In case people haven\'t seen this MIBBI had a publication in Nature Genetics this month... Toward interoperable bioscience data.
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.
Nat Genet. 2012 Jan 27;44(2):121-6
Oh and yes I do I have vested interest but I hope this is of interest to people.
Chris Taylor from the EBI has been in touch and he\'s produced a reference tool for omic data in terms of the standards in reporting requirements. You can find it at: http://mibbi.sourceforge.net/MICheckout.htm
I\'ve just taken a look and what strikes me is how much more detail we\'ve included in CIMR (MSI in old acronyms) compared with MIAME and how its going to be impossible to expect anyone to go through the whole CIMR list. I think we (the metabolomic community) need to work on that rather urgently. I like the mass spectrometry description - that\'s really useful to have in mind if we\'re going to produce something joined up across approaches. Any thoughts?
|Hi Stewart, What sort of things do you want to measure? We\'ve had some success using HILIC to look at TCA cycle intermediates and amino acids. We tend to do things in a targetted manner but happy to share our chromatography if it sounds of interet. Best wishes, Jules
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.
Metabomeeting is coming up at the end of the month. Is there anything we want feedback on for the work around MSI? I\'m happy to promote Adam\'s work and ISA-TAB but what would we like feedback on?
I wanted to get the ball rolling for resurrecting the discussions concerning MSI. I’ve just had published a paper that may be of interest to anyone involved in standards which can be found at A Metadata description of the data in \"A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.\" Griffin JL, Atherton HJ, Steinbeck C, Salek RM. BMC Res Notes. 2011 Jul 29;4(1):272. MetaboLights is making good progress at producing a central repository for metabolomics but we would like some feedback about where we are going and also I’m aware of other initiatives – with a workshop at nih in September and advances by metabolomics Australia. I would be interested in feedback on the paper and also whether a TC might be useful.
Hi Dan. For our lipidomic studies at MRC HNR we\'re currently using a commercial standards mixture for blood serum and while this was a good first solution to the problem of what to run alongside real samples to assess the variability of the assay from batch to batch but it wasn\'t that similar to the sera we were looking at, less similar still to plasma and nothing like adipose tissue or liver tissue. For liver tissue we resorted to a batch lot of Tesco\'s finest chopped liver but hardly a solution to the problem. From my experience for the lipidomics though you have to use complex standards alongside some reference standards in order to re-create some of the complexity of the real samples.
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?
