamide. This software package will normalize each gel to “housekeeping proteins”, filter out background noise, and create virtual gels using Ideal Gaussian Representations of experimental gels. In addition, this software allows statistical analysis of gels to determine which differences are significant and which are not. At each stage, PDQuest will show the spot of interest on all of the gels; sometimes, the user can make their own judgment call on whether the difference is significant or not. The features of PDQuest are too numerous to mention here, but a trip to the Bio-Rad website will help you find out that every feature has been built into this package.
PDQuest is a robust and nimble software that took minutes to accomplish what had taken us hours to do and it contained many of the features we needed. Our first experience with the software was quite user friendly. Once we had the gel images on the screen, we clicked on the automated detection and matching tool. Next we selected the faintest spot, the smallest spot (usually the same spot as the faintest spot), and the largest spot cluster. The first round of spots was shown on the screen to make sure all the spots we were interested in were identified. Next the default parameters were left for matching the spots between gels. That was it. Then, we were able to click through spots that were of interest to us. The program showed us where the spots were on each of the gels, the relative signal intensity, and a graphical representation of the relative signal intensity of the same spot in multiple gels.
Overall, this software is user friendly and even the beginner can quickly obtain data from multiple gels. This program can accommodate a wide array of uses, and this review only scratches the surface of PDQuests’ features. Our lab is extremely impressed by this software package, and would strongly recommend it to any lab involved in proteomics.
Jeffrey Perry
Lab Manager
University of Michigan
Ann Arbor, Michigan