The analytical methods presented here are fit-for-purpose and performance-enhanced adaptions of preceding methods, each developed in 2012 and in continuous use since in a high-volume industrial-scale research environment. These methodologies are readily implemented for human urine and blood product analyses and adaptable to other clinical sample types. They are paired with bespoke open-source software for the targeted extraction of known metabolites and pre-processing of the data in order to generate high quality and high-fidelity datasets. The platform is scalable, enabling the analysis of 80 sample assays/day/instrument on a regular schedule which is operationally convenient for laboratories of any size.