HERMES: a molecular formula-oriented method to target the metabolome

Roger Giné; Jordi Capellades; Josep M. Badia; Dennis Vughs; Michaela Schwaiger-Haber; María Vinaixa; Andrea M. Brunner; Gary J. Patti; Óscar Yanes

doi:10.1101/2021.03.08.434466

BioinformaticsbioRxivMar 8, 2021

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HERMES: a molecular formula-oriented method to target the metabolome

Roger Giné iD, Jordi Capellades iD, Josep M. Badia iD, Dennis Vughs iD, Michaela Schwaiger-Haber iD, María Vinaixa iD, Andrea M. Brunner iD, Gary J. Patti iD, Óscar Yanes iD

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Abstract

Comprehensive metabolome analyses are hampered by low identification rates of metabolites due to suboptimal strategies in MS and MS2 acquisition, and data analysis. Here we present a molecular formula-oriented and peak detection-free method, HERMES, that improves sensitivity and selectivity for metabolite profiling in MS and structural annotation in MS2. An analysis of environmental water, E. coli, and human plasma extracts by HERMES showed increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared to iterative data-dependent acquisition (DDA). HERMES is available as an R package with a user-friendly graphical interface to allow data analysis and interactive tracking of compound annotations.