Introducing Progenesis SpotCheck, for monitoring the reproducibility of your 2D gel running

spotcheck_logo In my last blog post, I talked about the need to minimise subjectivity in your analysis. It’s an area of great importance, as recognised by the Fixing Proteomics campaign, so I’m really excited to be able to introduce Progenesis SpotCheck.

SpotCheck is a new workflow in Progenesis SameSpots that assesses the reproducibility of your gel-running. It uses the following 3-step approach:

  1. Using a single sample, run a set of gels to the standard you want to maintain, analysing them in Progenesis SameSpots.
  2. Convert this analysis into a SpotCheck gold standard, specifying the required similarity in subsequent runs of the same sample.
  3. Monitor subsequent gel running — performed at later dates, by other users, or even other labs — by comparing the gels to your gold standard.

The end result is a straightforward pass-or-fail verdict, indicating whether the gel has met your quality requirements. All comparisons are based on automatic quantification of spot volumes, statistically validating the gels for maximum reproducibility. The person using the SpotCheck software is never asked to use their own judgement to decide whether the gel passes.

While SpotCheck’s currently still in its beta programme, we’ve already had some brilliant feedback. Dr David Jackson, a Research Fellow in Gel Proteomics, is just one person heaping praise upon it:

“It’s a very convenient and user-friendly module, and definitely of a lot of use for multi-batch experiments run over time and between different users as well as across sites. It allows the gel runner to carry out a QC easily without having to export to a statistician.

The end result, showing the most variable spots, is helpful for quickly narrowing down the cause of any fails. So, as well as a QC checker, it could also help in terms of speeding up or easing investigation of why things are problematic with your 2D gel protocol.”

Now, I wouldn’t blame you for being wary of such comments prior to the software’s release, but I really am quite proud of what we’ve done here. In the coming weeks, I hope to reveal a bit more of SpotCheck. For now, though, it’s back to making a few final tweaks. In the meantime, if you’d like more information on Progenesis SameSpots or would like to be notified of the release of the SpotCheck module, please just get in touch. Until next time… 🙂

Follow-up posts