Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Metabolites
Ivana BlaženovićOliver Fiehn

Abstract

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

References

Dec 9, 2004·The American Journal of Clinical Nutrition·S Jill JamesJames A Neubrander
Dec 31, 2005·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Mar 21, 2007·Journal of Chemical Information and Modeling·Stephen E SteinPeter J Linstrom
Oct 13, 2007·Nucleic Acids Research·Kirill DegtyarenkoMichael Ashburner
Jun 21, 2008·Journal of Chemical Information and Modeling·Huixiao HongWeida Tong
Aug 2, 2008·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Erwan WernerJean-Claude Tabet
Nov 19, 2008·Bioinformatics·Sebastian BöckerAnton Pervukhin
Mar 6, 2010·Nature Protocols·Hye Kyong KimRobert Verpoorte
Jul 14, 2010·Journal of Mass Spectrometry : JMS·Hisayuki HoraiTakaaki Nishioka
Dec 25, 2010·Analytical Chemistry·Florian RascheSebastian Böcker
Feb 4, 2011·Bioanalytical Reviews·Tobias Kind, Oliver Fiehn
Mar 2, 2011·PloS One·Nikolaos PsychogiosDavid S Wishart
Mar 23, 2011·Journal of Computational Chemistry·Chun Wei Yap
Apr 27, 2012·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Faizan SahigaraRoberto Todeschini
Nov 20, 2012·Nucleic Acids Research·David S WishartAugustin Scalbert
Jan 11, 2013·Journal of Mass Spectrometry : JMS·Michael A StravsJuliane Hollender
Jan 25, 2013·Journal of Cheminformatics·Stephen HellerIgor Pletnev
Mar 5, 2013·Journal of Cheminformatics·Kerstin ScheubertSebastian Böcker
Mar 16, 2013·Journal of Mass Spectrometry : JMS·Michael Gerlich, Steffen Neumann
Sep 1, 2007·Metabolomics : Official Journal of the Metabolomic Society·Lloyd W SumnerMark R Viant
Oct 4, 2013·Analytical Chemistry·Oliver RübelBenjamin P Bowen
Oct 8, 2013·Rapid Communications in Mass Spectrometry : RCM·Cris LapthornFrank S Pullen
Dec 18, 2013·Annual Review of Physical Chemistry·Thomas WyttenbachMichael T Bowers
Jan 31, 2014·Environmental Science & Technology·Emma L SchymanskiJuliane Hollender
Mar 20, 2014·Analytical Chemistry·Giuseppe PagliaGiuseppe Astarita
Apr 23, 2014·Natural Product Reports·Franziska HufskySebastian Böcker
Jan 1, 2013·Metabolites·Kai DührkopSebastian Böcker
Jan 1, 2013·Metabolites·Christoph RuttkiesSteffen Neumann

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Citations

May 30, 2019·Natural Product Reports·Alexander E Fox RamosMehdi A Beniddir
Mar 19, 2019·Annual Review of Analytical Chemistry·María Eugenia MongeFacundo M Fernández
Jun 19, 2019·FEMS Microbiology Letters·Cynthia M GrimLaura M Sanchez
Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
Aug 24, 2019·Journal of the American Society for Mass Spectrometry·Erin S Baker, Gary J Patti
Sep 10, 2019·Mass Spectrometry Reviews·Ana Margarida RodriguesCarla António
Sep 27, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Michaela HoenigsbergerRainer Schuhmacher
Oct 22, 2019·Preparative Biochemistry & Biotechnology·Olga Nehir OztelErdal Karaoz
Feb 14, 2020·Metabolomics : Official Journal of the Metabolomic Society·Henrik CarlssonKim Kultima
Oct 28, 2019·Clinical and Translational Science·Ryan S FunkMara L Becker
Mar 20, 2020·Molecular Omics·Anton RibbenstedtJonathan P Benskin
May 23, 2020·Critical Reviews in Food Science and Nutrition·Shubo LiHongshun Yang
May 15, 2020·Nature Protocols·Allegra T AronPieter C Dorrestein
Sep 26, 2019·Angewandte Chemie·Connor W ColeyKlavs F Jensen
Jun 27, 2020·Metabolites·Andrew D McEachranAntony J Williams
Dec 22, 2019·Nature Communications·Xavier Domingo-AlmenaraGary Siuzdak
May 31, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Dedi SatriaKuniyoshi Shimizu
Oct 24, 2019·World Journal of Microbiology & Biotechnology·Rajeshwari SinhaPratyoosh Shukla
Mar 19, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gaole ZhangDe-An Guo
Sep 23, 2020·Nature Metabolism·Vanessa LinkeJoshua J Coon
Sep 24, 2020·International Journal of Molecular Sciences·Aneta BalcerczykGilles J P Rautureau
Feb 19, 2019·Chemical Science·Jaqueline A PicacheJohn A McLean
Jun 19, 2019·Analytical and Bioanalytical Chemistry·Christoph RuttkiesMartin Krauss
Sep 25, 2019·Metabolites·Jan StanstrupSteffen Neumann
Dec 19, 2019·Metabolites·Ali RazzaqFozia Saleem
Jun 18, 2020·Metabolites·Ulf W LiebalLars M Blank
Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Catherine DebordeRoland Molinié
Jan 25, 2020·Science·Roel VermeulenGary W Miller

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Methods Mentioned

BETA
NMR
metabolomic profiling
SPLASH
Nuclear

Software Mentioned

BitBucket
CASMI
MacOS
Dragon
Zenodo
mzCloud
MAGMa
FAIMS
MOLD2
MS

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