Optimizing targeted/untargeted metabolomics by automating gas chromatography/mass spectrometry workflows

•Automated analysis of GC-GC/MS data to produce detailed metabolomic databases.•Mass spectrum subtraction of target compounds to identify non-target compounds.•Quantitative targeted and non-target analysis by GC/MS analysis.

New database building and MS subtraction algorithms have been developed for automated, sequential two-dimensional gas chromatography/mass spectrometry (GC-GC/MS). This paper reports the first use of a database building tool, with full mass spectrum subtraction, that does not rely on high resolution MS data. The software was used to automatically inspect GC-GC/MS data of high elevation tea from Yunnan, China, to build a database of 350 target compounds. The database was then used with spectral deconvolution to identify 285 compounds by GC/MS of the same tea. Targeted analysis of low elevation tea by GC/MS resulted in the detection of 275 compounds. Non-targeted analysis, using MS subtraction, yielded an additional eight metabolites, unique to low elevation tea.