Metabolomics by Gas Chromatography-Mass Spectrometry: Combined Targeted and Untargeted Profiling

Oliver Fiehn

Research output: Contribution to journalArticlepeer-review

212 Scopus citations


Gas chromatography-mass spectrometry (GC-MS)-based metabolomics is ideal for identifying and quantitating small-molecule metabolites (<650 Da), including small acids, alcohols, hydroxyl acids, amino acids, sugars, fatty acids, sterols, catecholamines, drugs, and toxins, often using chemical derivatization to make these compounds sufficiently volatile for gas chromatography. This unit shows how GC-MS-based metabolomics allows integration of targeted assays for absolute quantification of specific metabolites with untargeted metabolomics to discover novel compounds. Complemented by database annotations using large spectral libraries and validated standard operating procedures, GC-MS can identify and semiquantify over 200 compounds from human body fluids (e.g., plasma, urine, or stool) per study. Deconvolution software enables detection of more than 300 additional unidentified signals that can be annotated through accurate mass instruments with appropriate data processing workflows, similar to untargeted profiling using liquid chromatography-mass spectrometry. GC-MS is a mature technology that uses not only classic detectors (quadrupole) but also target mass spectrometers (triple quadrupole) and accurate mass instruments (quadrupole-time of flight). This unit covers sample preparation from mammalian samples, data acquisition, quality control, and data processing.

Original languageEnglish (US)
Pages (from-to)30.4.1-30.4.32
JournalCurrent Protocols in Molecular Biology
StatePublished - Apr 1 2016


  • compound identification
  • GC-MS
  • mass spectrometry
  • multivariate statistics
  • pathway mapping
  • precision medicine
  • structure elucidation

ASJC Scopus subject areas

  • Molecular Biology


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