SpotCheck is a separate QC workflow within SameSpots v4.1 which allows you to quickly and objectively measure whether a 2D gel meets your lab’s quality requirements.
Whether you use SameSpots for your 2D analysis, or another software package, you can follow this simple workflow to check the quality of all your gel images. Once you’ve created a gold standard, you can test unlimited gels against it free of charge.
There are 3 short steps in this process:
Analyse the gel images that represent your gold standard
To get started with SpotCheck you need a gold standard. This is used as a baseline to objectively measure the quality of your gels.
Select at least 3 images of gels that contain the same sample run using the same protocol. The gold standard should only contain gels that you’re happy represent the quality you want maintained in your lab.
The gold standard is generated by doing a SameSpots analysis up to the point where you have aligned all of the gel images and detected spots – it is a very fast process. You are then ready to convert your experiment to a SpotCheck gold standard.
Convert analysis into SpotCheck gold standard
This is a simple process where you define the pass criteria that subsequent test images need to meet.
The default in the software is set to 80% of spots falling within 3 standard deviations of the gold standard – but you are able to adjust these numbers depending on the stringency of the quality control check you wish to perform.
Monitor subsequent gel running
You can set up gold standards for each sample that you use, and then compare subsequent test images to make sure the gel running is maintained at an acceptable quality.
Gold standards can be shared between users and different labs so you can manage the quality of gels that are analysed as part of the same project. This can help QC within a lab where different people and equipment may be involved in the gel running process and also collaboration across labs.
Steps in this process:
- Import test image
Your images go through a process of automatic image quality assessment with feedback to help you optimise image capture - vital for accurate image analysis.
- Align test image to gold standard experiment
The test image is automatically aligned to the gold standard experiment.
- Image passed or failed the QC check
You get an immediate pass or fail assessment and a colour coded whole image view to show you which spots passed, and which spots failed. A group of spots which failed in a certain area of the gel may help you troubleshoot your gel running.
- Report – you can generate a PDF report.