We attended HUPO 2011 last week so here are the highlights of what HUPO and its members, including us, were up to during a very busy four days in Geneva.
The past ten years of HUPO and the future
HUPO celebrate its 10th Anniversary and the theme of the meeting was Translational Proteomics, or moving proteomics from a discovery phase and applying it to clinical research and molecular medicine.
From the talks and discussions over the four days generating results that are meaningful for biological studies and clinical application was being achieved in some labs. But, in private, I also heard the level of research and quality of results required for this is not yet accessible to all labs.
HUPO 2011: Looking back at the challenges and celebrating achievements of the last 10 years of proteomics (left) and specifically what HUPO has achieved with a lavish circus night (right).
(1) Moore J B , Weeks M E Adv Nutr 2011;2:355-364 & my own analysis of PubMed using “proteomics” search term
The packed workshops and symposia dedicated to education and practical solutions for translational proteomics ahead of the opening ceremony showed many labs are still learning what they need to meet the challenge including new technologies, quality control, standardisation and reproducibility. These requirements have been at the forefront in developing Progenesis products and Will Dracup, our company CEO, gave his presentation on quality control & reproducibility during the Symposium on New Technologies and Standardisation.
The topics of quality control, standardisation and reproducibility were repeated at many scientific presentations during the week including the Proteomics Standards Initiative (PSI) and EUPA Company afternoon.
Putting data in context of biological information
Another theme that dominated over the four days was the need for putting data into the context of biology, in particular systems biology and mapping pathways. Many people, during sessions and in conversation afterwards, were challenging the mind set that proteomics experiments should generate longer and longer lists of identified proteins. It’s not enough to know what is there but also how much of each protein there is and how the proteins are organised.
On the first full day of scientific talks, Prof Ruedi Aebersold said this to a packed lecture hall, starting by challenging many of the assumptions in proteomics experiments today including:
- Identify proteins and you identify function
- Identify a proteome and you identify all functions
- Increased protein abundance means more activity and a functional change
In the poster sessions, quantification of proteins, relative and absolute, was a big part of the work presented. A quick analysis of the 1,040 posters revealed that ~70% of them included a term for MS quantification and 40% of these included a term for absolute quantification. This is the first step to put discoveries in context of potential biomarkers, but as Prof Aebersold described, proteins work in regulatory complexes and networks. So, quantified and identified protein discoveries need a context of how they are organised at the cellular level to explain function and dysfunction that is useful for clinical research and personalised medicine.
Nonlinear Dynamics at HUPO 2011
As well as attending the scientific meetings we were there to show the latest developments for label-free LC-MS quantitative proteomics data analysis, having just released Progenesis LC-MS v4.0. This was promoted on a previous blog-post and an update email had gone out to all our customers eligible for a free update during the meeting. News travelled quickly and we had many people coming to the booth to see what was new (PDF 1.3MB).
The new features of Progenesis LC-MS of most interest to booth visitors were also the ones most relevant to the themes of scientific talks including:
- Add additional information to lists of quantified proteins. Lists of interesting proteins can be exported for further analysis in any external bioinformatics package, and results can be imported back into Progenesis LC-MS as a custom column to build up supplementary data on proteins of interest.
- Multivariate statistical tests applied to protein measurements. Correlation analysis allows you to group proteins that have similar expression patterns and helps you relate results back to the biological processes you are studying.
Demonstrating support for workflows that increase protein and proteome coverage also generated a lot of discussion and we look forward to seeing it applied in publications.
It was not just Progenesis LC-MS on show, other products were represented across at least ten posters that we knew about:
- Progenesis LC-MS (P1501, P1601, P1475, P1659, OC031)
- Progenesis SameSpots (P1401, P1433, P1754)
- Progenesis MALDI (P1857)
You can search for these abstracts online at the HUPO 2011 website to find out more details of what our customers are doing with their software.
And yes we did also enjoy meeting customers old and new at the social events and experiencing the beautiful (if expensive!) city of Geneva. As we were just packing up to leave, we met the organiser of next year’s HUPO annual congress. We’ll look forward to that and seeing how the good foundations laid in Geneva translate to results shown on the ground in Boston.