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Computational mass spectrometry for small molecules

Kerstin Scheubert1*, Franziska Hufsky12 and Sebastian Böcker1

Author Affiliations

1 Chair of Bioinformatics, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena, Germany

2 Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany

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Journal of Cheminformatics 2013, 5:12  doi:10.1186/1758-2946-5-12

Published: 1 March 2013


The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline.

Mass spectrometry; Metabolomics; Spectral library; Molecular formula identification; Structure elucidation; Fragmentation trees; Networks