Golm Metabolome Database: Difference between revisions

Revision as of 22:25, 29 November 2012

Revision as of 07:34, 1 December 2012

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The '''Golm Metabolome Database (GMD)''' <ref>{{cite journal | title= Decision tree supported substructure prediction of metabolites from GC-MS profiles|author= Hummel J, Strehmel N, Selbig J, Walther D and Kopka J|journal= [[Metabolomics]] |volume=6 |pages=322-333322–333 |year=2010 |doi=10.1007/s11306-010-0198-7 | issue= 2}}</ref><ref>{{cite journal | title= Retention index thresholds for compound matching in GC-MS metabolite profiling|author= Strehmel N, Hummel J, Erban A, Strassburg K and Kopka J |journal= [[Journal of Chromatography B]] |volume=871 |pages=182-190182–190 |year=2008 |doi=10.1016/j.jchromb.2008.04.042 | issue= 2}}</ref><ref>{{cite book |last1=Hummel |first1=Jan|last2=Selbig |first2=Joachim|last3=Walther |first3=Dirk|last4=Kopka |first4=Joachim |editor-first=John |editoreditor1-last1last=Nielsen |editoreditor2-last2last=Jewett |title=Metabolomics |publisher=Springer Berlin Heidelberg |dateyear=2007 |pages=75-9675–96 |chapter=The Golm Metabolome Database: a database for GC-MS based metabolite profiling |isbn=978-3-540-74719-2 |doi=10.1007/4735_2007_0229}}</ref><ref>{{cite journal | title= GC-MS libraries for the rapid identification of metabolites in complex biological samples|author= Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR and Kopka J |journal= [[FEBS letters]] |volume=579 |pages=1332-13371332–1337 |year=2005 |doi=10.1016/j.febslet.2005.01.029 | issue= 6}}</ref><ref>{{cite journal | title= [e-mail]: the Golm Metabolome Database|author= Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR and Steinhauser D |journal= [[Bioinformatics]] |volume=21 |pages=1635-16381635–1638 |year=2005 |doi=10.1093/bioinformatics/bti236 | issue= 8}}</ref> is a [[gas chromatography–mass spectrometry| gas chromatography (GC) – mass spectrometry (MS)]] reference library dedicated to [[metabolite]] profiling experiments and comprises mass spectral and retention index (RI) information for non-annotated mass spectral tags (MSTs, mass spectral information with [[retention time]] attached indices) together with data of a multitude of already identified metabolites and reference substances. The GMD is hosted at the [[Max Planck Institute for Molecular Plant Physiology|Max Planck Institute of Molecular Plant Physiology]] in [[Golm (Potsdam)|Golm]] district of [[Potsdam]], Germany.

== Background ==

Gas chromatography (GC) coupled to mass spectrometry (MS) is one of the most widespread routine technologies applied to the large scale screening and discovery of novel biomarkers in [[metabolomics]]. However, the majority of MSTs currently measured in plant [[metabolomic]] [[profiling]] experiments remains unidentified due to the lack of authenticated pure reference substances and the expensive and time-consuming effort to maintain mass spectral RI libraries required for compound identification by GC-MS.

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Aiming at the classification and identification of un-identified MSTs, the GMD accessed the information on available reference compounds as a source of training data to apply [[decision trees]] (DT) as a supervised [[machine learning]] approach. Single structure feature extraction was applied to classify the metabolite space of the GMD prior to DT training. DT-based prediction of the most frequent substructures classify low resolution GC-MS mass spectra of the linked (potentially unknown) metabolite with respect to the presence or absence of the chemical moieties.

The web-based frontend supports conventional mass spectral and RI comparison by ranked hit lists as well as advanced DT supported substructure prediction. Batch processing is enabled via [[Simple Object Access Protocol]] (SOAP)-based web services while web-based data access services expose particular data base entities adapting [[Representational State Transfer]] (ReST) principles and mass spectral standards such as [[NIST]]-MSP and [[JCAMP]]-DX.

==See Alsoalso==

* [[Human Metabolome Database]]

* [[MassBank (database)|MassBank]]

==References==

{{reflist}}

==External links==

* [http://gmd.mpimp-golm.mpg.de GMD website]

{{Uncategorized|date=December 2012}}