, Volume 9, Supplement 1, pp 44–66 | Cite as

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

  • Warwick B. DunnEmail author
  • Alexander Erban
  • Ralf J. M. Weber
  • Darren J. Creek
  • Marie Brown
  • Rainer Breitling
  • Thomas Hankemeier
  • Royston Goodacre
  • Steffen Neumann
  • Joachim Kopka
  • Mark R. Viant
Original Article


Metabolomics has advanced significantly in the past 10 years with important developments related to hardware, software and methodologies and an increasing complexity of applications. In discovery-based investigations, applying untargeted analytical methods, thousands of metabolites can be detected with no or limited prior knowledge of the metabolite composition of samples. In these cases, metabolite identification is required following data acquisition and processing. Currently, the process of metabolite identification in untargeted metabolomic studies is a significant bottleneck in deriving biological knowledge from metabolomic studies. In this review we highlight the different traditional and emerging tools and strategies applied to identify subsets of metabolites detected in untargeted metabolomic studies applying various mass spectrometry platforms. We indicate the workflows which are routinely applied and highlight the current limitations which need to be overcome to provide efficient, accurate and robust identification of metabolites in untargeted metabolomic studies. These workflows apply to the identification of metabolites, for which the structure can be assigned based on entries in databases, and for those which are not yet stored in databases and which require a de novo structure elucidation.


Capillary electrophoresis Metabolomics Metabolite identification Structure elucidation Mass spectrometry Gas chromatography Liquid chromatography Ultra performance liquid chromatography DIMS 



WD and MB gratefully acknowledge support from the National Institute for Health Research (NIHR) Manchester Biomedical Research Centre and the UK NorthWest Development Agency (NWDA). RW thanks both the British Heart Foundation (PG/10/036/28341) and UK Engineering and Physical Sciences Research Council (EP/J501414/1) for support. RG is very grateful to the UK BBSRC for financial support. DJC is funded by an Australian National Health and Medical Research Council (NHMRC) Training Fellowship.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Warwick B. Dunn
    • 1
    • 2
    Email author
  • Alexander Erban
    • 3
  • Ralf J. M. Weber
    • 4
    • 5
  • Darren J. Creek
    • 6
    • 7
  • Marie Brown
    • 1
    • 2
  • Rainer Breitling
    • 8
    • 9
  • Thomas Hankemeier
    • 10
    • 11
  • Royston Goodacre
    • 12
    • 13
  • Steffen Neumann
    • 14
  • Joachim Kopka
    • 3
  • Mark R. Viant
    • 4
    • 5
  1. 1.Centre for Advanced Discovery & Experimental Therapeutics (CADET), Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
  2. 2.School of BiomedicineUniversity of ManchesterManchesterUK
  3. 3.Max Planck Institute for Molecular Plant Physiology (MPIMP)Potsdam-GolmGermany
  4. 4.Centre for Systems BiologyUniversity of BirminghamBirminghamUK
  5. 5.School of BiosciencesUniversity of BirminghamBirminghamUK
  6. 6.Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
  7. 7.Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleAustralia
  8. 8.Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
  9. 9.Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
  10. 10.Division of Analytical Biosciences, LACDRLeiden UniversityLeidenThe Netherlands
  11. 11.Netherlands Metabolomics Centre, LACDRLeiden UniversityLeidenThe Netherlands
  12. 12.Manchester Centre for Integrative Systems BiologyUniversity of ManchesterManchesterUK
  13. 13.School of Chemistry, Manchester Interdisciplinary BiocentreUniversity of ManchesterManchesterUK
  14. 14.Department of Stress and Developmental BiologyLeibniz Institute of Plant BiochemistryHalleGermany

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