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Metabolites
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Recent Developments in Sample Preparation and Analysis in Mass Spectrometry-Based...
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Recent Developments in Sample Preparation and Analysis in Mass Spectrometry-Based Metabolomics 2nd Edition

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Metabolomic Profiling Technology".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 7675

Special Issue Editors

Dr. Artem D. Rogachev

E-Mail Website
Guest Editor
1. N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk, Russia
2. Department of Medicinal Chemistry, Novosibirsk State University, Novosibirsk, Russia
Interests: liquid chromatography; mass spectrometry; bioanalysis; metabolomics; method development and validation; pharmacokinetics
Special Issues, Collections and Topics in MDPI journals
Dr. Vladimir Ivanisenko

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
Interests: bioinformatics

Special Issue Information

Dear Colleagues,

Currently, metabolomic studies of living organisms can shed light on intrinsic processes that provide clues to understanding possible mechanisms of pathology development and disease biomarkers. Based on metabolomic screening data, new statistical models are currently being created to improve diagnosis.

Metabolomics studies can be performed on different biomatrices, such as whole blood, plasma, serum, urine, and tissue samples. As all these matrices have distinct biological properties, appropriate sample preparation protocols should be used. There are also different approaches for screening metabolites via gas/liquid chromatography or capillary electrophoresis coupled with mass spectrometry.

In this Special Issue, we present the current advances in sample preparation and/or analysis for screening metabolites of different classes and origins. Both scientific articles and reviews on these topics are welcome.

Dr. Artem Rogachev
Dr. Vladimir Ivanisenko
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

  • metabolite profiling
  • sample preparation
  • sample analysis
  • liquid chromatography
  • gas chromatography
  • mass spectrometry

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Published Papers (3 papers)

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Research

13 pages, 688 KiB  
Article
Untargeted Plasma Metabolomic Profiling in Patients with Depressive Disorders: A Preliminary Study
by Alexander A. Chernonosov, Irina A. Mednova, Lyudmila A. Levchuk, Ekaterina O. Mazurenko, Olga V. Roschina, German G. Simutkin, Nikolay A. Bokhan, Vladimir V. Koval and Svetlana A. Ivanova
Metabolites 2024, 14(2), 110; https://doi.org/10.3390/metabo14020110 - 6 Feb 2024
Viewed by 2046
Abstract
Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work [...] Read more.
Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work was a metabolomic analysis of blood serum to classify patients with depressive disorders and healthy individuals using Compound Discoverer software. Using high-resolution mass spectrometry, blood plasma samples from 60 people were analyzed, of which 30 were included in a comparison group (healthy donors), and 30 were patients with a depressive episode (F32.11) and recurrent depressive disorder (F33.11). Differences between patient and control groups were identified using the built-in utilities in Compound Discoverer software. Compounds were identified by their accurate mass and fragment patterns using the mzCloud database and tentatively identified by their exact mass using the ChemSpider search engine and the KEGG, ChEBI, FDA UNII-NLM, Human Metabolome and LipidMAPS databases. We identified 18 metabolites that could divide patients with depressive disorders from healthy donors. Of these, only two compounds were tentatively identified using the mzCloud database (betaine and piperine) based on their fragmentation spectra. For three compounds ((4S,5S,8S,10R)-4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one, (2E,4E)-N-(2-hydroxy-2-methylpropyl)-2,4-tetradecadienamide and 17α-methyl-androstan-3-hydroxyimine-17β-ol), matches were found in the mzCloud database but with low score, which could not serve as reliable evidence of their structure. Another 13 compounds were identified by their exact mass in the ChemSpider database, 9 (g-butyrobetaine, 6-diazonio-5-oxo-L-norleucine, 11-aminoundecanoic acid, methyl N-acetyl-2-diazonionorleucinate, glycyl-glycyl-argininal, dilaurylmethylamine, 12-ketodeoxycholic acid, dicetylamine, 1-linoleoyl-2-hydroxy-sn-glycero-3-PC) had only molecular formulas proposed, and 4 were unidentified. Thus, the use of Compound Discoverer software alone was not sufficient to identify all revealed metabolites. Nevertheless, the combination of the found metabolites made it possible to divide patients with depressive disorders from healthy donors. Full article
(This article belongs to the Special Issue Recent Developments in Sample Preparation and Analysis in Mass Spectrometry-Based Metabolomics 2nd Edition)
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15 pages, 1648 KiB  
Article
Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques
by Jeong-Hun Mok, Minjoong Joo, Seonghyeon Cho, Van-An Duong, Haneul Song, Jong-Moon Park and Hookeun Lee
Metabolites 2024, 14(1), 34; https://doi.org/10.3390/metabo14010034 - 3 Jan 2024
Cited by 2 | Viewed by 2170
Abstract
Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and [...] Read more.
Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through quantitative comparisons of the identified protein counts. Nevertheless, the specific differences in these comparisons have been minimally investigated. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, the Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for the identification of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA-processing proteins. Thus, FASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, regarding the choice of extraction method, the single-phase method identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction method identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences among small molecules are primarily identified due to the varying polarities of extraction solvents. These results, obtained by considering variables such as human error and batch effects in the sample preparation step, offer comprehensive and detailed results not previously provided by existing studies, thereby aiding in the selection of the most suitable pre-processing approach. Full article
(This article belongs to the Special Issue Recent Developments in Sample Preparation and Analysis in Mass Spectrometry-Based Metabolomics 2nd Edition)
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35 pages, 5349 KiB  
Article
Unlocking Potentially Therapeutic Phytochemicals in Capadulla (Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics
by Ewart Smith, Ainsely Lewis, Suresh S. Narine and R. J. Neil Emery
Metabolites 2023, 13(10), 1050; https://doi.org/10.3390/metabo13101050 - 3 Oct 2023
Cited by 1 | Viewed by 2905
Abstract
Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to [...] Read more.
Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography–mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED). Full article
(This article belongs to the Special Issue Recent Developments in Sample Preparation and Analysis in Mass Spectrometry-Based Metabolomics 2nd Edition)
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