Development of a metabolic pathway-based pseudo-targeted metabolomics method using liquid chromatography coupled with mass spectrometry

The pseudo-targeted metabolomics approach was developed recently which combined the advantages of untargeted and targeted analysis. However, the current pseudo-targeted analysis method has limitations due to the technical characteristics. In this study, a novel metabolic pathway-based pseudo-targeted approach was proposed for urine metabolomics analysis using an ultra-high-performance liquid chromatography (UPLC)-MS/MS system operated in the multiple reaction monitoring (MRM) mode. MRM ion pairs were acquired from urine samples through untargeted analysis using UPLC-HRMS, as well as by searching for metabolites in related pathways in relevant databases and from previous relevant research, including amino acids, fatty acids, nucleosides, carnitines, glycolysis metabolites, and steroids. This improved pseudo-targeted method exhibited good repeatability and precision, and no complicated peak alignment was required. As a proof of concept, the developed novel method was applied to the discovery of urine biomarkers for patients with esophageal squamous cell carcinoma (ESCC). The results showed that ESCC patients had altered acylcarnitines, amino acids, nucleosides, and steroid derivative levels et al. compared to those of healthy controls. The novelty of this study lies in the fact that it provides an approach for acquiring MRM ion pairs not only from untargeted MS analysis but also from targeted searching for metabolites in related metabolic pathways. By improving the detection limit of low-abundance metabolites, it enlarges the range for the discovery of potential biomarkers. Our work provides a foundation for achieving pseudo-targeted metabolomics analysis on the widely used LC-MS/MS MRM platform.