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

被引：1140

作者：

Duhrkop, Kai ^{[1
]}

Fleischauer, Markus ^{[1
]}

Ludwig, Marcus ^{[1
]}

Aksenov, Alexander A. ^{[2
,3
]}

Melnik, Alexey V. ^{[2
,3
]}

Meusel, Marvin ^{[1
,4
]}

Dorrestein, Pieter C. ^{[2
,3
]}

Rousu, Juho ^{[5
]}

Bocker, Sebastian ^{[1
]}

机构：

[1] Friedrich Schiller Univ, Chair Bioinformat, Jena, Germany

[2] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[4] Saarland Univ, Helmholtz Ctr Infect Res & Pharmaceut Biotechnol, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, Saarbrucken, Germany

[5] Aalto Univ, Dept Comp Sci, Helsinki Inst Informat Technol, Espoo, Finland

来源：

NATURE METHODS | 2019年 / 16卷 / 04期

基金：

芬兰科学院;

关键词：

SPECTROMETRY DATA; IDENTIFICATION; FRAGMENTATION; PREDICTION; DATABASES; PRODUCTS;

D O I：

10.1038/s41592-019-0344-8

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：299 / +

页数：8

共 44 条

[31] Finding Maximum Colorful Subtrees in Practice [J].

Rauf, Imran ;

Rasche, Florian ;

Nicolas, Francois ;

Boecker, Sebastian .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2013, 20 (04) :311-321

[32]

Röst HL, 2016, NAT METHODS, V13, P741, DOI [10.1038/nmeth.3959, 10.1038/NMETH.3959]

[33] Extended-Connectivity Fingerprints [J].

Rogers, David ;

Hahn, Mathew .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2010, 50 (05) :742-754

[34] Critical Assessment of Small Molecule Identification 2016: automated methods [J].

Schymanski, Emma L. ;

Ruttkies, Christoph ;

Krauss, Martin ;

Brouard, Celine ;

Kind, Tobias ;

Duehrkop, Kai ;

Allen, Felicity ;

Vaniya, Arpana ;

Verdegem, Dries ;

Boecker, Sebastian ;

Rousu, Juho ;

Shen, Huibin ;

Tsugawa, Hiroshi ;

Sajed, Tanvir ;

Fiehn, Oliver ;

Ghesquiere, Bart ;

Neumann, Steffen .

JOURNAL OF CHEMINFORMATICS, 2017, 9

[35]

Senior JK., 1951, AM J MATH, V73, P663, DOI [10.2307/2372318, DOI 10.2307/2372318]

[36] Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning [J].

Shen, Huibin ;

Szedmak, Sandor ;

Brouard, Celine ;

Rousu, Juho .

DISCOVERY SCIENCE, (DS 2016), 2016, 9956 :427-441

[37] Metabolite identification through multiple kernel learning on fragmentation trees [J].

Shen, Huibin ;

Duhrkop, Kai ;

Bocker, Sebastian ;

Rousu, Juho .

BIOINFORMATICS, 2014, 30 (12) :157-164

[38] XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification [J].

Smith, CA ;

Want, EJ ;

O'Maille, G ;

Abagyan, R ;

Siuzdak, G .

ANALYTICAL CHEMISTRY, 2006, 78 (03) :779-787

[39] The Chemistry Development Kit (CDK): An open-source Java']Java library for chemo- and bioinformatics [J].

Steinbeck, C ;

Han, YQ ;

Kuhn, S ;

Horlacher, O ;

Luttmann, E ;

Willighagen, E .

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 2003, 43 (02) :493-500

[40] MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis [J].

Tsugawa, Hiroshi ;

Cajka, Tomas ;

Kind, Tobias ;

Ma, Yan ;

Higgins, Brendan ;

Ikeda, Kazutaka ;

Kanazawa, Mitsuhiro ;

VanderGheynst, Jean ;

Fiehn, Oliver ;

Arita, Masanori .

NATURE METHODS, 2015, 12 (06) :523-+

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