Table 1

Strengths and weaknesses of the core instrumentation used in metabolomics

triple quadrupole
Applications Targeted and untargetedTargeted and untargetedTargeted and untargetedTargeted
  • Non-destructive technique.

  • High reproducibility.

  • Quantitative analysis.

  • Relatively easy metabolite identification.

  • Robust and reproducible metabolite separation.

  • Available databases to aid metabolite identification, for example, NIST.

  • Quantitative analysis.

  • Less expensive compared with other MS platforms.

  • High resolution.

  • Accurate mass determination.

  • Thousands of metabolites detected in a single run.

  • Fragment fingerprinting using MSn experiments.

  • Derivatisation is rarely needed, though ionisation of the molecules is required.

  • High specificity when combined with retention time.

  • Quantitative analysis with the use of stable isotope labelled standards.

  • Direct flow injection can be used with short run times, suited for targeted analysis of chemically related compounds.

  • Derivatisation is rarely needed, though ionisation of the molecules is required.

  • Low sensitivity compared with MS.

  • Large sample volumes required compared with MS.

  • Up to 200 metabolites can be detected in a single run due to overlapping signals compared with thousands detected in MS applications.

  • Destructive technique.

  • Prior derivatisation process is needed.

  • Unsuitable for metabolites that thermally decompose.

  • Destructive technique.

  • Relatively expensive compared with other MS techniques.

  • Complex metabolite identification.

  • Noise and redundancy in untargeted data.

  • Lack of absolute quantification in untargeted applications.

  • Low reproducibility, requiring quality control samples.

  • Destructive technique.

  • Hypothesis driven.

  • Difficult method development.

  • GC-MS, gas chromatography–mass spectrometry; LC-MS/MS, liquid chromatography–tandem mass spectrometry; MS, mass spectrometry; NIST, National Institute of Standards and Technology; NMR, nuclear magnetic resonance; Q-TOF, quadrupole time-of-flight mass spectrometer.