Golm Metabolome Database: Difference between revisions

Revision as of 08:23, 29 November 2012

Revision as of 08:26, 29 November 2012

Line 1:

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=322-333 |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=182-190 |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 |editor-last1=Nielsen |editor-last2=Jewett |title=Metabolomics |publisher=Springer Berlin Heidelberg |date=2007 |pages=75-96 |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=1332-1337 |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=1635-1638 |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]] 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 metabolic 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.

As the communication of analytical results and other approach-related details such as mass spectral and RI reference information within the scientific community is becoming increasingly popular, open access platforms for information exchange, such as the GMD, are obligatory.

While for the mass spectral matching differences in the used detector technologies, namely quadrupole, ion trap and time of flight, can be deemed irrelevant, chromatography settings varying between different laboratories such as temperature programming, type of capillary column and choice of column manufacturer heavily affect the empirically determined RI properties. Procedures for the transfer of RI properties between chromatography variants are, therefore, highly relevant for a shared library use. The GMD assessed the accuracy of RI transfer between chromatography variants and implemented means to transfer empirical determined RI properties.