Higher mass loadability in comprehensive two-dimensional gas chromatography–mass spectrometry for improved analytical performance in metabolomics analysis

A major challenge in metabolomics analysis is the accurate quantification of metabolites in the presence of (extremely) high abundant metabolites. Quantification of metabolites at low concentrations can be complicated by co-elution and/or peak distortion when these metabolites elute close to high abundant metabolites. To increase the separation efficiency a comprehensive two-dimensional gas chromatographic–mass spectrometric method (GC × GC–MS) was set up, in which a polar first dimension column and an apolar second dimension column were used to maximize the peak capacity. The feasibility of using wider bore, thicker film columns in the second dimension to improve the mass loadability and inertness of the analytical system was investigated. Several column combinations with varying second dimension column dimensions were compared with a setup with a narrow bore column (0.1 mm I.D.) in the second dimension. With a wider bore column (0.32 mm I.D.) in the second dimension the mass loadability was improved 10-fold, and the more inert column surface of the thicker film second dimension column resulted in a more accurate (automated) quantification and improved linearity in the presence of high concentrations of matrix compounds or metabolites. These benefits amply compensated the observed decrease in peak capacity of 40% compared to the narrow bore (0.1 mm I.D.) thin film second dimension column. Compared to GC–MS and conventional GC × GC–MS, better performance for quantification of metabolites for typical metabolomics samples was achieved.