Special Issue "Metabolomics Methodologies and Applications"

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

Deadline for manuscript submissions: closed (20 December 2019).

Special Issue Editor

Dr. Helen G. Gika
E-Mail Website
Guest Editor
Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University Thessaloniki, 54124 Greece
Interests: bioanalysis of small molecules; metabolomics; human growth; healthy ageing; biomarker discovery; disease biomarkers; diagnostic/prognostic; patient stratification; food authenticity/geographical origin verification; investigation of gut microbiota host-guest interactions
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Special Issue Information

Dear Colleagues,

The 5th Metabolomics Workshop organized by the Aristotle University of Thessaloniki is the continuation of a series of meetings held in Greece since 2008 with the aim to highlight and discuss the latest research on metabolomics, with special focus on applied methodologies.

We welcome papers particularly, but not exclusively, presented at the 5th Metabolomics Workshop to be held in Thessaloniki, Greece with a focus on methodologies and workflows, analytical procedures for targeted and untargeted approaches, sample preparation, data treatment, metabolite identification and quantification, as well as applications in health sciences, nutrition, and food science, amongst others.

More information about the 5th Metabolomics Workshop 2019 can be found at:

http://biomic.web.auth.gr/workshop2019/

Dr. Helen G. Gika
Guest Editor

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 1600 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

  • Analytical and preanalytical procedures in metabolomics
  • Targeted metabolomics
  • Lipidomics
  • LC-MS, GC-MS, NMR
  • Data acquisition and processing
  • Metabolite identification and quantification
  • Health and disease
  • Nutritional biomarkers
  • Foodomics

Published Papers (4 papers)

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Research

Open AccessArticle
Use of Chemometrics for Correlating Carobs Nutritional Compositional Values with Geographic Origin
Metabolites 2020, 10(2), 62; https://doi.org/10.3390/metabo10020062 (registering DOI) - 10 Feb 2020
Abstract
Carobs unique compositional and biological synthesis enables their characterization as functional foods. In the present study, 76 samples derived from fruit and seeds of carobs, with origin from the countries of the Mediterranean region (Cyprus, Greece, Italy, Spain, Turkey, Jordan and Palestine) were [...] Read more.
Carobs unique compositional and biological synthesis enables their characterization as functional foods. In the present study, 76 samples derived from fruit and seeds of carobs, with origin from the countries of the Mediterranean region (Cyprus, Greece, Italy, Spain, Turkey, Jordan and Palestine) were analyzed for their nutritional composition, in order to identify potential markers for their provenance and address the carobs’ authenticity issue. Moisture, ash, fat, proteins, sugars (fructose, glucose, sucrose), dietary fibers and minerals (Ca, K, Mg, Na, P, Cu, Fe, Mn, Zn) were estimated following official methods. Due to the large number of data (76 samples × 17 parameters × 7 countries), chemometric techniques were employed to process them and extract conclusions. The samples of different geographical origin were discriminated with 79% success in total. The carobs from Cyprus, Italy and Spain were correctly classified without error. The main discriminators were found to be the dietary fibers, the carbohydrates and Cu, Zn and Mn, which emphasize their specific nutritional added value to the product and the country of origin impact. The results suggest that the proposed analytical approach is a powerful tool that enables the discrimination of carobs based on their country of origin. This research contributes to authenticity of carobs, adding value to local products. Full article
(This article belongs to the Special Issue Metabolomics Methodologies and Applications)
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Open AccessArticle
A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics
Metabolites 2020, 10(1), 28; https://doi.org/10.3390/metabo10010028 - 08 Jan 2020
Abstract
Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report [...] Read more.
Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment. Full article
(This article belongs to the Special Issue Metabolomics Methodologies and Applications)
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Open AccessArticle
Direct Implementation of Intestinal Permeability Test in NMR Metabolomics for Simultaneous Biomarker Discovery—A Feasibility Study in a Preterm Piglet Model
Metabolites 2020, 10(1), 22; https://doi.org/10.3390/metabo10010022 - 01 Jan 2020
Abstract
Measurement of intestinal permeability (IP) is often used in the examination of inflammatory gastrointestinal disorders. IP can be assessed by measurement of urinary recovery of ingested non-metabolizable lactulose (L) and mannitol (M). The present study aimed to examine how measurements of IP can [...] Read more.
Measurement of intestinal permeability (IP) is often used in the examination of inflammatory gastrointestinal disorders. IP can be assessed by measurement of urinary recovery of ingested non-metabolizable lactulose (L) and mannitol (M). The present study aimed to examine how measurements of IP can be integrated in a NMR-based metabolomics approach for a simultaneous quantification of L/M ratio and biomarker exploration. For this purpose, plasma and urine samples were collected from five-day-old preterm piglets (n = 20) with gastrointestinal disorders (subjected to intra-amniotic lipopolysaccharide (LPS, 1 mg/fetus)) after they had been administrated a 5% lactulose and 5% mannitol solution (15 mL/kg). The collected plasma and urine samples were analyzed by 1H NMR-based metabolomics. Urine L/M ratio measured by 1H NMR spectroscopy showed high correlation with the standard measurement of the urinary recoveries by enzymatic assays (r = 0.93, p < 0.05). Partial least squares (PLS) regressions and correlation analyses between L/M ratio and NMR metabolomics data revealed that L/M ratio was positively correlated with plasma lactate, acetate and succinate levels and negatively correlated with urinary hippuric acid and glycine. In conclusion, the present study demonstrated that NMR metabolomics enables simultaneous IP testing and discovery of biomarkers associated with an impaired intestinal permeability. Full article
(This article belongs to the Special Issue Metabolomics Methodologies and Applications)
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Open AccessArticle
Study of Fecal and Urinary Metabolite Perturbations Induced by Chronic Ethanol Treatment in Mice by UHPLC-MS/MS Targeted Profiling
Metabolites 2019, 9(10), 232; https://doi.org/10.3390/metabo9100232 - 16 Oct 2019
Cited by 1
Abstract
Alcoholic liver disease (ALD) as a consequence of ethanol chronic consumption could lead to hepatic cirrhosis that is linked to high morbidity and mortality. Disease diagnosis is still very challenging and usually clear findings are obtained in the later stage of ALD. The [...] Read more.
Alcoholic liver disease (ALD) as a consequence of ethanol chronic consumption could lead to hepatic cirrhosis that is linked to high morbidity and mortality. Disease diagnosis is still very challenging and usually clear findings are obtained in the later stage of ALD. The profound effect of ethanol on metabolism can be depicted using metabolomics; thus, the discovery of novel biomarkers could shed light on the initiation and the progression of the ALD, serving diagnostic purposes. In the present study, Hydrophilic Interaction Liquid Chromatography tandem Mass Spectrometry HILIC-MS/MS based metabolomics analyisis of urine and fecal samples of C57BL/6 mice of both sexes at two sampling time points was performed, monitoring the effect of eight-week ethanol consumption. The altered hepatic metabolism caused by ethanol consumption induces extensive biochemical perturbations and changes in gut microbiota population on a great scale. Fecal samples were proven to be a suitable specimen for studying ALD since it was more vulnerable to the metabolic changes in comparison to urine samples. The metabolome of male mice was affected on a greater scale than the female metabolome due to ethanol exposure. Precursor small molecules of essential pathways of energy production responded to ethanol exposure. A meaningful correlation between the two studied specimens demonstrated the impact of ethanol in endogenous and symbiome metabolism. Full article
(This article belongs to the Special Issue Metabolomics Methodologies and Applications)
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