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Challenges and Opportunities in Application of Mass Spectrometry for Metabolomics and Lipidomics

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Metabolomic Profiling Technology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 2636

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Special Issue Editors

Dr. Konstantinos Kouremenos

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Guest Editor

Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, VIC 3010, Australia
Interests: metabolomics; lipidomics; separation science; mass spectrometry; clinical chemistry; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Dr. David J. Beale

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Guest Editor

Environmental Metabolomics and Proteomics, Land & Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecoscience Precinct, Dutton Park, QLD 4160, Australia
Interests: metabolomics; environmental multi-omics; pesticide analysis; systems biology; environmental science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce the Special Issue titled "Challenges and Opportunities in Mass-Spectrometry-Based Metabolomics and Lipidomics", aiming to highlight new scientific applications in mass spectrometry-based metabolomics and lipidomics and address the associated challenges.

Metabolomics is an interdisciplinary field that brings together experts from various disciplines such as analytical chemistry, biochemistry, statistics, biology, computational science and medicine. Among the various analytical platforms available, mass spectrometry stands out as a primary tool for exploring the metabolome due to its high sensitivity and specificity in chemical analyses. It is often used in conjunction with separation techniques such as gas or liquid chromatography—and more recently ion mobility—to improve the analysis of complex samples.

While significant progress has been made in the metabolomics and lipidomics fields, several challenges remain. These include the annotation of metabolites in discovery-based studies, the validation of proposed biomarkers, the development of user-friendly visualization methods for interpreting multivariate analysis outputs, the standardization of large data processing workflows, the achievement of consistent results in inter-laboratory comparisons and the translation of findings into clinical settings.

We encourage researchers to submit their work to this Special Issue covering original research and review articles which address analytical challenges, new advances, and recent applications in mass-spectrometry-based metabolomics and lipidomics.

Dr. Konstantinos Kouremenos
Dr. David J. Beale
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
lipidomics
separation science
mass spectrometry
bioinformatics

Published Papers (3 papers)

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Research

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14 pages, 4142 KiB

Open AccessArticle

Genetic Upregulation of Activated Protein C Mitigates Delayed Effects of Acute Radiation Exposure in the Mouse Plasma

by Shivani Bansal, Yaoxiang Li, Sunil Bansal, William Klotzbier, Baldev Singh, Meth Jayatilake, Vijayalakshmi Sridharan, José A. Fernández, John H. Griffin, Hartmut Weiler, Marjan Boerma and Amrita K. Cheema

Metabolites 2024, 14(5), 245; https://doi.org/10.3390/metabo14050245 - 24 Apr 2024

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Abstract

Exposure to ionizing radiation, accidental or intentional, may lead to delayed effects of acute radiation exposure (DEARE) that manifest as injury to organ systems, including the kidney, heart, and brain. This study examines the role of activated protein C (APC), a known mitigator of radiation-induced early toxicity, in long-term plasma metabolite and lipid panels that may be associated with DEARE in APCHi mice. The APCHi mouse model used in the study was developed in a C57BL/6N background, expressing the D168F/N173K mouse analog of the hyper-activatable human D167F/D172K protein C variant. This modification enables increased circulating APC levels throughout the mouse’s lifetime. Male and female cohorts of C57BL/6N wild-type and APCHi transgenic mice were exposed to 9.5 Gy γ-rays with their hind legs shielded to allow long-term survival that is necessary to monitor DEARE, and plasma was collected at 6 months for LC-MS-based metabolomics and lipidomics. We observed significant dyslipidemia, indicative of inflammatory phenotype, upon radiation exposure. Additionally, observance of several other metabolic dysregulations was suggestive of gut damage, perturbations in TriCarboxylic Acid (TCA) and urea cycles, and arginine metabolism. We also observed gender- and genotype-modulated metabolic perturbations post radiation exposure. The APCHi mice showed near-normal abundance for several lipids. Moreover, restoration of plasma levels of some metabolites, including amino acids, citric acid, and hypoxanthine, in APCHi mice is indicative of APC-mediated protection from radiation injuries. With the help of these findings, the role of APC in plasma molecular events after acute γ-radiation exposure in a gender-specific manner can be established for the first time. Full article

(This article belongs to the Special Issue Challenges and Opportunities in Application of Mass Spectrometry for Metabolomics and Lipidomics)

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20 pages, 4688 KiB

Open AccessArticle

Integrative Analysis of Cytokine and Lipidomics Datasets Following Mild Traumatic Brain Injury in Rats

by Alexis N. Pulliam, Alyssa F. Pybus, David A. Gaul, Samuel G. Moore, Levi B. Wood, Facundo M. Fernández and Michelle C. LaPlaca

Metabolites 2024, 14(3), 133; https://doi.org/10.3390/metabo14030133 - 21 Feb 2024

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Abstract

Traumatic brain injury (TBI) is a significant source of disability in the United States and around the world and may lead to long-lasting cognitive deficits and a decreased quality of life for patients across injury severities. Following the primary injury phase, TBI is characterized by complex secondary cascades that involve altered homeostasis and metabolism, faulty signaling, neuroinflammation, and lipid dysfunction. The objectives of the present study were to (1) assess potential correlations between lipidome and cytokine changes after closed-head mild TBI (mTBI), and (2) examine the reproducibility of our acute lipidomic profiles following TBI. Cortices from 54 Sprague Dawley male and female rats were analyzed by ultra-high-performance liquid chromatography mass spectrometry (LC-MS) in both positive and negative ionization modes and multiplex cytokine analysis after single (smTBI) or repetitive (rmTBI) closed-head impacts, or sham conditions. Tissue age was a variable, given that two cohorts (n = 26 and n = 28) were initially run a year-and-a-half apart, creating inter-batch variations. We annotated the lipidome datasets using an in-house data dictionary based on exact masses of precursor and fragment ions and removed features with statistically significant differences between sham control batches. Our results indicate that lipids with high-fold change between injury groups moderately correlate with the cytokines eotaxin, IP-10, and TNF-α. Additionally, we show a significant decrease in the pro-inflammatory markers IL-1β and IP-10, TNF-α, and RANTES in the rmTBI samples relative to the sham control. We discuss the major challenges in correlating high dimensional lipidomic data with functional cytokine profiles and the implications for understanding the biological significance of two related but disparate analysis modes in the study of TBI, an inherently heterogeneous neurological disorder. Full article

(This article belongs to the Special Issue Challenges and Opportunities in Application of Mass Spectrometry for Metabolomics and Lipidomics)

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Review

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14 pages, 1057 KiB

Open AccessReview

Challenges in the Metabolomics-Based Biomarker Validation Pipeline

by Shenghan Li, Nikita Looby, Vinod Chandran and Vathany Kulasingam

Metabolites 2024, 14(4), 200; https://doi.org/10.3390/metabo14040200 - 03 Apr 2024

Viewed by 469

Abstract

As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine. Full article

(This article belongs to the Special Issue Challenges and Opportunities in Application of Mass Spectrometry for Metabolomics and Lipidomics)

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