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Metabolites
Special Issues
Metabolomics Methodologies and Applications
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Metabolomics Methodologies and Applications

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: closed (20 December 2019) | Viewed by 15987

Special Issue Editor

Dr. Helen G. Gika

E-Mail Website
Guest Editor
Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University Thessaloniki, Thessaloniki, Greece
Interests: bioanalysis of small molecules; metabolomics; QA/QC strategies in metabolomics; LC-MS; GC-MS; biomarker discovery; disease biomarkers; diagnostic/prognostic
Special Issues, Collections and Topics in MDPI journals

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 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

  • 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

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Published Papers (4 papers)

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Research

11 pages, 1442 KiB  
Article
Use of Chemometrics for Correlating Carobs Nutritional Compositional Values with Geographic Origin
by Rebecca Kokkinofta, Stelios Yiannopoulos, Marinos A. Stylianou and Agapios Agapiou
Metabolites 2020, 10(2), 62; https://doi.org/10.3390/metabo10020062 - 10 Feb 2020
Cited by 11 | Viewed by 2931
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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13 pages, 2845 KiB  
Article
A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics
by Álvaro Fernández-Ochoa, Rosa Quirantes-Piné, Isabel Borrás-Linares, María de la Luz Cádiz-Gurrea, PRECISESADS Clinical Consortium, Marta E. Alarcón Riquelme, Carl Brunius and Antonio Segura-Carretero
Metabolites 2020, 10(1), 28; https://doi.org/10.3390/metabo10010028 - 8 Jan 2020
Cited by 15 | Viewed by 4924
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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11 pages, 1154 KiB  
Article
Direct Implementation of Intestinal Permeability Test in NMR Metabolomics for Simultaneous Biomarker Discovery—A Feasibility Study in a Preterm Piglet Model
by Masoumeh Alinaghi, Duc Ninh Nguyen, Per Torp Sangild and Hanne Christine Bertram
Metabolites 2020, 10(1), 22; https://doi.org/10.3390/metabo10010022 - 1 Jan 2020
Cited by 7 | Viewed by 3690
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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16 pages, 2063 KiB  
Article
Study of Fecal and Urinary Metabolite Perturbations Induced by Chronic Ethanol Treatment in Mice by UHPLC-MS/MS Targeted Profiling
by Olga Deda, Christina Virgiliou, Amvrosios Orfanidis and Helen G. Gika
Metabolites 2019, 9(10), 232; https://doi.org/10.3390/metabo9100232 - 16 Oct 2019
Cited by 17 | Viewed by 3903
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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