Proteomics Methods Forum 2011 – a first report

The two-day Proteomics Method Forum (PMF), which we mentioned taking place at St. James’ Park in Newcastle, ended on Friday last week. As well as spending the breaks talking with people at our booth, we also enjoyed the program of interesting talks, with 7 out of 17 presentations citing our Progenesis LC-MS software.

PMF 2011 hosted at St. James' Park, Newcastle Nonlinear Dynamics attend PMF 2011

Achim Treumann opened the meeting by sharing results from a survey sent to all PMF attendees from past years. The aim was to find out what people were up to in proteomics, highlight areas causing problems, or where interest would be in the next 12 months. Full results will be available on the PMF website soon, but the survey data was used to create a meeting agenda with 4 relevant session titles:

  • Statistics
  • PTM
  • Data, Software, Metabolomics
  • Quantitation

Although, as Achim noted in his introduction, the survey results didn’t stress a need for a Metabolomics session, it was included anyway! I think anyone who attended will say it was a good choice, with the talks focussed on comparing proteomics and metabolomics approaches. The theme was presented at a good time for us and the audience to hear, as we have just released Progenesis CoMet for metabolomics data analysis, taking the Progenesis range beyond proteomics.

Some of the other highlights, in no particular order:

  • A somewhat surprising survey result that while most people were doing stats for quantitative proteomics, no one seemed to have any problems with it. Which means, as Achim said, either people have great understanding of statistical approaches or  they are unaware that they have problems.
  • A stats 101 talk by Kathryn Lilley probably helped people decide whether they do need to focus on how they apply experiment design and statistics.
  • How you can maximise qualitative penetrance and quantitative quality in label free proteomics, with less than 2 hours between injections, using gas phase fractionation to improve MS2 data quality from Duncan Smith.
  • The challenges of global accurate mass metabolomics and possible solutions from Karl Burgess, including identification ambiguities created by isomers, fragmentation or adduct formation;  heterogeneity of instruments used for metabolomics analysis and diversity of molecules in your experiment, with any small molecule a potential metabolite!
  • Why do metabolomics and proteomics,  part of a talk by Pedro Cutillas, highlighted some of the same challenges as Karl, including an example where 2000 metabolite masses were detected, 200 positively identified by accurate mass, but only 1 was validated after extensive work.
  • A possible future trend for reanalysing the proteomics data in public repositories e.g. PRIDE, TRANCHE, Human Proteinpedia, in the PMF 2011 survey results. Perhaps we’ll see more publications that are based on these in-silico studies?
  • The advantages of GC-MS for metabolomics, specifically metabolomics for bioprocessing and how it may have potential for proteomics, from David Knight.
  • The interactome game. A great ice-breaker with everyone allocated a protein; the aim to find the person with your interacting protein. The first pair of “interacting proteins” to the registration desk won drinks.

These are just some of  the notes and highlights I took while enjoying the event. If you were there, why not post your comment and opinion of PMF 2011 below?