Breath analysis by two-dimensional gas chromatography with dual flame ionisation and mass spectrometric detection – Method optimisation and integration within a large-scale clinical study

•New method for the analysis of exhaled breath VOCs by TD-GC × GC-FID/qMS.•Optimisation of flow modulation and dual detection alongside clinical requirements.•Addresses key challenges of using GC × GC for large-scale breath metabolomics. Precision medicine has spurred new innovations in molecular pathology leading to recent advances in the analysis of exhaled breath as a non-invasive diagnostic tool. Volatile organic compounds (VOCs) detected in exhaled breath have the potential to reveal a wealth of chemical and metabolomic information. This study describes the development of a method for the analysis of breath, based on automated thermal desorption (TD) combined with flow modulated comprehensive two-dimensional gas chromatography (GC×GC) with dual flame ionisation and quadrupole mass spectrometric detection (FID and qMS). The constrained optimisation and analytical protocol was designed to meet the practical demands of a large-scale multi-site clinical study, while maintaining analytical rigour to produce high fidelity data. The results demonstrate a comprehensive method optimisation for the collection and analysis of breath VOCs by GC×GC, integral to the standardisation and integration of breath analysis within large clinical studies.