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Topic: How can we share critical analytical information. (Read 12996 times) previous topic - next topic

How can we share critical analytical information.

In addition to a name, structure,  mass and elemental composition, it seems important that we begin to share information on fragmentation and retention time with it\'s associated chromatography.  Can /will current public databases be structured to accept this information  from the metabolomics community?  Please share your thoughts.

John

How can we share critical analytical information.

Reply #1 –
Hi John, we talked about including retention time as part of MSI and its in there as a recommendation. In the work we\'re doing with MetaboLights we\'ve adopted some of the descriptions the proteomics people do and RT is in there and I think its relatively straight froward to do that. A question I don\'t have the answer is where you store, and if you do, the information you use for the IDs. So in my mind you would just ID metabolites in one sample and wouldn\'t capture the spectra used for IDs (here I\'m guessing you do some tandem MS and maybe something else) so how do you report that in your original sample chromatogram/mass spectrum. Anyone have any thoughts on this?

How can we share critical analytical information.

Reply #2 –
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?

How can we share critical analytical information.

Reply #3 –
Hi,
in addition to Massbank (http://www.massbank.jp/?lang=en) mentioned by Oliver, the Golm Metabolome Database (GMD, http://gmd.mpimp-golm.mpg.de/ from Joachim Kopka\'s group is available for GC-MS reference spectra and retention index (RI) information as well (see example of Alanine 3TMS http://gmd.mpimp-golm.mpg.de/Spectrums/86f8aafa-61d0-493b-8804-8bed8764a1a8.aspx). The RI values are specific to column polarity and applied retention index markers. However, given that a library of spectra is provided to Joachim or me, we can map (transform) the Golm RI values into your variant. The quality of this mapping depends on the similarity between the column polarities.

best regards,
Jan Hummel

How can we share critical analytical information.

Reply #4 –
Thanks Oliver and Jan. Both these comments are very useful - and it would be good to get some feedaback from some others. Sorry that registering was a problem but it does stop a lot of spam. Anyway, do we have anymore opinions on these postings.

How can we share critical analytical information.

Reply #5 –
Dear all,
Can any one give suggestion to solve my problem
I have analyzed Drosophila melanogester  polar extract using GC-MS after methoxyamine hydrochloride derivatization and TMS protection. Due to high abundance of disaccharide peak intensities, i am unable to solve their mass spectra with the help of NIST and willy libraries. I have also analysed 4 standards of disaccharides. But the sample peak Rt were not matching with the standard Rt. I am using Thermo Quantum XLS triple quadrapole mass spectrometer. Can anay one suggest to identify disaccharides.
Ratnasekhar Ch
Rsearch srudent
CSIR-IITR
India

How can we share critical analytical information.

Reply #6 –
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.  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. Worked nice!