Fecal sample preparation for untargeted and targeted metabolomics and a reproducibility study in the targeted platform

Sample preparation is an essential step to obtain high quality data in MS-based clinical metabolomics. For screening metabolites in heterogeneous semi-solid biological samples through multiple platforms, an ideal sample preparation requires a fast and reproducible method to maximize metabolite detection/quantification. Herein, we propose an efficient and robust method for preparing fecal samples for metabolomics analyses in different MS platforms. We describe a step-wise method that was accordingly derivatized for metabolomics analysis by GCGC-MS, untargeted lipidomics analysis by UPLC-qTof-MS, targeted metabolomics analyses by LC-ESI-MS/MS. Our method has been focused on reducing aliquoting and producing a common sample that covers a large variety of polar and non-polar metabolites of interest for clinical research. Here we present results from the targeted platform for a broad coverage of n=25 metabolites that represent liver-gut axis metabolism. Our platform test cohort consisted of 475 samples from patients with a history of harmful drinking and healthy controls.