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

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.