Progenesis SameSpots v4.1: the SpotCheck workflow

This week, Progenesis SameSpots v4.1 emerged from its beta programme and was released for download. By far the most noteworthy new feature is the addition of the SpotCheck workflow. This directly supports the first of the four key steps in reproducible proteomics1, as defined by the Fixing Proteomics campaign: achieving reproducibility in your gel running.

The way that SpotCheck does this uses a very simple, 3-step process, at the heart of which is a new type of file called a gold standard:

  1. Analyse a set of gel images that represents the high level of quality you want to maintain
  2. Convert the analysis to a SpotCheck gold standard, specifying how closely subsequent gels must match it
  3. Compare images from subsequent gels to the gold standard, getting a pass/fail verdict

The first step involves nothing more than aligning the images and detecting spots; at that point, we have all the measurements we’ll need. The second step requires that you set 2 simple parameters to use when comparing gels to the gold standard:

step2_pass_criteria

The final step – the comparison of subsequent gel images to your gold standard – is a simple matter of selecting the image and aligning it to the images in the gold standard. When this is done, you’re presented with the results, indicating whether or not the gel meets your quality requirements:

blog_spotcheck_success

And that really is all there is to it; it may be a simple process, but it’s an incredibly powerful tool in helping you ensure the proteomics work you’re doing is reproducible. And by using automatic statistical measures to assess your gels, you can be confident the verdict is an objective and repeatable one.

If you’d like to try it yourself, just download the latest version of SameSpots and have a run through the SpotCheck tutorial. You can also learn more about the software in the frequently asked questions (FAQs). As ever, we’d love to hear any comments you have, as well as any suggestions for further improvements.

[1] The four key steps to reproducible proteomics are outlined on the website of the Fixing Proteomics Campaign, a non-commercial, technique-independent campaign dedicated to solving the experimental challenges that stop proteomics delivering on its potential.

One Trackback

  1. By First report from HUPO 2010 « Nonlinear Dynamics' Blog on September 20, 2010 at 10:07 am

    […] SameSpots v4.1, incorporating the SpotCheck workflow for monitoring the quality of your gel […]

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