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Metabolites
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Metabolomic Fingerprinting: Challenges and Opportunities
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Metabolomic Fingerprinting: Challenges and Opportunities

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

Deadline for manuscript submissions: 30 May 2025 | Viewed by 1886

Special Issue Editors

Dr. Christina Virgiliou

E-Mail Website
Guest Editor
Analytical Chemistry Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: metabolomics; HRMS; method development; lipidomics; HILIC; ion mobility; biomarker identification; GC-MS; bioanalysis; foodomics; toxicological analysis
Dr. Olga-Angeliki Begou

E-Mail Website
Guest Editor
1. School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2. Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 57001 Thermi, Greece
Interests: mass spectrometry; validation; analytical chemistry; high-performance liquid chromatography (HPLC); analytical method development; quality control of chemicals, foods, and pharmaceuticals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are organizing a Special Issue entitled “Metabolomic Fingerprinting: Challenges and Opportunities” for Metabolites (MDPI).

The holistic analysis and simultaneous study of a wide array of small endogenous molecules from biological systems is one of the greatest strengths of metabolomic fingerprinting. However, metabolomics-based studies continue to face significant analytical challenges, mainly due to endogenous compounds' vast chemical diversity and varying concentration ranges. These challenges require specialized and advanced analytical techniques, as no single method can reveal all the properties of metabolites. Techniques such as High-Resolution Mass Spectrometry (HRMS), Two-Dimensional Liquid Chromatography (2D-LC), Capillary Electrophoresis (CE), Gas Chromatography (GC), and Ion Mobility Spectrometry (IMS) have propelled the progress of metabolic coverage, facilitating the discovery of new biomarkers and the understanding of their physiological mechanisms. These technologies provide high sensitivity and separation capabilities but also require advanced optimization and data analysis strategies. Their use allows for a deeper exploration of complex biological samples, aiding in discovering new biomarkers and understanding biochemical processes that impact health and disease. This Special Issue aims to showcase the latest approaches and methodologies related to the application of cutting-edge technologies, emphasizing both the technical challenges and the potential opportunities they present for a more comprehensive understanding of the multifaceted metabolomic profiles of biological systems.

We welcome articles and reviews, among other papers, to this Special Issue.

We look forward to receiving your contributions.

Dr. Christina Virgiliou
Dr. Olga-Angeliki Begou
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

  • metabolomics/metabonomics
  • mass spectrometry
  • metabolome
  • HRMS
  • hyphenated techniques

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Published Papers (2 papers)

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Research

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21 pages, 3701 KiB  
Article
LC-MS-Based Global Metabolic Profiles of Alternative Blood Specimens Collected by Microsampling
by Marlene N. Thaitumu, Daniel Marques De Sá e Silva, Philippine Louail, Johannes Rainer, Glykeria Avgerinou, Anatoli Petridou, Vassilis Mougios, Georgios Theodoridis and Helen Gika
Metabolites 2025, 15(1), 62; https://doi.org/10.3390/metabo15010062 - 16 Jan 2025
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Abstract
Blood microsampling (BμS) has recently emerged as an interesting approach in the analysis of endogenous metabolites but also in metabolomics applications. Their non-invasive way of use and the simplified logistics that they offer renders these technologies highly attractive in large-scale studies, especially the [...] Read more.
Blood microsampling (BμS) has recently emerged as an interesting approach in the analysis of endogenous metabolites but also in metabolomics applications. Their non-invasive way of use and the simplified logistics that they offer renders these technologies highly attractive in large-scale studies, especially the novel quantitative microsampling approaches such as VAMs or qDBS. Objectives: Herein, we investigate the potential of BµS devices compared to the conventional plasma samples used in global untargeted mass spectrometry-based metabolomics of blood. Methods: Two novel quantitative devices, namely, Mitra, Capitainer, and the widely used Whatman cards, were selected for comparison with plasma. Venous blood was collected from 10 healthy, overnight-fasted individuals and loaded on the devices; plasma was also collected from the same venous blood. An extraction solvent optimization study was first performed on the three devices before the main study, which compared the global metabolic profiles of the four extracts (three BµS devices and plasma). Analysis was conducted using reverse phase LC-TOF MS in positive mode. Results: BµS devices, especially Mitra and Capitainer, provided equal or even superior information on the metabolic profiling of human blood based on the number and intensity of features and the precision and stability of some annotated metabolites compared to plasma. Despite their rich metabolic profiles, BµS did not capture metabolites associated with biological differentiation of sexes. Conclusions: Overall, our results suggest that a more in-depth investigation of the acquired information is needed for each specific application, as a metabolite-dependent trend was obvious. Full article
(This article belongs to the Special Issue Metabolomic Fingerprinting: Challenges and Opportunities)
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Review

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28 pages, 2607 KiB  
Review
Underlying Mechanisms of Chromatographic H/D, H/F, cis/trans and Isomerism Effects in GC-MS
by Dimitrios Tsikas
Metabolites 2025, 15(1), 43; https://doi.org/10.3390/metabo15010043 - 11 Jan 2025
Viewed by 791
Abstract
Charge-free gaseous molecules labeled with deuterium 2H (D) atoms elute earlier than their protium-analogs 1H (H) from most stationary GC phases. This effect is known as the chromatographic H/D isotope effect (hdIEC) and can be calculated by [...] Read more.
Charge-free gaseous molecules labeled with deuterium 2H (D) atoms elute earlier than their protium-analogs 1H (H) from most stationary GC phases. This effect is known as the chromatographic H/D isotope effect (hdIEC) and can be calculated by dividing the retention times (tR) of the protiated (tR(H) ) to those of the deuterated (tR(D)) analytes: hdIEC = tR(H)/tR(D). Analytes labeled with 13C, 15N or 18O have almost identical retention times and lack a chromatographic isotope effect. Derivatives of cis- and trans-analytes such as cis- and trans-fatty acids also differ in their retention times. Analytes that contain trans-C=C-double bonds elute earlier in gas chromatography-mass spectrometry (GC-MS) than their cis-C=C-double bonds containing congeners. The chromatographic cis/trans-effect (ctEC) can be calculated by dividing the retention times of the cis- by those of the trans-analytes: ctEC = tR(c)/tR(t). In the present work, the hdIEC and ctEC values of endogenous and exogenous substances were calculated from previously reported GC-MS analyses and found to range each between 1.0009 and 1.0400. The examination suggests that the H/D-isotope effects and the cis/trans-effects observed in GC-MS are based on differences in the inter-molecular interaction strengths of the analyte derivatives with the stationary phase of GC columns. The deuterium atoms, being larger than the H atoms of the analytes, attenuate the interaction of the skeleton of the molecules with the GC stationary phase. The angulation of trans-analytes decreases the interaction of the skeleton of the molecules with the GC stationary phase, as only parts of the molecules are close enough to the GC stationary phase to interact. Other chromatographic effects caused by hydrogen (H) and fluorine (F) atoms and by stereo-isomerism are considered to be based on a similar mechanism due to the different orientation of the side chains. Full article
(This article belongs to the Special Issue Metabolomic Fingerprinting: Challenges and Opportunities)
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