Talk:Metabolomics

From Wikipedia, the free encyclopedia

Molecular and Cellular Biology WikiProject
MCB Portal
This article is within the scope of the Molecular and Cellular Biology WikiProject. To participate, visit the WikiProject for more information. The WikiProject's current monthly collaboration is focused on improving Restriction enzyme.

Article Grading: The article has not been rated for quality and/or importance yet. Please rate the article and then leave comments here to explain the ratings and/or to identify the strengths and weaknesses of the article. Click here for an overview of how to rate this article.

Hi -- I have taken the liberty to put down some of my thoughts on metabolomics. Any suggestions as to what else would be useful -- what about links to some metabolomics sites? Or what about citations to some of the more significant (peer-reviewed) scientific papers? thanks --jake b 10:10, 16 Oct 2004 (UTC)

The additions that you've made look really good. The only other things I think could be added are about matching experimental data to compund libraries, and the statistic and bioinformatic analysis of results. Oliver Fiehn's group at the Max-Planck-Institut has a good list of publications, I can't tell if they're they're fee for public access since I'm on a university network [1].--nixie 21:32, 16 Oct 2004 (UTC)
"Matching experimental data to compound libraries" -- fully agree with you, but it's a big job! Also think your suggestion about data analysis is a good one, I might add some bits in a day or two and let some more experienced biostatisticians correct where necessary. Do you feel like adding some external links, starting with the MPI one (or even just that for now)?? many thanks ... --jake b 21:46, 17 Oct 2004 (UTC)
I can quiz a girl in my lab, she's just started her PhD on a metabolomics project, the details are mind boggling- but a basic outline of an experiment would be good.--nixie 01:44, 18 Oct 2004 (UTC)

I've made a few changes: deleted one reference (seemed gratuitous, and more 'journalistic' than authoritative). Main thing I tried to do was rewrite the 'analytical technologies' section as it had got a bit confused, with reference to HPLC twice. comments? jake b 18:51, 24 Jun 2005 (UTC)

I'm not an expert in NMR, but I'm pretty sure some of the statements made on this page are incorrect. For example, it says "All kinds of small molecule metabolite can be measured simultaneously", but that's not true of any NMR techniques I know. For NMR you typically need to isolate your compound of interest in a very pure form for analysis. If significant impurities are present, you won't be able to properly characterize the analyte. This, along with lack of sensitivity, is among the major drawbacks of all NMR techniques. HPLC combined with mass spectrometry is popular in part because it eliminates the need to isolate pure compounds, as the separation is done on-line. Some scientists use HPLC combined with NMR, but this is a much more difficult set-up and I don't know if it's pratical for metabolomics. 146.6.144.113 19:29, 15 November 2005 (UTC)BDD

There are now (many many) publications using 1H NMR as a profiling tool -- typically, you obtain a spectrum of a complex mixture, and then use some kind of multivariate data analysis to detect which spectral regions vary (according to e.g. experimental treatment). You can then (try to) relate these back to specific metabolites. HPLC-NMR isn't really close to being a standard technique for metabolomics; main problems are that (a) sensitivity is an even bigger problem, and (b) RPHPLC is poor for highly polar metabolites, i.e. most of them. jake b 10:08, 19 December 2005 (UTC)

I have a couple of suggestions: 1. Implement a Metabobox similar to the Drugbox (Template:Drugbox) to be used in constructing metabolite entries so that all entries have a consistent look and feel. 2. I know of a really great website, the Human Metabolome Database [2], that could be used as a source for some of the initial entries. --Metabolite 17:15, 23 May 2007 (UTC)

Contrary to the statement on the main page, Arthur Robinson did NOT invent the field, and certainly did not author the first paper in the area of metabolic profiling. The 20-odd references to this author are mostly redundant, and do not represent the field. It's pretty clear that this is simply self-aggrandizing self-citation. —Preceding unsigned comment added by 74.87.29.154 (talk) 00:17, 26 May 2008 (UTC) I have attempted to edit the numerous references to A. Robinson, by removing citations of conference proceedings, two other articles that were apparently not peer-reviewed, as well as a number of papers that do not relate to metabolomics, but rather to protein chemistry. The justification was provided above. These edits were immediately reverted, with no explanation. —Preceding unsigned comment added by 74.87.29.154 (talk) 01:21, 26 May 2008 (UTC)

[edit] References

I cut these unlinked refs. Some could go back, but they should be justified.

  • Pauling, L.C., Robinson, A.B., Teranishi, R., and Cary, P., Quantitative Analysis of Urine Vapor and Breath by Gas-Liquid Partition Chromatography, Proc. Natl. Acad. Sci. (1971) 68, 2374-2376.
  • Teranishi, R. and Mon, T.R. and Robinson, A.B., Cary, P., and Pauling, L.C., Gas Chromatography of Volatiles from Breath and Urine, Analytical Chemistry 44 (1972) pp 18-20.
  • Robinson, A.B. and Pauling, L.C., Quantitative Chromatographic Analysis in Orthomolecular Medicine, Orthomolecular Psychiatry, 1973, ed. D. Hawkins, pp 35-53.
  • Robinson, A.B., Partridge, D., Turner, M., Teranishi, R., and Pauling, L.C., An Apparatus for the Quantitative Analysis of Volatile Compounds in Urine, J. Chromatography (1973) 85, pp 19-29.
  • Matsumoto, K.E., Partridge, D.H., Robinson, A.B., and Pauling, L.C. and Flath, R. A., Mon, T.R., and Teranishi, R., The Identification of Volatile Compounds in Human Urine, J. Chromatography 85 (1973) pp 31-34.
  • Pauling, L.C. and Robinson, A.B., Techniques of Orthomolecular Medicine, First Conference on the Analysis of Multicomponent Mixtures and their Application to Health-Related Problems (1973) 1, pp 1-7.
  • Robinson, A.B., Cary, P., Dore, B., Keaveny, I., Brenneman, L., Turner, M. and Pauling, L., Orthomolecular Diagnosis of Mental Retardation and Diurnal Variation in Normal Subjects by Low-Resolution Gas-Liquid Chromatography of Urine, Int. Research Comm. Sys. (1973) 70, p 3.
  • Robinson, A.B. and Westall, F.C., The Use of Urinary Amine Measurement for Orthomolecular Diagnosis of Multiple Sclerosis, J. Orth. Psych. (1974) 3, pp 1-10.
  • Robinson, A.B., Westall, F.C., and Ellison, G.W., Multiple Sclerosis: Urinary Amine Measurement for Orthomolecular Diagnosis, Life Sciences (1974) 14 pp 1747-1753.
  • Robinson, A.B. and Pauling, L.C., Techniques of Orthomolecular Diagnosis, Clinical Chemistry (1974) 20 pp 961-965.
  • Robinson, A.B., Orthomolecular Medicine – Diagnosis and Therapy, Proc. 8th Annual Conference National Society For Autistic Children (1974) pp 1-8.
  • Robinson, A.B., Looking for Optimum Health: A Guided Tour Through the Linus Pauling Institute (1975) Prevention, pp 89-96.
  • Robinson, A.B., Weiss, M., Reynolds, W.E., and Robinson, L.R., Use of Mass Spectrometry for Orthomolecular Diagnosis (1975) Proceedings Twenty-Third Annual Conference on Mass Spectrometry and Allied Topics, pp 182-184.
  • Rosenberg, R.N., Robinson, A.B., and Partridge, D., Urine Vapor Pattern for Olivopontocerebellar Degeneration (1975) Clinical Biochemistry 8, pp 365-368.
  • Dirren, H., Robinson, A.B., and Pauling, L.C., Sex-Related Patterns in the profiles of Human Urinary Amino Acids, Clinical Chemistry (1975) 21, pp 1970-1975.
  • Robinson, A.B., Willioughby, R., and Robinson, L.R., Age Dependent Amines, Amides, and Amino Acid Residues in Drosophila Melanogaster, Experimental Gerontology (1976) 11, pp 113-120.
  • Robinson, A.B., Dirren, H., and Sheets, A. and Miquel, J. and Lundgren, P.R., Quantitative Aging Pattern in Mouse Urine Vapor as Measured by Gas-Liquid Chromatography, Experimental Gerontology (1976) 11, pp 11-16.
  • Robinson, A.B., Pauling, L.C., and Aberth, W., A Controversy: Diagnosis of Infectious Hepatitis (1977) Clinical Chemistry 23, pp 908-910.
  • Robinson, A.B., Molecular Clocks, Molecular Profiles, and Optimum Diets: Three Approaches to the Problem of Aging (1979) Mechanisms of Ageing and Development 9, pp 225-236.
  • Robinson, A.B. and Robinson, L.R., Quantitative Measurement of Human Physiological Age by Profiling of Body Fluids and Pattern Recognition (1991) Mechanisms of Ageing and Development 59, pp 47-67.
  • Tomita M., Nishioka T. (2005), Metabolomics: The Frontier of Systems Biology, Springer, ISBN 4-431-25121-9
  • Wolfram Weckwerth W. (2006), Metabolomics: Methods And Protocols (Methods in Molecular Biology), Humana Press, ISBN 1-58829-561-3
  • Dunn, W.B. and Ellis, D.I. (2005), Metabolomics: current analytical platforms and methodologies. Trends in Analytical Chemistry 24(4), 285-294.
  • Ellis, D.I. and Goodacre, R. (2006) Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy. Analyst 131, 875-885. DOI:10.1039/b602376m
  • Wishart, D.S., Tzur, D., Knox, C., Eisner, R., Guo, A.C., Young, N., Cheng, D., Jewell, K., Arndt, D., Sawhney, S., Fung, C., Nikolai, L., Lewis, M., Coutouly, M.-A., Forsythe, I., Tang, P., Shrivastava, S., Jeroncic, K., Stothard, P., Amegbey, G., Block, D., Hau, D.D., Wagner, J., Miniaci, J., Clements, M., Gebremedhin, M., Guo, N., Zhang, Y., Duggan, G.E., Macinnis, G.D., Weljie, A.M., Dowlatabadi, R., Bamforth, F., Clive, D., Greiner, R., Li, L., Marrie, T., Sykes, B.D., Vogel, H.J., Querengesser, L. (2007) HMDB: The Human Metabolome Database. Nucleic Acids Research 35(Database issue), pp D521-6.

PMID: 17202168

  • Claudino, W.M., Quatronne, A., Pestrim, M., Biganzoli, L., Bertini and Di Leo, A.(2007) Metabolomics: Available Results, Current Research Projects in Breast Cancer, and Future *Applications. J Clin Oncol May 14; [Epub ahead of print].

http://lab.bcb.iastate.edu/projects/plantmetabolomics/

  • Ellis, D.I., Dunn, W.B., Griffin, J.L., Allwood, J.W. and Goodacre, R. (2007) Metabolic Fingerprinting as a Diagnostic Tool. Pharmacogenomics, 8(9), 1243-1266.

--Kkmurray (talk) 21:58, 28 November 2007 (UTC)