MetSoc2015 – Bridging the gap between community and industry

At the end of June, I, along with some of my colleagues, headed across to San Francisco, CA, for Metabolomics 2015. This was my third time attending this conference so I was looking forward to seeing some old faces, as well as new ones. I was also curious to see whether the same hot topics from last year were still a focus.

We arrived before the conference was officially underway, so we took the opportunity to explore the busy city around us. Cycling across the Golden Gate Bridge wasn’t on my bucket list, but in hindsight I think it should have been; it was awesome.

The impressive Golden Gate BridgeAli cycling across the Golden Gate Bridge

As with other years, compound identification was a hot topic, and one of the first sessions of the conference was focussed on this area. Due to problems with the projector, the session began with an impromptu open discussion where people shared details on what libraries they were using, and what criteria they require before trusting an identification in a publication. We’ve recently added the option to search the ChemSpider libraries in Progenesis QI so it was good to hear ChemSpider is a popular choice. While ChemSpider proved popular, there’s still the issue of the huge number of possible identifications it can retrieve so it was great to be able to demonstrate the soon-to-be-released Progenesis QI v2.1 which allows filtering of ChemSpider searches using theoretical fragmentation.

Speaking of theoretical fragmentation, Dr. Steffan Neumann from the Leibbniz Institute of Plant Biochemistry, stated that “in-silico fragmentation is the next best thing if there is no reference spectra library around”. Steffan is head of the group that developed MetFrag, the basis for the theoretical fragmentation done in Progenesis QI – he was pleased with the work we’d done using this, and that the source code, with unit tests, is available on GitHub for the rest of the community.

MetFrag isn’t the only area where we’ve been working with the metabolomics community – we recently implemented the option to search LipidBlast, a computer-generated MS/MS database produced by the Metabolomics Fiehn Lab. Progenesis QI v2.1 will also include support for the NIST MS/MS libraries. Of course, as well as using tools developed by community projects, we also recently released Progenesis SDF Studio v1.0, a free compound database management tool – just one of our ways of saying “thank you”. In other industries it’s quite common for commercial organisations and community projects to work together for software development, so it’s great that the metabolomics world is starting to see the benefits of this, and I’m very pleased to be a part of it.

There was a great turn out for the talksAli, Jon and Mark busy on the Nonlinear booth

If you’re working on a project you would like to integrate with Progenesis QI, get in touch – we’d love to hear from you.

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