Visualisation of a mass spectrum in the Golm Metabolome Database

Golm Metabolome Database Metabolite Profile 1

Golm Metabolome Database Metabolite Profile 2

Golm Metabolome Database Metabolite Profile 3

The Golm Metabolome Database (GMD) is a 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 In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a ...

attached indices) together with data of a multitude of already identified metabolites and reference substances. The GMD is hosted at the

Max Planck Institute of Molecular Plant Physiology The Max Planck Institute of Molecular Plant Physiology (german: Max-Planck-Institut für molekulare Pflanzenphysiologie) is a German research institute for molecular plant physiology, based in the Golm district of Potsdam, Brandenburg. Founded ...

in Golm district of

Potsdam Potsdam () is the capital and, with around 183,000 inhabitants, largest city of the German state of Brandenburg. It is part of the Berlin/Brandenburg Metropolitan Region. Potsdam sits on the River Havel, a tributary of the Elbe, downstream o ...

, 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 Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...

. 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 the different mass detector technologies, namely

quadrupole A quadrupole or quadrapole is one of a sequence of configurations of things like electric charge or current, or gravitational mass that can exist in ideal form, but it is usually just part of a multipole expansion of a more complex structure refl ...

ion trap An ion trap is a combination of electric and/or magnetic fields used to capture charged particles — known as ions — often in a system isolated from an external environment. Atomic and molecular ion traps have a number of applications in phy ...

and

time of flight Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium. This information can then be used to measure velocity or path length, or as a w ...

, can be deemed irrelevant, the chromatography settings 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 assesses the accuracy of RI transfer between chromatography variants and implements means to transfer empirically determined RI properties. Aiming at the classification and identification of un-identified MSTs, the GMD accesses the information on available reference compounds. These compounds serve as training set of data to apply

decision trees A decision tree is a decision support tool that uses a tree-like model of decisions and their possible consequences, including chance event outcomes, resource costs, and utility. It is one way to display an algorithm that only contains condit ...

(DT) as a supervised

machine learning Machine learning (ML) is a field of inquiry devoted to understanding and building methods that 'learn', that is, methods that leverage data to improve performance on some set of tasks. It is seen as a part of artificial intelligence. Machine ...

approach. Structural feature extraction was applied to classify the metabolite space of the GMD prior to DT training. DT-based predictions 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 is a salt of a fatty acid used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are used as ...

(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.

References

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External links

GMD website
Mass spectrometry software Organic compounds Chemical databases Metabolomic databases Biological databases

Background

See also

References

External links