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Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics

Damont, Annelaure, Olivier, Marie‐Françoise, Warnet, Anna, Lyan, Bernard, Pujos‐Guillot, Estelle, Jamin, Emilien L., Debrauwer, Laurent, Bernillon, Stéphane, Junot, Christophe, Tabet, Jean‐Claude, Fenaille, François
Journal of mass spectrometry 2019 v.54 no.6 pp. 567-582
bioinformatics, databases, infrastructure, ions, liquid chromatography, mass spectrometry, metabolites, metabolomics
Nowadays, high‐resolution mass spectrometry is widely used for metabolomic studies. Thanks to its high sensitivity, it enables the detection of a large range of metabolites. In metabolomics, the continuous quest for a metabolite identification as complete and accurate as possible has led during the last decade to an ever increasing development of public MS databases (including LC‐MS data) concomitantly with bioinformatic tool expansion. To facilitate the annotation process of MS profiles obtained from biological samples, but also to ease data sharing, exchange, and exploitation, the standardization and harmonization of the way to describe and annotate mass spectra seemed crucial to us. Indeed, under electrospray (ESI) conditions, a single metabolite does not produce a unique ion corresponding to its protonated or deprotonated form but could lead to a complex mixture of signals. These MS signals result from the existence of different natural isotopologues of the same compound and also to the potential formation of adduct ions, homomultimeric and heteromultimeric ions, fragment ions resulting from “prompt” in‐source dissociations. As a joint reflection process within the French Infrastructure for Metabolomics and Fluxomics (MetaboHUB) and with the purpose of developing a robust and exchangeable annotated MS database made from pure reference compounds (chemical standards) analysis, it appeared to us that giving the metabolomics community some clues to standardize and unambiguously annotate each MS feature was a prerequisite to data entry and further efficient querying of the mass spectral database. The use of a harmonized notation is also mandatory for interlaboratory MS data exchange. Additionally, thorough description of the variety of MS signals arising from the analysis of a unique metabolite might provide greater confidence on its annotation.