SIRIUS: decomposing isotope patterns for metabolite identification

By Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin. Bioinform., 2008

331 citations recorded by the source corpus.

Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still remain uncharacterized. Determination of the sum formula is a crucial step in the identification of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set. Results: We present a method for determining the sum formula of a metabolite solely from its mass and the natural distribution of its isotopes. Our input is a measured isotope pattern from a high resolution mass spectrometer, and we want to find those molecules that best match this pattern. Our method is computationally efficient, and results on experimental data are very promising: for orthogonal time-of-flight mass spectrometry, we correctly identify sum formulas for >90% of the molecules, ranging in mass up to 1000 Da. Availability: SIRIUS is available under the LGPL license at http://bio.informatik.uni-jena.de/sirius/ Contact: anton.pervukhin@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Ecology, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/aba341ed9cd8a930b4114f8b0727c8b35888b239

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Citations in the corpus

Computational mass spectrometry for small molecules (2013, methodology): “Decomp [100,101] for arbitrary alphabets of elements requires only little memory swift in practice SIRIUS [102,103] ∗ implementing Decomp approach for MS decomposing real-valued masses “Seven Golden Rules” [104] to ﬁlter molecular formulas”
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “The stand-alone SIRIUS GUI software [101] is used to calculate fragmentation trees and, subsequently, molecular formulas [102].”
Metabolomics in pesticide research and development: review and future perspectives (2011, neutral): “…Kind and Fiehn (2007) SIRIOUS http://bio.informatik.uni-jena.de/sirius/download/index.html Böcker et al. (2009) TargetSearch http://www.bioconductor.org/packages/2.5/bioc/html/TargetSearch.html Cuadros-Inostroza et al. (2009) VANTED…”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, methodology): “For most inputs, a Round Robin algorithm, originally developed for the SIRIUS metabolite identification tool [57], is used.”