Talk:Metabolomics

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Untitled[edit]

Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" (This definition is ridiculous, I think these people have been watching too much CSI! Chemical fingerprint Horatio?) —Preceding unsigned comment added by 155.198.149.176 (talk) 17:50, 29 July 2009 (UTC)

I think perhaps a better definition to start with might be from Oliver Fiehn, i.e. "a comprehensive analysis in which all the metabolites of a biological system are identified and quantified" (Plant Mol Biol (2002) 48:155-71).Amaher (talk) 03:53, 5 January 2010 (UTC)

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'm going to add some things on databases, please feel free to add and remove as necessary. Also I'm putting everything in alphabetical order as to not step on peoples toes. FYI I removed a link about proteomics soc as it has very little to do with metabolomics/metabonomics. --Hpbenton (talk) 00:54, 11 January 2009 (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)

References[edit]

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)


I've removed these refs which were collectively used as one citation. Most of them are very good papers but they tend to already have been cited elsewhere in the article (or, at least, other papers from these groups are represented)

  • First[citation needed] book on metabolomics — Harrigan, G. G. & Goodacre, R. (eds) (2003). RMetabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Kluwer Academic Publishers (Boston). ISBN 1-4020-7370-4. 
  • Fiehn O, Kloska S, Altmann T (February 2001). "Integrated studies on plant biology using multiparallel techniques". Current Opinion in Biotechnology 12 (1): 82–6. doi:10.1016/S0958-1669(00)00165-8. PMID 11167078. 
  • Fiehn O (2001). "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks". Comparative and Functional Genomics 2 (3): 155–68. doi:10.1002/cfg.82. PMC 2447208. PMID 18628911. 
  • Weckwerth, W. Metabolomics in systems biology. Annu. Rev. Plant Biol. 54, 669–689 (2003).
  • Goodacre, R., Vaidyanathan, S., Dunn, W. B., Harrigan, G. G. & Kell, D. B. Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol. 22, 245–252 (2004).
  • Nicholson, J. K., Holmes, E., Lindon, J. C. & Wilson, I. D. The challenges of modeling mammalian biocomplexity. Nature Biotechnol. 22, 1268–1274 (2004). Stresses the role of intestinal microorganisms in contributing to the human metabolome.
  • van der Greef, J., Stroobant, P. & van der Heijden, R. The role of analytical sciences in medical systems biology. Curr. Opin. Chem. Biol. 8, 559–565 (2004).
  • Kell, D. B. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296–307 (2004).
  • Dunn, W.B. and Ellis, D.I. (2005) Metabolomics: current analytical platforms and methodologies. Trends in Analytical Chemistry 24(4), 285-294.
  • Ellis DI, Goodacre R (August 2006). "Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy". The Analyst 131 (8): 875–85. doi:10.1039/b602376m. PMID 17028718. 

--Amaher (talk) 23:35, 18 January 2010 (UTC)

Last section[edit]

I don't want to stand on anyone's toes, but I think the section I've removed from the article and pasted below reads like an advert for one company's technologies and has no references so shouldn't be included. Otherwise the rest of the article seems quite informative. Terri G (talk) 14:58, 21 November 2008 (UTC)

'Application of metabolomics to drug discovery and development' The use of biomarkers to improve drug discovery and development is a well established paradigm that, unfortunately, has yet to be achieved. While expectations have been set for biomarker discovery to be the engine for improved discovery and development, the mechanisms for achieving this remain unclear. In an attempt to clarify the approaches to help speed the development and approval of medical and pharmaceutical products, the US Food and Drug Administration developed the Critical Path initiatives in 2006. Within these guidelines, the importance of using qualified biomarkers is defined for the areas of: drug candidate safety testing, dose range identification, dose response evaluation, clinical trial subject selection, and using the biomarker as a surrogate endpoint to determine product efficacy. With these agency-defined objectives as a guideline, researchers are now beginning to fully leverage the benefits of biochemical biomarkers, by improving the prioritisation of drug candidates. Recently, Metabolon has developed a series of defined metabolomics-based solutions to address these needs. The first of these, mSelect, is designed to identify the leading drug candidate in early stage discovery. For example, in addition to interacting with the intended target, many drug candidates are likely to have unanticipated affects on other pathways. These effects can lead to safety issues that do not surface until late in the development process. With mSelect, metabolomics is used to isolate significantly altered biochemical biomarkers from dosed cell cultures. Through further analysis, the effected biochemical pathways are also identified so researchers can effectively assess the broad biological impact of each candidate drug. Using these data, the most promising lead compound(s) can continue to the next phase of development. Ideally, further evaluation of lead candidates throughout the discovery and development processes would be based on a consistent set of qualified biomarkers. Metabolomics offers a promising approach to achieve this objective because of the highly conserved nature of biochemical biomarkers across species. In addition, processing of biological samples from various sources can be examined on the same platforms, thus reducing variability introduced by differences in analytical equipment. Metabolon’s second solution, mVivo, is designed to evaluate the changes in drug-induced biochemical biomarkers during pre-clinical animal model testing. In many ways, this solution is similar to mSelect except that it is used in conjunction with routine animal studies and utilises various sample types such as plasma or biopsy material. mVivo can monitor the metabolism of the drug as well as measuring all of the other changes related to the action of the chemical. Finally, mProveClinical, the third solution, is designed to evaluate drug effects on biochemical biomarkers in first-in-human clinical studies. Currently, drug development companies make large investments to advance a compound to the point where the first tests in man can take place. However, since these studies are designed to test for drug safety, there is a relatively small amount of rich biomarker data derived from these studies. In addition to the traditional safety assessments performed at this stage of evaluation, with mProveClinical a preliminary read of the drug-induced effects on thepreviously identified biomarkers can be achieved. By applying these three solutions on a single metabolomics platform, researchers can leverage highly conserved biochemical biomarkers in a stepwise manner throughout the drug discovery and development process. Findings at each stage can be compared to the earlier results, whether in tissue culture, animals, or humans, to fully leverage biomarkers as a tool for rationale decisions ultimately leading to more reliable product development.


Edits regarding separation methods[edit]

I have made a few edits to this page today - there were several instances where the article stated that metabolomics requires "extraction of metabolites" and "separation of analytes". This is a misleading generalisation since NMR-based methods do not require "separation" or "extraction" of any metabolites - just a spot of D2O and away you go. In general the article itself can do with a massive clean up. --Amaher (talk) 23:57, 7 January 2010 (UTC)

History section[edit]

The history section of this article is mostly original research and as such does not belong in Wikipedia. This article is about Metabolomics, which means that the History section should detail the background to the field with respect to what people have published within the Metabolomics field. I'm going to clean this up very soon to align this section more closely with Wikipedia guidelines contained in WP:OR--Amaher (talk) 01:59, 11 January 2010 (UTC)

OK I have made substantial additions to the History section - based on sources that were written by modern day metabolomics people and published in peer-reviewed journals. I have left the Arthur Robinson section in for now but it needs citations (i.e. ones that specifically relate it to modern day metabolomics - rather than the primary sources) as do a few other things in there. Let me know what you think. --Amaher (talk) 03:08, 11 January 2010 (UTC)
I've removed a number of the Robinson refs since it was giving undue weight to this group and thus not in alignment with WP guidelines (WP:NPOV). Although I have left some of the info in and cleaned up the ref list by adding an inline citation since some people in the field have acknowledged the contribution of this group. Although it still problably should only have refs from modern players in the field. I'll come back to this soon.--Amaher (talk) 11:09, 17 January 2010 (UTC)