Literature DB >> 30886413

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.

Kai Dührkop1, Markus Fleischauer1, Marcus Ludwig1, Alexander A Aksenov2,3, Alexey V Melnik2,3, Marvin Meusel1,4, Pieter C Dorrestein2,3, Juho Rousu5, Sebastian Böcker6.   

Abstract

Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 (https://bio.informatik.uni-jena.de/sirius/), which provides a fast computational approach for molecular structure identification. SIRIUS 4 integrates CSI:FingerID for searching in molecular structure databases. Using SIRIUS 4, we achieved identification rates of more than 70% on challenging metabolomics datasets.

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Year:  2019        PMID: 30886413     DOI: 10.1038/s41592-019-0344-8

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  152 in total

Review 1.  Software tools, databases and resources in metabolomics: updates from 2018 to 2019.

Authors:  Keiron O'Shea; Biswapriya B Misra
Journal:  Metabolomics       Date:  2020-03-07       Impact factor: 4.290

2.  A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.

Authors:  Jordan E Bisanz; Paola Soto-Perez; Cecilia Noecker; Alexander A Aksenov; Kathy N Lam; Grace E Kenney; Elizabeth N Bess; Henry J Haiser; Than S Kyaw; Feiqiao B Yu; Vayu M Rekdal; Connie W Y Ha; Suzanne Devkota; Emily P Balskus; Pieter C Dorrestein; Emma Allen-Vercoe; Peter J Turnbaugh
Journal:  Cell Host Microbe       Date:  2020-04-28       Impact factor: 21.023

Review 3.  Metabolome response to anthropogenic contamination on microalgae: a review.

Authors:  Léa Gauthier; Juliette Tison-Rosebery; Soizic Morin; Nicolas Mazzella
Journal:  Metabolomics       Date:  2019-12-21       Impact factor: 4.290

4.  High-resolution MS/MS metabolomics by data-independent acquisition reveals urinary metabolic alteration in experimental colitis.

Authors:  Zhixiang Yan; Ting Li; Bin Wei; Panpan Wang; Jianbo Wan; Yitao Wang; Ru Yan
Journal:  Metabolomics       Date:  2019-04-30       Impact factor: 4.290

5.  Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.

Authors:  Anupriya Tripathi; Yoshiki Vázquez-Baeza; Julia M Gauglitz; Mingxun Wang; Kai Dührkop; Mélissa Nothias-Esposito; Deepa D Acharya; Madeleine Ernst; Justin J J van der Hooft; Qiyun Zhu; Daniel McDonald; Asker D Brejnrod; Antonio Gonzalez; Jo Handelsman; Markus Fleischauer; Marcus Ludwig; Sebastian Böcker; Louis-Félix Nothias; Rob Knight; Pieter C Dorrestein
Journal:  Nat Chem Biol       Date:  2020-11-16       Impact factor: 15.040

6.  A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products.

Authors:  Raphael Reher; Hyun Woo Kim; Chen Zhang; Huanru Henry Mao; Mingxun Wang; Louis-Félix Nothias; Andres Mauricio Caraballo-Rodriguez; Evgenia Glukhov; Bahar Teke; Tiago Leao; Kelsey L Alexander; Brendan M Duggan; Ezra L Van Everbroeck; Pieter C Dorrestein; Garrison W Cottrell; William H Gerwick
Journal:  J Am Chem Soc       Date:  2020-02-21       Impact factor: 15.419

7.  Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics Using Probabilistic Modeling.

Authors:  Ramtin Hosseini; Neda Hassanpour; Li-Ping Liu; Soha Hassoun
Journal:  Metabolites       Date:  2020-05-03

8.  Staring into the void: demystifying microbial metabolomics.

Authors:  Cynthia M Grim; Gordon T Luu; Laura M Sanchez
Journal:  FEMS Microbiol Lett       Date:  2019-06-01       Impact factor: 2.742

9.  Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.

Authors:  Kai Dührkop; Louis-Félix Nothias; Markus Fleischauer; Raphael Reher; Marcus Ludwig; Martin A Hoffmann; Daniel Petras; William H Gerwick; Juho Rousu; Pieter C Dorrestein; Sebastian Böcker
Journal:  Nat Biotechnol       Date:  2020-11-23       Impact factor: 54.908

Review 10.  Microbial natural product databases: moving forward in the multi-omics era.

Authors:  Jeffrey A van Santen; Satria A Kautsar; Marnix H Medema; Roger G Linington
Journal:  Nat Prod Rep       Date:  2020-08-28       Impact factor: 13.423

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