Overcoming common challenges in differential protein expression analysis

Are you spending hours on tedious spot editing, but want to put your time to better use? SameSpots, our 2D gel image analysis software, can help… and it can also give you reproducible results between different users.

Using our Image QC feature, SameSpots saves users time by quality checking images and flagging any issues prior to any analysis. This step is important as poor image quality can make gel analysis difficult. It can increase subjectivity and may mean your results are less accurate. Image QC checks images for the following:

• That they are greyscale
• That they are free from saturation
• That they have a high bit-depth
• That they have a high dynamic range
• And that they have not been compressed or edited prior to analysis

If any issues are detected, you also have the opportunity within the system to make minor changes, without changing the original image. This includes flipping images horizontally and vertically, rotating images 90° clockwise or anticlockwise, inverting the image and cropping the image.

To see how SameSpots and its image quality checker can be used in your lab environment contact us for a free trial.

How intelligent alignment and automation lead to more accurate identification of spot patterns

We’re often asked if DIGE gels can be used within SameSpots and the answer is, ‘yes’. The DIGE experiments can be set up before alignment and the SameSpots software automatically deals with all measurement calculations.

We use alignment, which takes two images and overlays them in the same co-ordinate space, so that a spot on image A will be in the same location at the matching spot on image B.

Images can be accurately compared as alignment removes the positional variation between images, which may be introduced during the gel running and imaging processes. This allows for all images to be overlaid on each other and a single spot pattern to be detected. This image alignment delivers 100 per cent matching, with no missing values in your data, for valid multivariate statistics.

The software then uses intelligent automation to analyse results and produce automatically calculated dendrograms of spot relationships.

Delivering confidence in your 2D gel electrophoresis image analysis

The software is easy to use, with our experienced team providing you with a guided walkthrough of the workflow so you can quickly get to grips with the 2D gel electrophoresis image analysis software.

Once up and running, typical analysis takes just five minutes per gel with either single-stain or 2D DIGE images.

Quick tags can also be used: these are useful for quickly highlighting proteins that show significant changes. Therefore, you can focus your attention on these ‘interesting’ spots for further analysis with mass spectrometry. You can also import protein identifications back into your 2-DE analysis and report alongside quantitative results.