Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

Journal of Cheminformatics
Ivana BlaženovićOliver Fiehn

Abstract

In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hi...Continue Reading

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Citations

Feb 21, 2018·Environmental Science and Pollution Research International·Andrew D McEachranElizabeth Guthrie Nichols
Dec 1, 2017·Journal of Cheminformatics·Antony J WilliamsAnn M Richard
Jun 27, 2020·Metabolites·Andrew D McEachranAntony J Williams
Apr 25, 2019·Metabolites·Yannick Djoumbou-FeunangDavid S Wishart
Aug 4, 2019·Scientific Data·Andrew D McEachranAntony J Williams
Sep 27, 2019·Environmental Health Perspectives·Dinesh Kumar Barupal, Oliver Fiehn
Mar 7, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Qing FangHai Deng
Apr 5, 2019·Nature Communications·Xiaotao ShenZheng-Jiang Zhu
Jun 19, 2019·Analytical and Bioanalytical Chemistry·Christoph RuttkiesMartin Krauss
Sep 1, 2018·Journal of Cheminformatics·Andrew D McEachranAntony J Williams
Oct 16, 2020·The Science of the Total Environment·Ingus PerkonsVadims Bartkevics
Jan 8, 2021·Journal of Cheminformatics·Rick HelmusEmma L Schymanski
Mar 4, 2021·Journal of the American Society for Mass Spectrometry·Michael J TaylorChristopher R Anderton
Mar 12, 2021·Emerging Topics in Life Sciences·Sophie Alvarez, Michael J Naldrett
Mar 10, 2021·Journal of Cheminformatics·Emma L SchymanskiEvan E Bolton
Mar 25, 2021·Briefings in Bioinformatics·Christoph A Krettler, Gerhard G Thallinger
Feb 18, 2020·Reproductive Toxicology·Julia E RagerRebecca C Fry
Aug 20, 2021·Journal of the American Society for Mass Spectrometry·Ting JiangTracey J Woodruff
Jan 5, 2019·Analytical Chemistry·Ivana BlaženovićOliver Fiehn
Apr 17, 2019·Analytical Chemistry·Hongchao JiZhimin Zhang
Oct 16, 2021·Nature Biotechnology·Martin A HoffmannSebastian Böcker

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Software Mentioned

MacOS
MIDAS
Molecular Structure Correlator ( Agilent
ChemSpider
MAGMA
MOLGEN
MetFrag
CASMI
MS search
InChIKey

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