Recognition from Sweden for SameSpots

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.

Another happy Progenesis SameSpots user :-)

It’s always great to hear from our customers, and yesterday we got some feedback from Dr. Marcel Koken from CNRS UMR 6539 LEMAR (Laboratoire des sciences de l’environnement marin) in France. He said, “A few months ago, a "SameSpots" demo session gave us the impression of an easy-to-use application. Now, we have finally bought the program … and our initial idea has been completely corroborated; very easy to use and very reliable results!”

If you would like to see how easy to use Progenesis SameSpots is, then you can always take a look for yourself. Keep an eye out for the email you receive when you download the software with your licence code to analyse your own images. If you don’t have any images to hand, then why not take a look at the tutorial images?

Happy Friday

North East Leads the Way in Groundbreaking Research

We’ve joined forces with Northumbria University on one of four EPSRC CASE awards that RTC North helped secure in the region. The project is aiming to improve the production of biofuels and with the approach we’re taking, we want to show that the LC-MS analysis results can be reproduced across-labs. Our first data will be presented at the London Biological Mass Spectrometry Discussion Group on March 18th 2010.

The research is being led by Professor Gary Black and carried out by Northumbria PhD student Andrew Porter from Gateshead. He’s using traditional scientific laboratory culturing techniques to grow a bacteria commonly found in soil called Cellvibrio japonicas and see if the bacteria is able to use Miscanthus giganteus and sugarcane bagasse  biomass as a sole carbon and energy source. Working with Professor Black the proteins involved will be isolated and analysed  in labs at Northumbria University and at North East Proteome Analysis Facility (NEPAF) using our Progenesis LC-MS software. I’m the industrial supervisor, which is something new for me and I’m looking forward to getting involved and learning a lot from this 100% locally sourced research project.

In this picture (L to R): PhD student Andrew Porter with Prof. Gary Black from Northumbria University & me (Paddy Lavery) as industrial supervisor from Nonlinear Dynamics.

We’ve got a lot of experience supporting projects with the goal of curing diseases, so biofuel research is a new, exciting field for us and the EPSRC CASE awards can help bring bright things to us, Northumbria University and our region.  Andrew’s work should keep talent and attention here as well as helping biofuel to become a real alternative energy source.

Nonlinear and Northumbria also have an opportunity to be pioneers here.  If we’re successful, the results of this research will support a good message. That is, if you take the right approach, anyone can go from initial discovery research to validated results that can be reproduced in other labs. I’m hoping it will send ripples out beyond Newcastle and it also links up with The Fixing Proteomics Campaign that we already work with.

Out with the old, and in with the new!

Well this is my first ever blog-post, so bear with me! I’ve been reading some tips on how to write good blog posts and they range from trying to inject a bit of humour to keeping a really focussed message. Well I’m not a comedian, and I have been known to drift off every now and then so we’ll just have to see how it goes……:-))

It’s been a really busy past 6 months and now it’s time to reveal to the world what we’ve been working on. To start 2010, we have a brand new website which shows off our new look and is packed full of interesting and useful information relating to the world of proteomics research. And to top that, we also have a new version of Progenesis SameSpots v4.0.

I’m not going to bore you with all the new features in v4.0, you’ll be able to find that out yourself by having a look. So if you want to try it on your own data then you can download it  with some free image licenses to get you started.

We have lots of customers singing the praises of our software, and so you can see who some of our users are, they have kindly given us permission to share with you what they think. Jesper Hedberg of AstraZeneca RD in Sweden recently said, “Previously, we always considered 2D image alignment and analysis to be one of the big bottlenecks in 2D gel proteomics. SameSpots has completely changed that. 2D gel analysis is now easy and we do much more 2D experiments.”

I hope his words encourage you to take a look!