ProteoMMX 2.0 “Strictly Quantitative”

Last week I attended the ProteoMMX 2.0 meeting here in my home town of Chester with my colleague, Martin Wells. Chester is a very beautiful old city, full of Roman archeological remains, which contrasted with the cutting edge scientific program and presentations. 

Prof. Rob Beynon opened the meeting with a bit of history. A reminder about the first meeting 2 years ago, which was disrupted by the Icelandic volcano, Eyjafjallajökull.  This prevented speakers from attending the meeting but at the eleventh hour speakers skyped in and gave their presentations.  This sums up the spirit of the ProteoMMX meeting, which is cosy, down-to-earth and inclusive.

This conference was themed ‘Strictly Quantitative’ and it was. The program was preceded by a Quantitative Proteomics and Data Analysis training course, organised by the Biochemical Society.  We participated in this course with a presentation on the challenges and solutions you face with relative quantification of proteins by 2D DIGE and label free LC-MS/MS. Specifically this covered:

  • Experimental design that can answer the biological questions
  • Like for like measure of abundance across all samples to make relative comparisons
  • Correction for differences in sample loading
  • Reliable measure of variance within experimental groups
  • Statistical tools to confidently find differences that are significant and likely to be true
  • Identification workflow to annotate the measured features
  • Confirmation that other measurements are in consensus

There was a lot of interest, both from people just starting out in proteomics and those who have been addressing the pains of quantitative analysis for some time.  For me it was interesting to hear first-hand the issues that quantitative proteomics scientists face.  The word ‘challenging’ was one of the words I heard the most, although I think some scientists would have preferred to use some other words instead sometimes!

One presentation in the main program showed that, based on publication volume, the use of label-free workflows has taken over as the primary tool for proteomic quantitation. A summary of all the presentations can be found in the final abstract book. There were a lot of scientists using Progenesis LC-MS presenting at the event.  There was recognition of Progenesis LC-MS’s ability to handle large datasets and large sample numbers so that statistically meaningful results can be obtained.  This ties in with our passion for helping to improve reproducibility in proteomics and why we have cofounded the Fixing Proteomics campaign.

There were 28 posters including one from Andrew Porter, Northumbria University, a PhD student we sponsor. His poster demonstrated proteomic analysis of C. japonicas using 2D gels and label free LC-MS with gas phase fractionation. The conclusion was that the two techniques were complementary in uncovering this organism’s proteome.  If you are interested to read more, a copy of Andrew’s poster is available here and you can download both Progenesis SameSpots and Progenesis LC-MS to try with your own data.

The meeting was very well organised indeed and Waters hosted an evening reception for all the delegates at the wonderfully quirky ‘Oddfellows’.  This has the well known ‘upside down room’ pictured here.oddfellows

It was at Oddfellows that I heard my favourite utterance of the conference.  This was when I introduced two scientists to each other and they realised they had both worked at the same institute but at different times.  “I purified an enzyme there!!!”.  Pure proteomics pleasure.