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

TLDR

GC‑MS–based metabolomics is a mature, versatile platform for identifying and quantifying small‑molecule metabolites (<650 Da) across diverse classes, employing derivatization and a range of detectors from quadrupole to quadrupole‑time‑of‑flight mass spectrometers. The unit demonstrates how GC‑MS metabolomics integrates targeted absolute quantification of selected metabolites with untargeted profiling to uncover novel compounds. The methodology includes mammalian sample preparation, GC‑MS data acquisition, quality control, and downstream data processing. GC‑MS can identify and semi‑quantify over 200 metabolites in human fluids per study, and deconvolution software reveals more than 300 additional signals that can be annotated with accurate‑mass instruments and suitable workflows. © 2016 John Wiley & Sons, Inc.

Abstract

Abstract Gas chromatography–mass spectrometry (GC‐MS)–based metabolomics is ideal for identifying and quantitating small‐molecule metabolites (&lt;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. © 2016 by John Wiley &amp; Sons, Inc.