Methods in Molecular Biology™ Volume 358, 2007, pp 19-38

Nonsupervised Construction and Application of Mass Spectral and Retention Time Index Libraries From Time-of-Flight Gas Chromatography-Mass Spectrometry Metabolite Profiles

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Gas chromatography-mass spectrometry (GC-MS) is routinely applied to the metabolite profiling of biological samples. Time-of-flight (TOF)-GC-MS metabolite profiling is based on highly reproducible electron impact ionization. Single chromatograms may comprise 200–1000 mass spectral components. The nature and composition of these mass spectral components depend on the choice of metabolite extraction, type of biological sample, and experimental condition. The components represent mass spectral tags (MSTs) of volatile metabolites or metabolite derivatives. Identification of MSTs is the major challenge in GC-MS metabolite profiling. We describe methods suitable for the automated construction of mass spectral and retention time index databases from large sets of TOF-GC-MS profiles. Application of these libraries for automated identification by pure reference compounds and classification of hitherto unidentified MSTs from biological sources is demonstrated.