Skip to main content ↑ ↓

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - Oliver Fiehn

3
Compound identification / Re: Metabolomics and clinical practice
the problem is 'clinical routine'. It is really difficult to get legal approvals (e.g. in the United States, FDA), and to convince insurance companies to cover costs. Easily a decade, even if everything is perfect. Multiple studies on various cohorts of patients are needed before a clinical organization would consider discussing the topic, after meta-analysis (comparison) of those study outcomes.
5
Mass Spectrometry Interest Group / How can we share critical analytical information.
Hi,
it\'s interesting to see that 74 people have \'viewed\' John Shockcor\'s question, but only one person replied.
I am not quite clear why we need to register for that discussion? Maybe Jules Griffin could bring that up at the Society\'s board meetings. Just by the statistics alone (74 views, one reply) it appears that registering is an unnecessary hurdle.

Anyway. Here\'s my reply.

* for mass spectra, the best repository so far is MassBank, and we surely hope to extend and further utilize it in coordination with other repositories (in Europe, U.S. and Canada)...MassBank contributors still \'own\' their spectra, so that\'s why you cannot batch download spectra. I think we should build a repository that is open access to everyone, in which contributors get credit (like \"this QTOF mass spectrum at 20V collision energy and ....parameters was contributed by XXYY from ZZZ institute in WWWcity, country). The parameters should be queryable, so that people could download \'all spectra\' or \'just the QTOF spectra\' according to their needs.

* for retention times, in GC these are standardized ages ago as \'retention index\'. Retention indices differ a little bit between different columns of the same type when purchase from different vendors (e.g. the popular 5% diphenydimethylpolysiloxane columns from, say, J&W versus Restek), but those retention indices do not differ wildly and one can nicely use RI values from one column and apply it on a similar column of a different vendor. Joachim Kopka published on that a couple of years ago, and we have also most recently published a paper (\'the volatile compound BinBase database\' in BMC bioinformatics) where we had used the Adams MS library for matching our experimental spectra. Worked nice! So, my general advice is: use GC when you can (GC stands for \'Good Chromatography\', by the way...:)  )

* for HPLC or UPLC, retention mechanisms and phases vary so much, that no generic retention index has ever been developed. What I would like to know, at least, is the retention factor (!) k, to ensure that people report peaks that are reasonably retained and away from the void volume. Secondly, if any academic or industry would like to take that job, it would  be nice to get a mixture of, say, 5 artificial compounds (not-natural) that would ionize under both positive and negative ESI and that would exert large difference in polarity, say, from XlogP -2 to 10. With those 5 compounds sold as a mixture from, e.g., Sigma-Aldrich, one could demand that people should report their retention times on their specific column and their specific solvents etc RELATIVE TO THOSE STANDARDS. It would not be a retention index, but it would at least follow the idea and make the \'science\' more reproducible....

Further comments?