Skip to main content

Annotation of LC/ESI-MS Mass Signals

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4414))

Abstract

Mass spectrometry is the work-horse technology of the emerging field of metabolomics. The identification of mass signals remains the largest bottleneck for a non-targeted approach: due to the analytical method, each metabolite in a complex mixture will give rise to a number of mass signals. In contrast to GC/MS measurements, for soft ionisation methods such as ESI-MS there are no extensive libraries of reference spectra or established deconvolution methods. We present a set of annotation methods which aim to group together mass signals measured from a single metabolite, based on rules for mass differences and peak shape comparison.

Availability: The software and documentation is available as an R package on http://msbi.ipb-halle.de/

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Böcker, S., Letzel, M.C., Lipták, Z., Pervukhin, A.: Decomposing metabolomic isotope patterns. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 12–23. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  2. Fiehn, O., Kopka, J., Dörmann, P., Altmann, T., Trethewey, R., Willmitzer, L.: Metabolite profiling for plant functional genomics. Nature Biotechnology 18, 115 (2000)

    Article  Google Scholar 

  3. Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., Kanehisa, M.: Organizing and computing metabolic pathway data in terms of binary relations. Pac. Symp. Biocomput., 175–186 (1997)

    Google Scholar 

  4. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., et al.: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34(Database issue), 354–357 (2006)

    Article  Google Scholar 

  5. Oliver, S.G., Winson, M.K., Kell, D.B., Baganz, F.: Systematic functional analysis of the yeast genome. Trends Biotechnol. 16(9), 373–378 (1998)

    Article  Google Scholar 

  6. von Roepenack-Lahaye, E., Degenkolb, T., Zerjeski, M., Franz, M., Roth, U., et al.: Profiling of Arabidopsis Secondary Metabolites by Capillary Liquid Chromatography Coupled to Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry. Plant Physiology 134, 548–559 (2004)

    Article  Google Scholar 

  7. Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M., Asahi, H., Kurokawa, K., et al.: KNApSAcK: A comprehensive species-metabolite relationship database. In: Plant Metabolomics. Biotechnology in Agriculture and Forestry, pp. 165–181. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  8. Smith, C.A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification. Analytical Chemistry 78(3), 779–787 (2006)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Sepp Hochreiter Roland Wagner

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer Berlin Heidelberg

About this paper

Cite this paper

Tautenhahn, R., Böttcher, C., Neumann, S. (2007). Annotation of LC/ESI-MS Mass Signals. In: Hochreiter, S., Wagner, R. (eds) Bioinformatics Research and Development. BIRD 2007. Lecture Notes in Computer Science(), vol 4414. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71233-6_29

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-71233-6_29

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71232-9

  • Online ISBN: 978-3-540-71233-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics