Comparison of Kit-Based Metabolomics with Other Methodologies in a Large Cohort, towards Establishing Reference Values

Abstract

Metabolic profiling is an omics approach that can be used to observe phenotypic changes, making it particularly attractive for biomarker discovery. Although several candidate metabolites biomarkers for disease expression have been identified in recent clinical studies, the reference values of healthy subjects have not been established. In particular, the accuracy of concentrations measured by mass spectrometry (MS) is unclear. Therefore, comprehensive metabolic profiling in large-scale cohorts by MS to create a database with reference ranges is essential for evaluating the quality of the discovered biomarkers. In this study, we tested 8700 plasma samples by commercial kit-based metabolomics and separated them into two groups of 6159 and 2541 analyses based on the different ultra-high-performance tandem mass spectrometry (UHPLC-MS/MS) systems. We evaluated the quality of the quantified values of the detected metabolites from the reference materials in the group of 2541 compared with the quantified values from other platforms, such as nuclear magnetic resonance (NMR), supercritical fluid chromatography tandem mass spectrometry (SFC-MS/MS) and UHPLC-Fourier transform mass spectrometry (FTMS). The values of the amino acids were highly correlated with the NMR results, and lipid species such as phosphatidylcholines and ceramides showed good correlation, while the values of triglycerides and cholesterol esters correlated less to the lipidomics analyses performed using SFC-MS/MS and UHPLC-FTMS. The evaluation of the quantified values by MS-based techniques is essential for metabolic profiling in a large-scale cohort.

Identification of predictive biomarkers for diagnosis and radiation sensitivity of uterine cervical cancer using wide‐targeted metabolomics

“…Targeted metabolomic analysis was performed as previously described, 15,21 using an ACQUITY UPLC connected to a triple-quadrupole mass spectrometer (Xevo TQ-XS, Waters Corporation, Milford, MA), and a MxP ® Quant 500 kit (Biocrates Life Science AG). The 10 μL blank solution, calibration standard solution, quality control solution supplied with the kit and plasma samples were transferred to individual wells of a 96-well plate.…”

Widespread natural selection on metabolite levels in humans

“…Recent technological advancements allowed the detection of hundreds of metabolic compounds that can potentially be used as biomarkers for diseases or drug targets. However, different operating standards and the lack of reference values obtained from healthy subjects lead to large discrepancies in detected metabolite levels across different platforms and laboratories, impeding metabolic profiling 19 and downstream analyses, like ours. The MR analysis results demonstrate that many metabolites have causal effect on clinically relevant, complex traits, although, in line with transcriptome-wide MR analyses 20 , these effects are minor.…”

Identification of predictive biomarkers for endometrial cancer diagnosis and treatment response monitoring using plasma metabolome profiling

“…Pooled normal human plasma was purchased from Innovative Research (Novi, MI, USA; Lot 26,393) and was used for global quality control (gQC). The other chemicals and reagents used are described in previous studies [ 15 , 16 , 21 , 22 ].…”