Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research

Ramos, Alexander E. Fox; Pogam, Pierre Le; Alcover, Charlotte; N’Nang, Elvis Otogo; Cauchie, Gaëla; Hazni, Hazrina; Awang, Khalijah; Bréard, Dimitri; Echavarren, Antonio M.; Frédérich, Michel; Gaslonde, Thomas; Girardot, Marion; Grougnet, Raphaë͏l; Kirillova, Mariia S.; Kritsanida, Marina; Lémus, Christelle; Ray, Anne‐Marie Le; Lewin, Guy; Litaudon, Marc; Mambu, Lengo; Michel, Sylvie; Miloserdov, Fedor M.; Muratore, Michael E.; Richomme-Peniguel, Pascal; Roussi, Fanny; Evanno, Laurent; Poupon, Erwan; Champy, Pierre; Beniddir, Mehdi A.

doi:10.1038/s41597-019-0028-3

Cited by 40 publications

(53 citation statements)

References 21 publications

(18 reference statements)

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“…GNPS-MassIVE now performs >6,000 analysis jobs and has >200,000 page views a month (excluding developers), with the predominant analysis being molecular networking. As a result, GNPS-based analysis has been used for the discovery of hundreds of new molecules in the past few years, ranging from immune regulators to antimicrobials, including antiviral agents and protease inhibitors 9,[30][31][32][33] . Here, we provide a detailed protocol for generating a publishable and reproducible molecular network from a mass spectrometry dataset.…”

Section: Intmentioning

confidence: 99%

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

et al. 2020

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Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS 2 ) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS 2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS 2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS 2 data with sample information (metadata) and annotated MS 2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS 2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90-to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

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Section: Intmentioning

confidence: 99%

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

et al. 2020

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“…To this effect, a molecular networking dereplication pipeline was developed based on the implementation of an in-house MS/MS database (Fig. 1), inspired by the MIADB project spearheaded by Beniddir and co-workers 56 . Pure lichen metabolites from Siegfried Huneck’s chemical library maintained in Berlin, in addition to an in-house chemical library from the laboratory in Rennes, were used to constitute the MS/MS database labelled LDB: Lichen DataBase.…”

Section: Background and Summarymentioning

confidence: 99%

A database of high-resolution MS/MS spectra for lichen metabolites

et al. 2019

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While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights (https://www.ebi.ac.uk/metabolights/MTBLS999) while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist’s viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.

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“…Monoterpene indole alkaloids (MIAs) are an important class of secondary plant metabolites found in hundreds of species among the Alangiaceae, Apocynaceae, Gelsemiaceae, Icacinaceae, Loganiaceae, Nyssaceae and Rubiaceae plant families, including more than 3000 known structures …”

Section: Introductionmentioning

confidence: 99%

“…Unfortunately, this process is compromised due the scarcity of studies focused on the fragmentation patterns under collision‐induced dissociation for MIAs . More recently, the ability to process MS data on open‐access platforms, such as Global Natural Products Social Molecular Networking (GNPS), using modern tools such as molecular networking (MN) and Library Search (LS), among others, has greatly assisted in the steps of data interpretation and screening of unknown MIAs …”

Section: Introductionmentioning

confidence: 99%

Molecular networking‐based dereplication of strictosidine‐derived monoterpene indole alkaloids from the curare ingredient Strychnos peckii

Santos

Angolini

Neves

et al. 2020

Rapid Comm Mass Spectrometry

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Rationale Monoterpene indole alkaloids (MIAs) are a large group of biologically active compounds produced by hundreds of plant species in numerous plant families, such as Apocynaceae, Loganiaceae and Rubiaceae. Although this diversity is biosynthetically intermediated by strictosidine, there are no works focused on the fragmentation patterns under collision‐induced dissociation of strictosidine‐derived alkaloids. Methods Initially, the alkaloid fingerprint of Strychnos peckii was established using leaf spray with tandem mass spectrometry (LS‐MS/MS). Then, high‐performance liquid chromatography coupled to tandem mass spectrometry (HPLC/MS/MS) analyses were carried out to focus on the patterns of neutral losses in product ion scan experiments with the leaf aqueous extract. Finally, the product ion spectra from a set of presumable strictosidine‐type derivatives were analyzed and organized via molecular networking (MN), and dereplicated by manual interpretation of MS/MS spectra. Results LS‐MS/MS allowed the tentative identification of strictosidine‐derived alkaloids in the leaves of S. peckii, showing useful neutral losses for the dereplication of strictosidine analogues by HPLC/MS/MS experiments. The use of MN combined with manual interpretation of the fragmentation patterns highlighted characteristic fragmentation pathways, and allowed the tentative identification of strictosidine, desoxycordifoline, strictosidinic acid, 10‐hydroxystrictosidine, 5‐carboxystrictosidine, lyaloside, 3,4‐dehydrostrictosidine and strictosidine lactam. Conclusions The use of MN combined with the analysis of the fragmentation patterns proved to be a useful strategy for the dereplication of strictosidine‐derived MIAs from S. peckii, highlighting known and unprecedented structures, as well as useful diagnostic product ions. Therefore, this workflow is an effective approach for the characterization of strictosidine‐type alkaloids in future dereplication works.

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Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research

Cited by 40 publications

References 21 publications

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

A database of high-resolution MS/MS spectra for lichen metabolites

Molecular networking‐based dereplication of strictosidine‐derived monoterpene indole alkaloids from the curare ingredient Strychnos peckii

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