Computational mass spectrometry for small molecules

By Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker. 2013

156 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. I. Blaženović
2. Jian Ji
3. Tobias Kind
4. Oliver Fiehn
5. Felicity Allen
6. David S. Wishart
7. Russ Greiner
8. Sebastian Böcker

In Molecular Biology

1. David S. Wishart
2. Tobias Kind
3. Oliver Fiehn
4. I. Blaženović
5. Jian Ji
6. Felicity Allen
7. Russ Greiner
8. Jianguo Xia

In Spectroscopy

1. David S. Wishart
2. Oliver Fiehn
3. Felicity Allen
4. Tobias Kind
5. I. Blaženović
6. Russ Greiner
7. Jian Ji
8. Jianguo Xia

Citations in the corpus

• Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification (2013, methodology): “2007), using mass spectrometry, compare a collected MS or MS/MS spectrum for an unknown compound against a database containing reference MS or MS/MS spectra (Stein and Scott 1994; Scheubert et al. 2013; Tautenhahn et al. 2012).”
• Non-target screening with high-resolution mass spectrometry: critical review using a collaborative trial on water analysis (2015, unknown): “[13–15]).”
• Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, background): “Most of the approaches below have been discussed in much greater technical detail in a series of excellent reviews [88–91].”