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Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of...
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Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 8206

Special Issue Editors

Dr. Xian Luo

E-Mail Website
Guest Editor
The Metabolomics Innovation Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
Interests: mass spectrometry; LC-MS; metabolomics; metabolic flux
Dr. Wesley Baker

E-Mail Website
Guest Editor
Division of Neurology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Interests: functional near-infrared spectroscopy; diffuse correlation spectroscopy; cerebral hemodynamics; multimodal neuromonitoring; neurocritical care bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Comprehensive metabolomic profiling of cells and tissues can help us discover new drug targets, find biomarkers for disease diagnosis, and study absorption, distribution, metabolism and excretion (ADME) of drugs. MS is one of the most powerful analytical platforms. However, achieving high-coverage analysis of metabolites in cells and tissues is still very challenging. In a real-world situation, a limited amount of tissues can be collected from animal models or patients. Although a large number of cells can be acquired from cell culturing, only a small number of primary cells, which are more useful in biological study, can be isolated from patients. Profiling single cell metabolome in tumors can provide valuable information regarding cancer heterogeneity. Therefore, it is desirable to develop more sensive MS technique for realizing comprehensive metabolomic analysis of cells and tissues. More than that, there are various of other challenges in cell and tissue metabolomic profiling: data processing (e.g., efficiently extract meaningful signal sfrom raw data), linking with other -omics techniques (e.g., genomics, transcriptomics, proteomics) and metabolite identification. This Special Issue highlights the development of MS for comprehensive analysis of metabolites in cells and tissues. The Special Issue covers, but is not limited to, untargeted metabolomic profiling of cells and tissues, targeted metabolites analysis in cells and tissues, single cell metabolomics, developing new algorithms to improve data processing and metabolite identification rate,  novel chemical derivatization method development, and application of cellular and tissue metabolomics in clinical diagnosis. 

Dr. Xian Luo
Dr. Wesley Baker
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

  • mass spectrometry
  • metabolomics
  • tissue analysis
  • bioinformatics
  • cellular metabolomics

Published Papers (5 papers)

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15 pages, 1939 KiB  
Article
Optimized Mass Spectrometry Detection of Thyroid Hormones and Polar Metabolites in Rodent Cerebrospinal Fluid
by Ryann M. Fame, Ilhan Ali, Maria K. Lehtinen, Naama Kanarek and Boryana Petrova
Metabolites 2024, 14(2), 79; https://doi.org/10.3390/metabo14020079 - 23 Jan 2024
Viewed by 1282
Abstract
Thyroid hormones (TH) are required for brain development and function. Cerebrospinal fluid (CSF), which bathes the brain and spinal cord, contains TH as free hormones or as bound to transthyretin (TTR). Tight TH level regulation in the central nervous system is essential for [...] Read more.
Thyroid hormones (TH) are required for brain development and function. Cerebrospinal fluid (CSF), which bathes the brain and spinal cord, contains TH as free hormones or as bound to transthyretin (TTR). Tight TH level regulation in the central nervous system is essential for developmental gene expression, which governs neurogenesis, myelination, and synaptogenesis. This integrated function of TH highlights the importance of developing precise and reliable methods for assessing TH levels in CSF. We report an optimized liquid chromatography–mass spectrometry (LC-MS)-based method to measure TH in rodent CSF and serum, applicable to both fresh and frozen samples. Using this new method, we find distinct differences in CSF TH in pregnant dams vs. non-pregnant adults and in embryonic vs. adult CSF. Further, targeted LC-MS metabolic profiling uncovers distinct central carbon metabolism in the CSF of these populations. TH detection and metabolite profiling of related metabolic pathways open new avenues of rigorous research into CSF TH and will inform future studies on metabolic alterations in CSF during normal development. Full article
(This article belongs to the Special Issue Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues)
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15 pages, 2680 KiB  
Article
UPLC-QTOF-MS Based Comparison of Rotundic Acid Metabolic Profiles in Normal and NAFLD Rats
by Lvying Wu, Lei Xing, Yake Zou, Zichen Wang, Yuanyuan Gou, Lei Zhang and Su Guan
Metabolites 2023, 13(1), 38; https://doi.org/10.3390/metabo13010038 - 26 Dec 2022
Cited by 1 | Viewed by 1301
Abstract
Rotundic acid, the principal bioactive constituent of the herbal remedy “Jiubiying”, has been considered as a candidate compound for treating non-alcoholic fatty liver disease (NAFLD). However, the in vivo and in vitro metabolism of rotundic acid has remained unclear. With the aim of [...] Read more.
Rotundic acid, the principal bioactive constituent of the herbal remedy “Jiubiying”, has been considered as a candidate compound for treating non-alcoholic fatty liver disease (NAFLD). However, the in vivo and in vitro metabolism of rotundic acid has remained unclear. With the aim of elucidating its metabolic profile, a reliable approach that used ultra-high performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was applied for screening and identifying rotundic acid in vivo (plasma, feces, urine, and liver tissue of normal and NAFLD model rats) and in vitro (rat liver microsomes) metabolites. Herein, 26 metabolites of rotundic acid were identified, including 22 metabolites in normal rats, 20 metabolites in NAFLD model rats, and eight metabolites in rat liver microsomes. Among them, 17 metabolites were identified for the first time. These data illustrate that the pathological status of NAFLD affects the metabolism of rotundic acid. Furthermore, the major pathways of metabolism included phase Ⅰ (demethylation, desaturation, etc.) and phase Ⅱ (sulfation and glucuronidation) reactions, as well as a combined multiple-step metabolism. This work provides important information on the metabolism of rotundic acid and lays the foundation for its future clinical application. Full article
(This article belongs to the Special Issue Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues)
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15 pages, 2497 KiB  
Article
Sex Differences in the In Vivo Exposure Process of Multiple Components of Gelsemium elegans in Rats
by Meng-Ting Zuo, Meng-Die Gong, Xiao Ma, Wen-Bo Xu, Zi-Yuan Wang, Mo-Huan Tang, Yong Wu and Zhao-Ying Liu
Metabolites 2023, 13(1), 33; https://doi.org/10.3390/metabo13010033 - 24 Dec 2022
Cited by 1 | Viewed by 1385
Abstract
Asian Gelsemium elegans (G. elegans) has a wide range of pharmacological activities. However, its strong toxicity limits its potential development and application. Interestingly, there are significant gender differences in G. elegans toxicity in rats. This work aimed to elucidate the overall [...] Read more.
Asian Gelsemium elegans (G. elegans) has a wide range of pharmacological activities. However, its strong toxicity limits its potential development and application. Interestingly, there are significant gender differences in G. elegans toxicity in rats. This work aimed to elucidate the overall absorption, distribution, metabolism, and excretion (ADME) of whole G. elegans crude extract in female and male rats using high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC/QqTOF-MS), which facilitates determining the reasons for the gender differences in toxicity. A total of 25 absorbed bioactive components and 3 related produced metabolites were tentatively identified in female rats, while only 17 absorbed bioactive components and 3 related produced metabolites were identified in male rats. By comparison of peak intensities, most compounds were found to be more active in absorption, distribution and excretion in female rats than in male rats, which showed that female rats were more sensitive to G. elegans. This study was the first to investigate the multicomponent in vivo process of G. elegans in rats and compare the differences between sexes. It was hypothesized that differences in the absorption of gelsedine-type alkaloids were one of the main reasons for the sex differences in G. elegans toxicity. Full article
(This article belongs to the Special Issue Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues)
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17 pages, 5877 KiB  
Article
UPLC-LTQ-Orbitrap-Based Cell Metabolomics and Network Pharmacology Analysis to Reveal the Potential Antiarthritic Effects of Pristimerin: In Vitro, In Silico and In Vivo Study
by Mengying Lv, Qiaoling Liang, Zhaoyong Luo, Bo Han, Tengyang Ni, Yang Wang, Li Tao, Weiting Lyu, Jie Xiang and Yanqing Liu
Metabolites 2022, 12(9), 839; https://doi.org/10.3390/metabo12090839 - 05 Sep 2022
Cited by 5 | Viewed by 2041
Abstract
Rheumatoid arthritis (RA) is characterized by systemic inflammation and synovial hyperplasia. Pristimerin, a natural triterpenoid isolated from plants belonging to the Celastraceae and Hippocrateaceae families, has been reported to exhibit anti-inflammation and anti-proliferation activities. Our study aims to reveal the antiarthritic effects of [...] Read more.
Rheumatoid arthritis (RA) is characterized by systemic inflammation and synovial hyperplasia. Pristimerin, a natural triterpenoid isolated from plants belonging to the Celastraceae and Hippocrateaceae families, has been reported to exhibit anti-inflammation and anti-proliferation activities. Our study aims to reveal the antiarthritic effects of pristimerin and explore its potential mechanism using in vitro, in silico, and in vivo methods. In the present study, pristimerin treatment led to a dose-dependent decrease in cell viability and migration in TNF-α stimulated human rheumatoid arthritis fibroblast-like synoviocytes MH7A. Moreover, UPLC-LTQ-Orbitrap-based cell metabolomics analysis demonstrated that phospholipid biosynthesis, fatty acid biosynthesis, glutathione metabolism and amino acid metabolic pathways were involved in TNF-α induced MH7A cells after pristimerin treatment. In addition, the adjuvant–induced arthritis (AIA) rat model was employed, and the results exhibited that pristimerin could effectively relieve arthritis symptoms and histopathological damage as well as reduce serum levels of TNF-α, NO and synovial expressions of p-Akt and p-Erk in AIA rats. Furthermore, network pharmacology analysis was performed to visualize crucial protein targets of pristimerin for RA treatment, which showed that the effects were mediated through the MAPK/Erk1/2, PI3K/Akt pathways and directing binding with TNF-α. Taken together, our study not only offered new insights into the biochemical mechanism of natural compounds for RA treatment, but also provided a strategy that integrated in vitro, in silico and in vivo studies to facilitate screening of new anti-RA drugs. Full article
(This article belongs to the Special Issue Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues)
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10 pages, 1371 KiB  
Technical Note
Effects of Solvent Evaporation Methods and Short-Term Room Temperature Storage on High-Coverage Cellular Metabolome Analysis
by Xian Luo and Liang Li
Metabolites 2023, 13(10), 1052; https://doi.org/10.3390/metabo13101052 - 05 Oct 2023
Viewed by 971
Abstract
Cellular metabolomics provides insights into the metabolic processes occurring within cells and can help researchers understand how these processes are regulated and how they relate to cellular function, health, and disease. In this technical note, we investigated the effects of solvent evaporation equipment [...] Read more.
Cellular metabolomics provides insights into the metabolic processes occurring within cells and can help researchers understand how these processes are regulated and how they relate to cellular function, health, and disease. In this technical note, we investigated the effects of solvent evaporation equipment and storage condition on high-coverage cellular metabolomics. We previously introduced a robust CIL LC-MS-based cellular metabolomics workflow that encompasses various steps, including cell harvest, metabolic quenching, cell lysis, metabolite extraction, differential chemical isotope labeling, and LC-MS analysis. This workflow has consistently served as the cornerstone of our collaborative research and service projects. As a core facility catering to users with diverse research needs and financial resources, we have encountered scenarios requiring short-term sample storage. For example, the need often arises to transport samples at room temperature from user sites to our core facility. Herein, we present a study in which we compared different solvent evaporation methods (specifically, the nitrogen blowdown evaporator, SpeedVac concentrator, and lyophilizer) and diverse storage conditions (including dried samples stored in a freezer, samples stored in a freezer with methanol, dried samples stored at room temperature, and samples stored at room temperature with methanol). Our findings indicate that the choice of solvent evaporation equipment did not significantly impact the cellular metabolome. However, we observed a noteworthy change in the metabolome after 7 days of storage when cells were stored with methanol, regardless of whether they were kept at −80 °C or room temperature, in contrast to cells that were dried and frozen. Importantly, we detected no significant alterations in cells that were dried and stored at room temperature. In conclusion, to ensure the production of high-quality CIL LC-MS metabolomics results, we strongly recommend that, in situations where low-temperature storage is not feasible, cell samples should be thoroughly dried before storage or shipment at room temperature. Full article
(This article belongs to the Special Issue Mass Spectrometry: A Powerful Tool for Comprehensive Metabolomic Profiling of Cells and Tissues)
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