Molecular networking and collision cross section prediction for structural isomer and unknown compound identification in plant metabolomics: a case study applied to Zhanthoxylum heitzii extracts

Calabrese, Valentina; Schmitz-Afonso, Isabelle; Prevost, Candice; Afonso, Carlos; Elomri, Abdelhakim

doi:10.1007/s00216-022-04059-7

Cited by 9 publications

(3 citation statements)

References 90 publications

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“…Wang et al identified many components in Lanqin Oral Liquid (a Chinese patent medicine) by UPLC-IM-QTOF-MS and automatic peak annotation driven by UNIFI software. The CCS data correlation global natural products molecular networking platform (GNPS) can further identify targeted or nontargeted compounds with a high throughput. − …”

Section: Applications Of Im-ms For the Separation And Characterizatio...mentioning

confidence: 99%

Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules

et al. 2023

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Section: Applications Of Im-ms For the Separation And Characterizatio...mentioning

confidence: 99%

Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules

et al. 2023

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“…While these MS tools are nowadays routinely applied in metabolomics for the characterization of natural compounds in plants (Calabrese et al, 2022(Calabrese et al, , 2023 or human biofluids (Zhu et al, 2021), applications in ecotoxicological research remains still very limited (Taylor et al, 2009;Duarte, et al, 2022) and totally unexplored in Gammarids.…”

Section: Metabolomics and Lipidomics Approachesmentioning

confidence: 99%

Challenges and perspectives in MS-based omics approaches for ecotoxicology studies: An insight on Gammarids sentinel amphipods

Calabrese

Salvador²,

Clément³

et al. 2023

Front. Anal. Sci.

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The aquatic environment is one of the most complex biosystems, as organism at all trophic levels may be exposed to a multitude of pollutants. As major goals, ecotoxicology typically investigates the impact of toxic pollutants on the ecosystems through the study of sentinel organisms. Over the past decades, Mass Spectrometry (MS)-based omics approaches have been extended to sentinel species both in laboratory and field exposure conditions. Single-omics approaches enable the discovery of biomarkers mirroring the health status of an organism. By covering a restricted set of the molecular cascade, they turn out to only partially satisfy the understanding of complex ecotoxicological effects. In contrast, a more complete understanding of the ecotoxicity pathways can be accessed through multi-omics approaches. In this perspective, we provide a state-of-the-art and a critical evaluation on further developments in MS-based single and multi-omics studies in aquatic ecotoxicology. As case example, literature regarding Gammarids freshwater amphipods, non-model sentinel organisms sensitive to pollutants and environmental changes and crucial species for downstream ecosystems, will be reviewed.

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“…To achieve more effective annotation of compounds, alternative strategies have been tested during the years, such as the use of additional intrinsic descriptors like collision cross-sectional area (CCS) [32,33], chemical derivatization prior to fragmentation [34], ionization in form of Li, Cu, Co, Ag (and so on), adducts [35][36][37], or alternative dissociation methods as photon or electron-activated dissociation [38]. Moreover, it is worth mentioning that compound annotation, especially in the presence of complex mixtures containing many isobars and isomers (as for complex lipids samples), might strongly be improved by hyphenation with peculiar chromatography techniques.…”

Section: Introductionmentioning

confidence: 99%

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

Calabrese,

Brunet,

Degli-Esposti

et al. 2024

Anal Bioanal Chem

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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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Molecular networking and collision cross section prediction for structural isomer and unknown compound identification in plant metabolomics: a case study applied to Zhanthoxylum heitzii extracts

Cited by 9 publications

References 90 publications

Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules

Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules

Challenges and perspectives in MS-based omics approaches for ecotoxicology studies: An insight on Gammarids sentinel amphipods

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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