Special Issue "Cell and Tissue Metabolomics"

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A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (30 June 2014)

Special Issue Editor

Guest Editor
Dr. Justin J.J. van der Hooft

Plant Products and Human Nutrition group, North Lab, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
Website | E-Mail
Phone: +441413308611
Interests: mass spectrometry; mass spectrometry fragmentation; nuclear magnetic resonance spectroscopy; metabolite identification; structural elucidation; metabolite annotation; automated metabolite annotation; polyphenols; bioavailability; metabolomics; urine

Special Issue Information

Dear Colleagues,

The last two decades we have witnessed an exciting development of metabolomics techniques and approaches. Without disregarding the other analytical tools, the two main analytical pillars are currently mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR). The total extracts of numerous plants, yeast, and human bio fluids were comprehensively characterised. With the equipment getting increasingly sensitive, we now see the first examples of cell and tissue metabolomes being, at least partially, resolved, with cancer cells and tissues being in the centre of attention.

Again the main challenges to be expected are: i) can we fully elucidate all detected metabolites, and ii) can we develop protocols for robust extraction and detection of the small metabolites? There are several interesting questions to be addressed: a) how can we learn from previous metabolomics studies, b) how can we organize the tremendous amount of data and metadata on metabolites in the most efficient way, and c) how can software tools help us solving the metabolomics challenges?

Herewith I invite you to contribute to this special issue of Metabolites: original research, a reviewing of the initial attempts, and ideas on how to tackle the cell and tissue metabolomics challenges in the nearby future are all welcome, from both the plant and human metabolomics field.

Dr. Justin J.J. van der Hooft

Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 quarterly 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 800 CHF (Swiss Francs).


Keywords

  • metabolomics
  • cell metabolomics
  • tissue metabolomics
  • metabolite annotation
  • metabolite identification
  • mass spectrometry
  • NMR
  • GC-MS
  • LC-MS
  • spectral databases
  • compound databases
  • sample preparation techniques
  • metabolic networks

Published Papers (4 papers)

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Research

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Open AccessArticle Metabolome Consistency: Additional Parazoanthines from the Mediterranean Zoanthid Parazoanthus Axinellae
Metabolites 2014, 4(2), 421-432; doi:10.3390/metabo4020421
Received: 1 April 2014 / Revised: 20 May 2014 / Accepted: 22 May 2014 / Published: 30 May 2014
Cited by 5 | PDF Full-text (1061 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ultra-high pressure liquid chromatography coupled to high resolution mass spectrometry (UHPLC-MS/MS) analysis of the organic extract obtained from the Mediterranean zoanthid Parazoanthus axinellae yielded to the identification of five new parazoanthines F-J. The structures were fully determined by comparison of fragmentation patterns with
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Ultra-high pressure liquid chromatography coupled to high resolution mass spectrometry (UHPLC-MS/MS) analysis of the organic extract obtained from the Mediterranean zoanthid Parazoanthus axinellae yielded to the identification of five new parazoanthines F-J. The structures were fully determined by comparison of fragmentation patterns with those of previously isolated parazoathines and MS/MS spectra simulation of in silico predicted compounds according to the metabolome consistency. The absolute configuration of the new compounds has been assigned using on-line electronic circular dichroism (UHPLC-ECD). We thus demonstrated the potential of highly sensitive hyphenated techniques to characterize the structures of a whole family of natural products within the metabolome of a marine species. Minor compounds can be characterized using these techniques thus avoiding long isolation processes that may alter the structure of the natural products. These results are also of interest to identify putative bioactive compounds present at low concentration in a complex mixture. Full article
(This article belongs to the Special Issue Cell and Tissue Metabolomics)
Open AccessArticle Comparative Analysis of Biological Sphingolipids with Glycerophospholipids and Diacylglycerol by LC-MS/MS
Metabolites 2014, 4(1), 98-114; doi:10.3390/metabo4010098
Received: 4 December 2013 / Revised: 8 January 2014 / Accepted: 20 January 2014 / Published: 27 January 2014
Cited by 15 | PDF Full-text (978 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Liquid chromatography-electrospray ionization mass spectrometry (LC-MS) is an effective and popular technique used in lipid metabolomic studies. Although many LC-MS methods enabling the determination of sphingolipid molecular species have been reported, they do not cover a broad range of sphingolipid metabolites with expanding
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Liquid chromatography-electrospray ionization mass spectrometry (LC-MS) is an effective and popular technique used in lipid metabolomic studies. Although many LC-MS methods enabling the determination of sphingolipid molecular species have been reported, they do not cover a broad range of sphingolipid metabolites with expanding glycerophospholipids (GPLs) and diacylglycerol (DAG). In this study, we developed an approach for the comprehensive analysis of sphingolipids, GPLs and DAG molecular species in a biological sample, without alkaline hydrolysis. After validating the reliability of this approach, we analyzed tissue lipids of sphingomyelin synthase 2-knockout mice and found that changes in sphingolipid metabolism in the liver affect the level of docosahexaenoic acid-containing GPLs. Our method analyzes GPLs and DAG, as well as sphingolipids within biological samples and, thus, will facilitate more comprehensive studies of sphingolipid metabolism in pathology and diagnostics. Full article
(This article belongs to the Special Issue Cell and Tissue Metabolomics)

Review

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Open AccessReview Unraveling Biochemical Pathways Affected by Mitochondrial Dysfunctions Using Metabolomic Approaches
Metabolites 2014, 4(3), 831-878; doi:10.3390/metabo4030831
Received: 29 June 2014 / Revised: 2 September 2014 / Accepted: 18 September 2014 / Published: 25 September 2014
Cited by 4 | PDF Full-text (709 KB) | HTML Full-text | XML Full-text
Abstract
Mitochondrial dysfunction(s) (MDs) can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to
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Mitochondrial dysfunction(s) (MDs) can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to alter the capacity of ATP production and are observed in several pathological states/diseases, including cancer, obesity, muscle and neurological disorders. The induction of MDs can also alter the secretion of several metabolites, reactive oxygen species production and modify several cell-signalling pathways to resolve the mitochondrial dysfunction or ultimately trigger cell death. Many metabolites, such as fatty acids and derived compounds, could be secreted into the blood stream by cells suffering from mitochondrial alterations. In this review, we summarize how a mitochondrial uncoupling can modify metabolites, the signalling pathways and transcription factors involved in this process. We describe how to identify the causes or consequences of mitochondrial dysfunction using metabolomics (liquid and gas chromatography associated with mass spectrometry analysis, NMR spectroscopy) in the obesity and insulin resistance thematic. Full article
(This article belongs to the Special Issue Cell and Tissue Metabolomics)
Open AccessReview Application of Stable Isotope-Assisted Metabolomics for Cell Metabolism Studies
Metabolites 2014, 4(2), 142-165; doi:10.3390/metabo4020142
Received: 13 January 2014 / Revised: 18 March 2014 / Accepted: 20 March 2014 / Published: 31 March 2014
Cited by 13 | PDF Full-text (579 KB) | HTML Full-text | XML Full-text
Abstract
The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to
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The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other “omics” analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research. Full article
(This article belongs to the Special Issue Cell and Tissue Metabolomics)

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

 

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