Full Scan Enhanced Dynamic Range MS Improves Metabolite Coverage and Cancer Cell Line Discrimination in Untargeted Metabolomics

Abstract Metabolite detection with mass spectrometry (MS) in untargeted metabolomics is limited by the wide concentration range of metabolites, where high-abundance ions can restrict the detection of low-abundance features. Full Scan enhanced Dynamic Range (eDR) MS addresses this limitation by partitioning the MS1 mass range into multiple subscans and mass windows, reducing ion competition during accumulation. Here, we systematically evaluated different eDR acquisition strategies for untargeted metabolomics. Across four hepatocellular carcinoma cell lines, Full Scan eDR MS increased detectable compounds up to ∼3.5-fold compared with Full Scan MS and improved signal-to-noise ratios of low-abundance compounds. Among equidistant configurations, 12 windows yielded the highest compound count, while custom window distributions enabled targeted enhancement of selected mass regions. In particular, allocating narrower windows to the low-m/z region selectively increased the detection of low-mass compounds. Increased MS1 coverage also translated into deeper MS2 coverage and increased metabolite identifications. This expanded coverage included cancer-relevant metabolites and improved the detection of metabolic differences between cancer cell lines. Overall, Full Scan eDR MS provides a flexible strategy to increase analytical depth in untargeted metabolomics while maintaining data quality. Customization of window size and distribution enables targeted expansion of the dynamic range within predefined mass regions, allowing MS acquisition to be tailored to sample composition and metabolites of interest.