Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study

Abstract

Large-scale metabolomic studies have become common, and the reliability of the peak data produced by the various instruments is an important issue. However, less attention has been paid to the large number of uncharacterized peaks in untargeted metabolomics data. In this study, we tested various criteria to assess the reliability of 276 and 202 uncharacterized peaks that were detected in a gathered set of 30 plasma and urine quality control samples, respectively, using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). The linear relationship between the amounts of pooled samples and the corresponding peak areas was one of the criteria used to select reliable peaks. We used samples from approximately 3000 participants in the Tsuruoka Metabolome Cohort Study to investigate patterns of the areas of these uncharacterized peaks among the samples and clustered the peaks by combining the patterns and differences in the migration times. Our assessment pipeline removed substantial numbers of unreliable or redundant peaks and detected 35 and 74 reliable uncharacterized peaks in plasma and urine, respectively, some of which may correspond to metabolites involved in important physiological processes such as disease progression. We propose that our assessment pipeline can be used to help establish large-scale untargeted clinical metabolomic studies.

Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry

“…Previous work also discovered uncharacterized peaks from CE-MS that might reflect the pathophysiology of the kidney in diabetic patients [ 22 ]. Therefore, we suggest that these uncharacterized peaks may have potential to predict AKI after the assessment of their reliability [ 36 ].…”

Current applications of capillary electrophoresis‐mass spectrometry for the analysis of biologically important analytes in urine (2017 to mid‐2021): A review

“…Recently, some effort has been put into assessing the reliability of the CE‐MS for the determination of urinary metabolite concentrations [ 73 ]. Additionally, testing the reliability of uncharacterized peaks in the urinary untargeted metabolomics was also performed [ 74 ] including relative migration‐time reproducibility and identification capabilities in an interlaboratory trial [ 75 ]. For annotation of metabolites with a higher confidence level, an internal library platform of 226 standards together with their in‐source fragment ions, adducts, and relative migration times was developed [ 76 ].…”

Editorial of Special Issue “Metabolomic Analysis in Health and Diseases”

“…Although most of such analyses had focused only on targeted data, they devised analyses for untargeted analytical data. They evaluated their methods using large-scale datasets of urine and plasma samples collected in a cohort study that included 3000 participants [9].…”