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Metabolites
Special Issues
Mass Spectral Libraries and Databases for Metabolomics
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Mass Spectral Libraries and Databases for Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Bioinformatics and Data Analysis".

Deadline for manuscript submissions: closed (15 July 2022)

Special Issue Editors

Dr. Annelaure Damont

E-Mail Website
Guest Editor
Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, F-91191 Gif sur Yvette, France
Interests: metabolomics; mass spectrometry; structural elucidation; organic analysis; isotope-assisted research
Dr. Guillaume Marti

E-Mail Website1 Website2 Website3
Guest Editor
Laboratoire de Recherche en Science Végétal (LRSV), University Toulouse 3, Centre National de Recherche Scientifique (CNRS), 31400 Toulouse, France
Interests: metabolomics; mass spectrometry; machine learning; chemometrics; big data

Special Issue Information

Dear Colleagues,

No matter the context (medical, toxicological, nutritional, environmental, etc.), metabolomics is currently facing an explosion in the amount of data generated from a single sample, especially when using mass spectrometry (MS)-based approaches. Driven by a desire to gain maximum knowledge about the organic content of a sample, metabolomic studies increasingly include untargeted tandem mass spectrometry protocols (such as data-dependent or -independent acquisitions) in their data acquisition workflows, and call upon diverse and complementary MS-based platforms (LC-MS, GC-MS, Ion Mobility Spectroscopy (IMS)-MS, etc.), generating data and metadata as complex as they are varied. In this context, mass spectral libraries and databases are of primary importance, both for data storage and management, but also to ensure reliable identification and shareable annotation of metabolites (including lipids and exposures) and facilitate the exploration of a large part of the metabolome that remains unknown or incompletely characterized.

This Special Issue of Metabolites, dedicated to “Mass Spectral Libraries and Databases for Metabolomics”, will cover various aspects ranging from spectral data collection and repository management to practical applications. Relevant contributions dealing with the (non-exhaustive) following topics are welcome: prerequisites (including QA/QC) for high-quality and FAIR (findable, accessible, interoperable, and reproducible) spectral data acquisition, data processing pipelines for building MS(/MS) libraries either from authentic standards or biological samples, database management systems, data import/export, spectral library enrichment with orthogonal information (e.g., collision cross-section), curation and product ion annotation strategies, spectral library-based molecular networking and unknown compound structural elucidation, in silico-generated MS/MS libraries. Manuscripts dealing with any other related issues are also warmly welcomed.

Dr. Annelaure Damont
Dr. Guillaume Marti
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Dr. Annelaure Damont
Dr. Guillaume Marti
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics
  • mass spectrometry
  • databases
  • library search
  • spectral data collection
  • high quality spectra
  • tandem mass spectra
  • fragmentation
  • reference compounds
  • matching
  • annotation
  • identification
  • molecular networking

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Published Papers (2 papers)

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12 pages, 1531 KiB  
Article
Dereplication of Cytochalasans and Octaketides in Cytotoxic Extracts of Endophytic Fungi from Casearia arborea (Salicaceae)
by Augusto L. Santos, Marisa Ionta, Renato O. Horvath, Marisi G. Soares, Daniele O. Silva, Eunizinis S. Kawafune, Marcelo J. P. Ferreira and Patricia Sartorelli
Metabolites 2022, 12(10), 903; https://doi.org/10.3390/metabo12100903 - 26 Sep 2022
Cited by 1 | Viewed by 2040
Abstract
Endophytes have been shown to be a source of novel drug prototypes. The Casearia genus is known for presenting cytotoxic clerodane diterpenes; however, there are few reports on secondary metabolites produced by its fungal microbiota. Thus, in the present study endophytic fungi obtained [...] Read more.
Endophytes have been shown to be a source of novel drug prototypes. The Casearia genus is known for presenting cytotoxic clerodane diterpenes; however, there are few reports on secondary metabolites produced by its fungal microbiota. Thus, in the present study endophytic fungi obtained from the fresh leaves of C. arborea were grown in potato dextrose broth and rice to perform a secondary metabolite prospection study. The cytotoxic profile of the crude extracts at 10 µg/mL was determined by a colorimetric assay on tumor cell lines. The endophytes producing cytotoxic extracts were identified through phylogenetic analysis and belong to Diaporthe and Colletotrichum species. Metabolites present in these extracts were organized in molecular networking format based on HRMS-MS, and a dereplication process was performed to target compounds for chromatographic purification. Metabolic classes, such as lipids, peptides, alkaloids, and polyketides were annotated, and octaketide and cytochalasin derivatives were investigated. Cytochalasin H was purified from the cytotoxic Diaporthe sp. CarGL8 extract and its cytotoxic activity was determined on human cancer cell lines A549, MCF-7, and HepG2. The data collected in the present study showed that molecular networking is useful to understand the chemical profile of complex matrices to target compounds, minimizing the cost and time spent in purification processes. Full article
(This article belongs to the Special Issue Mass Spectral Libraries and Databases for Metabolomics)
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12 pages, 444 KiB  
Article
Volatile Organic Compounds Frequently Identified after Hyperbaric Hyperoxic Exposure: The VAPOR Library
by Feiko J. M. de Jong, Paul Brinkman, Thijs T. Wingelaar, Pieter-Jan A. M. van Ooij and Rob A. van Hulst
Metabolites 2022, 12(5), 470; https://doi.org/10.3390/metabo12050470 - 23 May 2022
Cited by 9 | Viewed by 2738
Abstract
Diving or hyperbaric oxygen therapy with increased partial pressures of oxygen (pO2) can have adverse effects such as central nervous system oxygen toxicity or pulmonary oxygen toxicity (POT). Prevention of POT has been a topic of interest for several decades. One [...] Read more.
Diving or hyperbaric oxygen therapy with increased partial pressures of oxygen (pO2) can have adverse effects such as central nervous system oxygen toxicity or pulmonary oxygen toxicity (POT). Prevention of POT has been a topic of interest for several decades. One of the most promising techniques to determine early signs of POT is the analysis of volatile organic compounds (VOCs) in exhaled breath. We reanalyzed the data of five studies to compose a library of potential exhaled markers for the early detection of POT. GC-MS data from five hyperbaric hyperoxic studies were collected. Wilcoxon signed-rank tests were used to compare baseline- and postexposure measurements; all ion fragments that significantly varied were compared by similarity using the National Institute of Standards and Technology (NIST) library. All identified molecules were cross-referenced with open-source databases and other scientific publications on VOCs to exclude compounds that occurred as a result of contamination, and to identify the compounds most likely to occur due to hyperbaric hyperoxic exposure. After identification and removal of contaminants, 29 compounds were included in the library. This library of hyperbaric hyperoxic-related VOCs can help to advance the development of an early noninvasive marker of POT. It enables validation by others who use more targeted MS-related techniques, instead of full-scale GC-MS, for their exhaled VOC research. Full article
(This article belongs to the Special Issue Mass Spectral Libraries and Databases for Metabolomics)
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