Special Issue "Mass Spectrometry-Based Metabolomics: Challenges and Applications"

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

Deadline for manuscript submissions: 31 October 2019.

Special Issue Editors

Guest Editor
Dr. María Eugenia Monge Website E-Mail
Centro de Investigaciones en Bionanociencias, Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina
Interests: metabolomics; mass spectrometry; liquid chromatography; lipidomics; biomarker discovery for disease diagnosis; analytical chemistry; atmospheric chemistry; ambient mass spectrometry; chemometrics
Guest Editor
Dr. Christina M. Jones Website E-Mail
National Institute of Standards and Technology, Gaithersburg, United States
Interests: metabolomics; precision medicine; foodomics; lipidomics; mass spectrometry; analytical chemistry; metrology; liquid chromatography; ambient mass spectrometry; chemometrics

Special Issue Information

Dear Colleagues,

This Special Issue of Metabolites entitled “Mass Spectrometry-Based Metabolomics: Challenges and Applications” encourages authors to submit new scientific applications and challenges associated with mass spectrometry-based metabolomics in the format of research and review articles.

Metabolomics combines the expertise of analytical chemists, biochemists, statisticians, biologists, computational scientists, and medical doctors, among others, in a joint effort to holistically understand biochemical processes in complex biological systems through the analysis and characterization of small molecules (MW < 1500). Mass spectrometry is one of the primary analytical platforms used to explore the metabolome, as it is highly sensitive and versatile for chemical analyses. It is typically used in combination with additional separation techniques, such as gas or liquid chromatography, and/or ion mobility for enhancing peak capacity and, thereby, improving analysis of complex samples. Moreover, advancements in new, soft ambient ion generation techniques for surface sampling, and in situ analysis in real time, with little to no sample preparation, have broadened mass spectrometry-based metabolomics applications, tackling high-throughput analytical challenges.

Multidisciplinary efforts enrich the metabolomics field by addressing metabolite-related scientific questions through hypothesis-testing (targeted) and hypothesis-generating (untargeted) studies. These are designed to interrogate complex samples, such as biological fluids and tissues from human subjects, animal models, and plants, as well as samples from microorganisms, in vitro models, food, and marine environments, based on the original scientific question.

Many challenges have been identified thus far in the field, including metabolite annotation in discovery-based studies, the validation of proposed biomarkers, the development of user-friendly visualization methods for understanding multivariate analysis outputs, the standardization of large data processing workflows, the achievement of comparable results in inter-laboratory comparisons, and the translation of findings from health-related investigations into clinical settings.

Based on this brief overview, we are pleased to receive contributions from scientific groups around the world working to move this exciting, comprehensive, and versatile field forward.

Dr. María Eugenia Monge
Dr. Christina M. Jones
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 papers will be 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 1400 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
  • Lipidomics
  • Mass spectrometry
  • Multivariate analysis
  • Chemometrics
  • Biochemical processes

Published Papers (3 papers)

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Research

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Open AccessArticle
Polar Lipids in Starch-Rich Commodities to be Analyzed with LC-MS-Based Metabolomics—Optimization of Ionization Parameters and High-Throughput Extraction Protocols
Metabolites 2019, 9(8), 167; https://doi.org/10.3390/metabo9080167 - 12 Aug 2019
Abstract
Metabolomics-based approaches are still receiving growing attention with regard to food authenticity testing. Such studies require enormous sample numbers with negligible experimental or analytical variations to obtain statistically reliable results. In this context, an extraction protocol in line with optimized ionization parameters was [...] Read more.
Metabolomics-based approaches are still receiving growing attention with regard to food authenticity testing. Such studies require enormous sample numbers with negligible experimental or analytical variations to obtain statistically reliable results. In this context, an extraction protocol in line with optimized ionization parameters was developed in consideration of potential starch-derived matrix effects focusing on the polar lipids of potatoes. Therefore, well-known extractions (Bligh and Dyer, Folch, Matyash, and a n-hexane-based procedure) were compared in a non-targeted and a targeted approach regarding the extractability of their lipids such as phosphatidylcholines, phosphatidylethanolamines, galacto- and glucocerebrosides, di- and triglycerides, and acylated steryl glucosides. The selected Folch method was also scrutinized in view of its ability to remove the matrix’s starch and consequently improved by substituting trichlormethane with ethyl acetate as a “greener” Folch approach. Moreover, the challenge of starch-derived contamination and imminent ion suppression in the electrospray ionization source (ESI) was addressed by an optimization of ionization parameters varying desolvation settings, removing injection peaks, and increasing the angles and distances of the ESI-device. Long-term stability tests over five days were performed successfully with a combination of appropriate extraction and decreased desolvation settings during ionization. In conclusion, the present methodology provided the basis for on-going large-scale metabolomic studies with respect to the botanical origin of potatoes using UPLC-IMS-QToF (ultra-high performance liquid chromatography ion mobility spectroscopy quadrupole-time of flight mass spectrometer). Full article
(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics: Challenges and Applications)
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Open AccessArticle
Microbial Transformations of Organically Fermented Foods
Metabolites 2019, 9(8), 165; https://doi.org/10.3390/metabo9080165 - 10 Aug 2019
Abstract
Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, [...] Read more.
Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, we analyze the microbiome and metabolome of organically fermented vegetables, using a salt brine, which is a common ‘at-home’ method of food fermentation. We found that the natural microbial fermentation had a strong effect on the food metabolites, where all four foods (beet, carrot, peppers and radishes) changed through time, with a peak in molecular diversity after 2–3 days and a decrease in diversity during the final stages of the 4-day process. The microbiome of all foods showed a stark transition from one that resembled a soil community to one dominated by Enterobacteriaceae, such as Erwinia spp., within a single day of fermentation and increasing amounts of Lactobacillales through the fermentation process. With particular attention to plant natural products, we observed significant transformations of polyphenols, triterpenoids and anthocyanins, but the degree of this metabolism depended on the food type. Beets, radishes and peppers saw an increase in the abundance of these compounds as the fermentation proceeded, but carrots saw a decrease through time. This study showed that organically fermenting vegetables markedly changed their chemistry and microbiology but resulted in high abundance of Enterobacteriaceae which are not normally considered as probiotics. The release of beneficial plant specialized metabolites was observed, but this depended on the fermented vegetable. Full article
(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics: Challenges and Applications)
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Other

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Open AccessConcept Paper
Multi-Omics Analyses Detail Metabolic Reprogramming in Lipids, Carnitines, and Use of Glycolytic Intermediates between Prostate Small Cell Neuroendocrine Carcinoma and Prostate Adenocarcinoma
Metabolites 2019, 9(5), 82; https://doi.org/10.3390/metabo9050082 - 26 Apr 2019
Abstract
As the most common cancer in men, prostate cancer is molecularly heterogeneous. Contributing to this heterogeneity are the poorly understood metabolic adaptations of the two main types of prostate cancer, i.e., adenocarcinoma and small cell neuroendocrine carcinoma (SCNC), the latter being more aggressive [...] Read more.
As the most common cancer in men, prostate cancer is molecularly heterogeneous. Contributing to this heterogeneity are the poorly understood metabolic adaptations of the two main types of prostate cancer, i.e., adenocarcinoma and small cell neuroendocrine carcinoma (SCNC), the latter being more aggressive and lethal. Using transcriptomics, untargeted metabolomics and lipidomics profiling on LASCPC-01 (prostate SCNC) and LNCAP (prostate adenocarcinoma) cell lines, we found significant differences in the cellular phenotypes of the two cell lines. Gene set enrichment analysis on the transcriptomics data showed 62 gene sets were upregulated in LASCPC-01, while 112 gene sets were upregulated in LNCAP. ChemRICH analysis on metabolomics and lipidomics data revealed a total of 25 metabolite clusters were significantly different. LASCPC-01 exhibited a higher glycolytic activity and lower levels of triglycerides, while the LNCAP cell line showed increases in one-carbon metabolism as an exit route of glycolytic intermediates and a decrease in carnitine, a mitochondrial lipid transporter. Our findings pinpoint differences in prostate neuroendocrine carcinoma versus prostate adenocarcinoma that could lead to new therapeutic targets in each type. Full article
(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics: Challenges and Applications)
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