tagged: Analysis Center, Analysis strategy, composite image, fusion image, image warping, Ludesi 2D gel Analysis procedure, Ludesi Basic, Ludesi Pro, PTM, REDFIN, REDFIN Solo

Analysis strategies in REDFIN Solo and the Ludesi Basic and Pro analysis services

Posted by ludesi in 2DE Knowledge Base

Johan Ljunggren, Key Account Manager at Ludesi answers

Q: “How is the analysis strategy in REDFIN Solo different from the Basic and Pro analysis services?”

As you may already know, Ludesi has started to offer a pay-per-gel image analysis software -REDFIN Solo- where you do the image analysis yourself as opposed to our current service based offerings – Basic and Pro – where the analysis is performed by the Ludesi Analysis Center.

For the Solo option, we have chosen a different strategy of gel image analysis. We have opted to use a workflow where the user warps/aligns the images, and an artificial composite gel image is created based on this alignment.

The composite image is a combination of all the original images where additional weight is given to spots that are present in only a few gels so that these spots do not disappear or become too faint in the composite image. Spots are detected and spot borders are calculated in the composite image. The spot positions and borders are then copied to all the original gel images, and spot volumes are calculated from these images.

In contrast, in our service offerings Basic and Pro we use the approach of detecting spots and calculating borders in the original gel images. These spots are then matched between the gels according to a certain algorithm to determine which spots represent the same protein or PTM.

This strategy avoids some of the problems associated with the composite image approach, most prominently the tendency to create less accurate spot borders and to incorrectly detect several separate spots as a single spot.

This is especially common with gel sets that are difficult to warp and/or contain a great amount of variation, PTM’s, or artifacts. There is also a certain degree of bias involved in creating the composite image because the user must decide which gels to warp to which reference gel. Ludesi’s matching on the other hand uses an “all-to-all” method where all gels are treated equally.

The downside however, is that it is a pretty involved, time-consuming and difficult process to perform this type of analysis with good, consistent results. That is not a big problem with a service offering since we can do the analysis ourselves using our own, somewhat complicated software and trained staff. But we feel that to expose researchers to these complications would not be ideal.

That is why we have decided to go with the composite image approach for our Solo option. This makes it possible for even a novice user to complete the analysis with a reasonable amount of effort and a minimal amount of training. Especially for 2D gels with low variation and a clearly defined spot pattern the composite image approach will achieve very high quality results. Indeed, this type of workflow has been successfully incorporated in some of the leading 2D gel image analysis software on the market today.

As with most things, each analysis approach has its benefits and drawbacks, and it is advisable to carefully consider which type of analysis workflow is most suitable for a particular experiment.

For example, if you are expecting a high degree of biological variation and PTM’s we would recommend you to choose Ludesi Basic or Pro, as a composite image approach is not as suitable under these circumstances. If on the other hand, you find it easy to align your 2D gel images with each other, then composite image approach in REDFIN Solo will most likely results in very high quality and consistent results.

The ability to choose in REDFIN between Solo, Basic and Pro and their different analysis approaches on a project-by-project basis ensures that the most appropriate strategy can be applied every time.

This flexibility can be a deciding factor for the succesful completion of your 2D gel projects.