Journal of Inherited Metabolic Disease

, Volume 41, Issue 3, pp 355–366 | Cite as

Promises and pitfalls of untargeted metabolomics

  • Ilya Gertsman
  • Bruce A. Barshop


Metabolomics is one of the newer omics fields, and has enabled researchers to complement genomic and protein level analysis of disease with both semi-quantitative and quantitative metabolite levels, which are the chemical mediators that constitute a given phenotype. Over more than a decade, methodologies have advanced for both targeted (quantification of specific analytes) as well as untargeted metabolomics (biomarker discovery and global metabolite profiling). Untargeted metabolomics is especially useful when there is no a priori metabolic hypothesis. Liquid chromatography coupled to mass spectrometry (LC-MS) has been the preferred choice for untargeted metabolomics, given the versatility in metabolite coverage and sensitivity of these instruments. Resolving and profiling many hundreds to thousands of metabolites with varying chemical properties in a biological sample presents unique challenges, or pitfalls. In this review, we address the various obstacles and corrective measures available in four major aspects associated with an untargeted metabolomics experiment: (1) experimental design, (2) pre-analytical (sample collection and preparation), (3) analytical (chromatography and detection), and (4) post-analytical (data processing).


Compliance with ethical standards

Conflict of interest

Ilya Gertsman and Bruce A. Barshop declare that they have no conflict of interest.


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© SSIEM 2018

Authors and Affiliations

  1. 1.Biochemical Genetics and Metabolomics Laboratory, Department of PediatricsUniversity of California San DiegoCAUSA

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