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MassBank

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Encyclopedia of Lipidomics

MassBank (Horai et al. 2010) is a public repository for metabolomics and lipidomics research containing mass spectra from small chemical compounds (<3000 Da). The database comprises a collection of MSn spectra of primary metabolites, flavonoids, gibberellins, saponins, carotenoids, oligosaccharides, and phospholipids. Lipids came into the scope of MassBank in 2008, as they became the official database of the Mass Spectral Society in Japan. Spectra are acquired under various pre-separation techniques, ion sources, MS instrumentations, ion modes, and varying collision energies. The reason for this heterogeneous data collection lies in the fact that the observed fragment ions and intensities thereof vary highly depending on these setup parameters (Hopley et al. 2008), particularly if ESI is used as ion source. The stored spectra are experimentally error-free and noise-free measurements of single chemical compounds, and as such they are a high-quality source. Compound identification is...

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Abbreviations

MS:

Mass spectrometry

MSn spectra:

Fragmentation spectra where n corresponds to MS stage

ESI:

Electrospray ionization

SMILES:

Simplified Molecular Input Line Entry Specification, i.e., a chemical structure encoding in a string format

InChI:

International Chemical Identifier, i.e., an identifier for chemical substances

mzML:

XML format for storing MS output in a vendor independent form

Molfile format:

Format for describing the 3D structure of a molecule

SOAP:

Protocol for exchanging structured information, used especially for the programmatic access to web services

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KNApSAcK:

Database containing species-metabolite relationships

References

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Authors and Affiliations

  1. Computational Biotechnology and Bioinformatics Group, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Austria

    Jürgen Hartler

Authors
  1. Jürgen Hartler
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Correspondence to Jürgen Hartler .

Editor information

Editors and Affiliations

  1. Yong Loo Lin School of Medicine Centre for Life Sciences, Singapore, Singapore

    Markus R. Wenk

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© 2015 Springer Science+Business Media Dordrecht

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Hartler, J. (2015). MassBank. In: Wenk, M. (eds) Encyclopedia of Lipidomics. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7864-1_12-1

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  • DOI: https://doi.org/10.1007/978-94-007-7864-1_12-1

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  • Publisher Name: Springer, Dordrecht

  • Online ISBN: 978-94-007-7864-1

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