Golm Metabolome Database: Difference between revisions

Revision as of 18:23, 29 November 2012

Latest revision as of 17:35, 1 August 2025

(31 intermediate revisions by 19 users not shown)

Line 1:

[[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]]

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|Max Planck Institute of Molecular Plant Physiology]] in [[Golm (Potsdam)|Golm]] district of [[Potsdam]], Germany.

[[File:Golm Metabolome Database Metabolite Profile 2.png|thumb|profile of all metabolites in a single experiments]]

[[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 = DecisionHummel tree| supportedfirst1 substructure= predictionJ. of| metaboliteslast2 from= GC-MSStrehmel profiles|author= Hummelfirst2 J, Strehmel= N,. Selbig| J,last3 Walther= DBölling and| Kopkafirst3 J|journal= [[Metabolomics]]C. |volume last4 =6 Schmidt |pages=322-333 |yearfirst4 =2010 |doi=10S.1007/s11306-010-0198-7 | issuelast5 = 2}}</ref><ref>{{citeWalther journal| |first5 title= RetentionD. index| thresholdslast6 for= compoundKopka matching| infirst6 GC-MS= metaboliteJ. profiling|author chapter = StrehmelMass N,Spectral HummelSearch J,and ErbanAnalysis A,Using Strassburgthe KGolm andMetabolome KopkaDatabase J| doi = 10.1002/9783527669882.ch18 |journal title = [[JournalThe Handbook of ChromatographyPlant B]]Metabolomics |volume=871 |pages =182-190 321 | year=2008 |doi=10.1016/j.jchromb.2008.04.042 2013 | issueisbn = 29783527669882 }}</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= [e-mail]: 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.

== 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.

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 different mass spectral matching differences in the used detector technologies, namely

[[Quadrupole mass 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 MSBackbTsMSTs, 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 Alsoalso==

* [[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]]