|
[[File:Visualisation of a mass spectrum in the Golm Metabolome Database.png|thumb|GMD reference mass spectrum]][[File:Golm Metabolome Database Metabolite Profile 1.png|thumb|profile of a single metabolite across replicates of different experiments]]
{{AFC submission|d|blank|declinets=20121129013427|decliner=Rushbugled13|ts=20121129013123|u=Jahu54321|ns=5}}
[[File:Golm Metabolome Database Metabolite Profile 2.png|thumb|profile of all metabolites in a single experiments]]
<!-- This will add a notice to the bottom of the page and won't blank it! The new template which says that your draft is waiting for a review will appear at the bottom; simply ignore the old (grey) drafted templates and the old (red) decline templates. A bot will update your article submission. Until then, please don't change anything in this text box and press "Save page". -->
[[File:Golm Metabolome Database Metabolite Profile 3.png|thumb|relative metabolite concentrations in the replica groups of a single experiment]]
The '''Golm Metabolome Database''' ('''GMD''')<ref>{{ citeCite journalbook | titlelast1 = RetentionHummel index| thresholdsfirst1 for= compoundJ. matching| inlast2 GC-MS= metaboliteStrehmel profiling| author= Strehmelfirst2 = N ,. Hummel| J,last3 Erban= A,Bölling Strassburg| Kfirst3 and= KopkaC. J| last4 = Schmidt | journal first4 = [[JournalS. of| Chromatographylast5 B]]= Walther | volume first5 = 871 D. | pages last6 = 182-190 Kopka | year first6 = 2008 J. | chapter = Mass Spectral Search and Analysis Using the Golm Metabolome Database | doi = 10. 10161002/ j9783527669882. jchromb.2008.04.042ch18 | issuetitle = 2The Handbook of Plant Metabolomics | pages = 321 | year = 2013 | isbn = 9783527669882 }}</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 |url=https://archive.org/details/metabolomicspowe00niel |url-access=limited |publisher=Springer Berlin Heidelberg | dateyear=2007 |pages= [https://archive.org/details/metabolomicspowe00niel/page/n45 75 -96]–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| authorvauthors= 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 lettersLetters]] |volume=579 |pages= 1332-13371332–1337 |year=2005 |doi=10.1016/j.febslet.2005.01.029 | issue= 6 |pmid=15733837|doi-access=free }}</ref><ref>{{cite journal | title= GMD@CSB.DB: the Golm Metabolome Database| authorvauthors= 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 (journal)|Bioinformatics]] |volume=21 |pages= 1635-16381635–1638 |year=2005 |doi=10.1093/bioinformatics/bti236 | issue= 8 |pmid=15613389|doi-access=free |hdl=20.500.11850/33179 |hdl-access=free }}</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 [[Chromatography#Terms|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.▼
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= GMD@CSB.DB: 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]] (GC-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 [[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 metabolicbiomarkers in biomarkers[[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.
Due to the lack of mandatory standards it remains difficult to compare individual mass spectrums.
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. ▼While the different mass detector technologies, namely
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. ▼▲While for the[[Quadrupole mass spectral matching differences in the used detector technologies, namely analyzer|quadrupole ]], [[ion trap ]] and [[Time-of-flight mass spectrometry|time of flight ]], can be deemed irrelevant, the 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 assessedassesses the accuracy of RI transfer between chromatography variants and implementedimplements means to transfer empiricalempirically determined RI properties. <ref>{{cite journal | title= Retention index thresholds for compound matching in GC-MS metabolite profiling|vauthors=Strehmel N, Hummel J, Erban A, Strassburg K, Kopka J |journal= [[Journal of Chromatography B]] |volume=871 |pages=182–190 |year=2008 |doi=10.1016/j.jchromb.2008.04.042 |pmid=18501684 | issue= 2}}</ref>
▲Aiming at the classification and identification of un-identified MSTs, the GMD accessedaccesses the information on available reference compounds . asThese acompounds sourceserve ofas training set of data to apply [[decision trees]] (DT) as a supervised [[machine learning]] approach. Single structureStructural feature extraction was applied to classify the metabolite space of the GMD prior to DT training. DT-based predictionpredictions 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. <ref>{{cite journal | title= Decision tree supported substructure prediction of metabolites from GC-MS profiles|vauthors=Hummel J, Strehmel N, Selbig J, Walther D, Kopka J |journal= [[Metabolomics]] |volume=6 |pages=322–333 |year=2010 |doi=10.1007/s11306-010-0198-7 |pmid=20526350 | issue= 2|pmc=2874469 }}</ref>
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.
The GMD visualise quantitative metabolite pool size changes data.
==See also==
* [[Human Metabolome Database]]
* [[MassBank (database)|MassBank]]
==References==
{{reflist}}
==External links==
* [http://gmd.mpimp-golm.mpg.de GMD website]
[[Category:Mass spectrometry software]]
[[Category:Organic compounds]]
[[Category:Chemical databases]]
[[Category:Metabolomic databases]]
| 