Optimising a urinary extraction method for non-targeted GC–MS metabolomics

Abstract Urine is ideal for non-targeted metabolomics, providing valuable insights into normal and pathological cellular processes. Optimal extraction is critical since non-targeted metabolomics aims to analyse various compound classes. Here, we optimised a low-volume urine preparation procedure for non-targeted GC–MS. Five extraction methods (four organic acid [OA] extraction variations and a “direct analysis” [DA] approach) were assessed based on repeatability, metabolome coverage, and metabolite recovery. The DA method exhibited superior repeatability, and achieved the highest metabolome coverage, detecting 91 unique metabolites from multiple compound classes comparatively. Conversely, OA methods may not be suitable for all non-targeted metabolomics applications due to their bias toward a specific compound class. In accordance, the OA methods demonstrated limitations, with lower compound recovery and a higher percentage of undetected compounds. The DA method was further improved by incorporating an additional drying step between two-step derivatization but did not benefit from urease sample pre-treatment. Overall, this study establishes an improved low-volume urine preparation approach for future non-targeted urine metabolomics applications using GC–MS. Our findings contribute to advancing the field of metabolomics and enable efficient, comprehensive analysis of urinary metabolites, which could facilitate more accurate disease diagnosis or biomarker discovery.