, Volume 4, Issue 4, pp 393–405

The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry

  • Jesper Højer-Pedersen
  • Jørn Smedsgaard
  • Jens Nielsen
Original Article

DOI: 10.1007/s11306-008-0132-4

Cite this article as:
Højer-Pedersen, J., Smedsgaard, J. & Nielsen, J. Metabolomics (2008) 4: 393. doi:10.1007/s11306-008-0132-4


Mass spectrometry (MS) has been a major driver for metabolomics, and gas chromatography (GC)-MS has been one of the primary techniques used for microbial metabolomics. The use of liquid chromatography (LC)-MS has however been limited, but electrospray ionization (ESI) is very well suited for ionization of microbial metabolites without any previous derivatization needed. To address the capabilities of ESI-MS in detecting the metabolome of Saccharomyces cerevisiae, the in silico metabolome of this organism was used as a template to present a theoretical metabolome. This showed that in combination with the specificity of MS up to 84% of the metabolites can be identified in a high mass accuracy ESI-spectrum. A total of 66 metabolites were systematically analyzed by positive and negative ESI-MS/MS with the aim of initiating a spectral library for ESI of microbial metabolites. This systematic analysis gave insight into the ionization and fragmentation characteristics of the different metabolites. With this insight, a small study of metabolic footprinting with ESI-MS demonstrated that biological information can be extracted from footprinting spectra. Statistical analysis of the footprinting data revealed discriminating ions, which could be assigned using the in silico metabolome. By this approach metabolic footprinting can advance from a classification method that is used to derive biological information based on guilt-by-association, to a tool for extraction of metabolic differences, which can guide new targeted biological experiments.


Mass spectrometry Metabolic footprinting Saccharomyces cerevisiae Mass spectral library Metabolic marker 

Supplementary material

11306_2008_132_MOESM1_ESM.pdf (210 kb)
(PDF 210 kb)

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Jesper Højer-Pedersen
    • 1
  • Jørn Smedsgaard
    • 1
  • Jens Nielsen
    • 1
    • 2
  1. 1.Center for Microbial BiotechnologyTechnical University of DenmarkKongens LyngbyDenmark
  2. 2.Systems Biology, Department of Chemical and Biological EngineeringChalmers University of TechnologyGothenburgSweden

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