Compounds class for SIRIUS results.

This class is derived from compounds and contains additional specific SIRIUS data.

Details

Objects from this class are generated by generateCompoundsSIRIUS

Slots

fingerprints

A list with for each feature group result a data.table containing fingerprints obtained with CSI:FingerID.

S4 class hierarchy

• compounds

  • compoundsSIRIUS

References

Hoffmann MA, Nothias L, Ludwig M, Fleischauer M, Gentry EC, Witting M, Dorrestein PC, Dührkop K, Böcker S (2021). “High-confidence structural annotation of metabolites absent from spectral libraries.” Nature Biotechnology, 40(3), 411–421. ISSN 1546-1696. doi:10.1038/s41587-021-01045-9 . http://dx.doi.org/10.1038/s41587-021-01045-9.

Dührkop K, Nothias L, Fleischauer M, Reher R, Ludwig M, Hoffmann MA, Petras D, Gerwick WH, Rousu J, Dorrestein PC, Böcker S (2020). “Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.” Nature Biotechnology, 39(4), 462–471. ISSN 1546-1696. doi:10.1038/s41587-020-0740-8 . http://dx.doi.org/10.1038/s41587-020-0740-8.

Duhrkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Bocker S (2019). “SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.” Nature Methods, 16(4), 299–302. doi:10.1038/s41592-019-0344-8 .

Duhrkop K, Bocker S (2015). “Fragmentation Trees Reloaded.” In Przytycka TM (ed.), Research in Computational Molecular Biology, 65–79. ISBN 978-3-319-16706-0.

Duhrkop K, Shen H, Meusel M, Rousu J, Bocker S (2015). “Searching molecular structure databases with tandem mass spectra using CSI:FingerID.” Proceedings of the National Academy of Sciences, 112(41), 12580–12585. doi:10.1073/pnas.1509788112 .

Bocker S, Letzel MC, Liptak Z, Pervukhin A (2008). “SIRIUS: decomposing isotope patterns for metabolite identification.” Bioinformatics, 25(2), 218–224. doi:10.1093/bioinformatics/btn603 .

See also

compounds and generateCompoundsSIRIUS