When we launched Progenesis SameSpots to the world back in 2006 it was soon clear to me that because it was so different, explaining it’s new approach to 2D gel analysis and the benefits it gives would be a big job.
The things I read this week from Ernesto Silva, Asa Wheelock et al showed me how things have changed! Their publication “In the Eye of the Beholder: Does the Master see the SameSpots as the Novice” has rigorously evaluated the performance of Progenesis SameSpots and in particular the objectivity in the workflow, comparing analysis from a novice compared to an expert user was a nice way to do it. They also measured overall contribution of variance dependent on the background subtraction and normalization techniques, which I didn’t realise had such a big affect until I read the paper. I was relieved to read the default method in Progenesis SameSpots gave the best results but it’s hard for me to give an objective view 🙂 so I encourage you to read the whole thing and get the full story yourself.
The other thing that amazed me was that I’ve been promoting the benefits of speed, objectivity and statistics, and more recently reproducibility, since the launch of SameSpots. I sort of knew, but not completely, this was useful to people but this paper showed all of these things and why they’re so important!
Speed of analysis, particularly with any editing involved, was highlighted and times reduced from 6-8 hrs/gel to 1-2h/gel. The conclusion said it all by stating SameSpots “represents improvements both in reproducibility and objectivity” compared to other approaches and the less-experienced user got the same or better results compared to one of our experts.
Reading all this was great. It shows people understand what SameSpots is about and why we developed it to help everyone doing proteomics. That’s the most satisfying thing I can say as a marketeer at Nonlinear. It’s a real high point for me and made me proud to be a part of the company that develops Progenesis SameSpots.