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Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum

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Abstract

The past decades have marked the rise of metabolomics and lipidomics as the -omics sciences which reflect the most phenotypes in living systems. Mass spectrometry–based approaches are acknowledged for both quantification and identification of molecular signatures, the latter relying primarily on fragmentation spectra interpretation. However, the high structural diversity of biological small molecules poses a considerable challenge in compound annotation. Feature-based molecular networking (FBMN) combined with database searches currently sets the gold standard for annotation of large datasets. Nevertheless, FBMN is usually based on collision-induced dissociation (CID) data, which may lead to unsatisfying information. The use of alternative fragmentation methods, such as electron-activated dissociation (EAD), is undergoing a re-evaluation for the annotation of small molecules, as it gives access to additional fragmentation routes. In this study, we apply the performances of data-dependent acquisition mass spectrometry (DDA-MS) under CID and EAD fragmentation along with FBMN construction, to perform extensive compound annotation in the crude extracts of the freshwater sentinel organism Gammarus fossarum. We discuss the analytical aspects of the use of the two fragmentation modes, perform a general comparison of the information delivered, and compare the CID and EAD fragmentation pathways for specific classes of compounds, including previously unstudied species. In addition, we discuss the potential use of FBMN constructed with EAD fragmentation spectra to improve lipid annotation, compared to the classic CID-based networks. Our approach has enabled higher confidence annotations and finer structure characterization of 823 features, including both metabolites and lipids detected in G. fossarum extracts.

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Data availability

All the data are described within the manuscript. The raw data and metadata analyzed during the current study are available from the corresponding author on request.

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Funding

This work was supported by the French National Research Agency (ANR) (young investigator grant, ANR-18-CE34-0008 PLAN-TOX). VC was supported by a post-doctoral fellowship of the SENS research funding of the Université Claude Bernard Lyon 1. This work was performed within the framework of the EUR H2O’Lyon (ANR-17-EURE-0018) of Université de Lyon (UdL), within the program “Investissements d’Avenir” operated by the French National Research Agency (ANR). We thank the French GDR “Aquatic Ecotoxicology” framework which aims at fostering stimulating discussions and collaborations for more integrative approaches.

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  1. Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France

    Valentina Calabrese, Thomas Alexandre Brunet, Arnaud Salvador, Yohann Clément & Sophie Ayciriex

  2. Laboratoire d’écotoxicologie, INRAE, UR RiverLy, 69625, Villeurbanne, France

    Davide Degli-Esposti, Arnaud Chaumot & Olivier Geffard

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  1. Valentina Calabrese
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  2. Thomas Alexandre Brunet
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  3. Davide Degli-Esposti
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  8. Sophie Ayciriex
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Contributions

VC: conceptualization; methodology; formal analysis; investigation; data analysis; visualization; writing—original draft. TAB: methodology, investigation. DDE: writing—review and editing. AC, OG: resources; writing—review and editing. AS: writing—review and editing. YC: resources; writing—review and editing. SA: conceptualization; funding acquisition; supervision; writing—original draft; writing—review and editing.

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Correspondence to Valentina Calabrese or Sophie Ayciriex.

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Calabrese, V., Brunet, T.A., Degli-Esposti, D. et al. Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum. Anal Bioanal Chem 416, 2893–2911 (2024). https://doi.org/10.1007/s00216-024-05232-w

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