Liquid
chromatography–high-resolution mass spectrometry
(LC-HRMS) is the most popular platform for untargeted metabolomics
studies, but compound annotation is a challenge. In this work, we
developed a new LC-HRMS data-targeted extraction method called MetEx
for metabolite annotation. MetEx contains the retention time (t
R), MS1, and MS2 information of 30 620
metabolites from freely available spectral databases, including MoNA
and KEGG. The t
R values of 95.4% of the
compounds in our database were calculated by the GNN-RT model. The
MS2 spectra of 39.4% compounds were also predicted using CFM-ID. MetEx
was initially examined on a mixture of 634 standards, considering
chemical coverage and accurate metabolite assignment, and later applied
to human plasma (NIST SRM 1950), human urine, HepG2 cells, mouse liver
tissue, and mouse feces. MetEx correctly assigned 252 out of 253 standards
detected in our instruments. The platform also provided 8.0–44.2%
more compounds in the biological samples compared to XCMS, MS-DIAL,
and MZmine 2. MetEx is implemented and visualized in R and freely
available at .
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