Fragmentation trees reloaded

Journal of Cheminformatics
Sebastian Böcker, Kai Dührkop

Abstract

Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our me...Continue Reading

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Citations

Jul 12, 2016·Analytical Chemistry·Marvin MeuselSebastian Böcker
Aug 12, 2016·Analytical Chemistry·Nathaniel G MahieuGary J Patti
Mar 11, 2017·Environmental Science & Technology·P Lee Ferguson, Heather M Stapleton
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May 30, 2019·Natural Product Reports·Alexander E Fox RamosMehdi A Beniddir
Aug 4, 2020·Journal of Analytical Toxicology·Nick VerougstraeteChristophe Stove
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Jul 12, 2018·Nature·Naama KanarekDavid M Sabatini
Jul 25, 2019·Frontiers in Plant Science·Madeleine ErnstNina Rønsted
Jun 25, 2020·International Journal of Molecular Sciences·Alberto Dávila-LaraAxel Mithöfer
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Nov 1, 2017·Journal of Cheminformatics·Emma L SchymanskiSteffen Neumann
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May 24, 2021·Environmental Pollution·Kirsten E OverdahlP Lee Ferguson
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Sep 28, 2017·Journal of the American Society for Mass Spectrometry·Jennifer E ScholléeJuliane Hollender
Aug 2, 2019·Analytical Chemistry·Alexander E Fox RamosMehdi A Beniddir

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Software Mentioned

Chemistry Development Kit ( CDK )
GNPS
SIRIUS
PubChem
MassHunter
MOLGEN
MassBank

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