A Strategy for Uncovering the Serum Metabolome by Direct-Infusion High-Resolution Mass Spectrometry

Abstract

Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. However, metabolite assignment is limited by the inadequate mass accuracy and chemical space of the metabolome database. Here, a serum metabolome characterization method was proposed to make full use of the potential of DI-nESI-HRMS. Different from the widely used database search approach, unambiguous formula assignments were achieved by a reaction network combined with mass accuracy and isotopic patterns filter. To provide enough initial known nodes, an initial network was directly constructed by known metabolite formulas. Then experimental formula candidates were screened by the predefined reaction with the network. The effects of sources and scales of networks on assignment performance were investigated. Further, a scoring rule for filtering unambiguous formula candidates was proposed. The developed approach was validated by a pooled serum sample spiked with reference standards. The coverage and accuracy rates for the spiked standards were 98.9% and 93.6%, respectively. A total of 1958 monoisotopic features were assigned with unique formula candidates for the pooled serum, which is twice more than the database search. Finally, a case study of serum metabolomics in diabetes was carried out using the developed method.

Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics

“…While there have been many excellent studies in the metabolomics discipline conducted using direct infusion mass spectrometry (Maleki et al, 2018;Dou et al, 2023;Sun et al, 2023;Wolthuis et al, 2023) and flow injection mass spectrometry (Zang et al, 2018), chromatographic separations are commonly hyphenated to mass spectrometry. This coupling adds a further dimension of separation, beyond mass spectrometry itself, which in essence is a separation.…”