Assessment of automated trimethylsilyl derivatisation protocols for GC-MS-based untargeted metabolomic analysis of urine

GC-MS is a commonly used metabolomic platform for the analysis of urine. A key step in the preparation of samples for GC-MS is derivatisation, in particular, methoximation and trimethylsilylation. This paper presents an assessment of automated derivatisation protocols for GC-MS-based untargeted metabolomic analysis of rat urine. Automated batch and in-time (a sample ready for injection every 70 minutes) derivatisation protocols were tested using BSTFA and MSTFA. Principal component analysis determined differences based upon protocol tested (PC-1; 19%) and silylation reagent (PC-2; 17%) used. Of 249 compounds, 40 compounds were significantly different (P<0.05) based upon reagent and 154 compounds were significantly different (P<0.05) based upon protocol. A key outcome of this study was the demonstrated effects of derivatisation including reagent and protocol (i.e. reaction duration, temperature and mixing speed) on individual urinary metabolites. It is hoped that the current work will provide a reference on which to base future GC-MS-based untargeted and targeted metabolomic analyses of urine.