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

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

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 8003

Special Issue Editors

Dr. Konstantinos Kouremenos

E-Mail Website
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

E-Mail Website
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

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Published Papers (5 papers)

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Research

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13 pages, 1858 KiB  
Article
Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility
by Johanna von Gerichten, Kyle Saunders, Melanie J. Bailey, Lee A. Gethings, Anthony Onoja, Nophar Geifman and Matt Spick
Metabolites 2024, 14(8), 461; https://doi.org/10.3390/metabo14080461 - 19 Aug 2024
Viewed by 1042
Abstract
Identification of features with high levels of confidence in liquid chromatography–mass spectrometry (LC–MS) lipidomics research is an essential part of biomarker discovery, but existing software platforms can give inconsistent results, even from identical spectral data. This poses a clear challenge for reproducibility in [...] Read more.
Identification of features with high levels of confidence in liquid chromatography–mass spectrometry (LC–MS) lipidomics research is an essential part of biomarker discovery, but existing software platforms can give inconsistent results, even from identical spectral data. This poses a clear challenge for reproducibility in biomarker identification. In this work, we illustrate the reproducibility gap for two open-access lipidomics platforms, MS DIAL and Lipostar, finding just 14.0% identification agreement when analyzing identical LC–MS spectra using default settings. Whilst the software platforms performed more consistently using fragmentation data, agreement was still only 36.1% for MS2 spectra. This highlights the critical importance of validation across positive and negative LC–MS modes, as well as the manual curation of spectra and lipidomics software outputs, in order to reduce identification errors caused by closely related lipids and co-elution issues. This curation process can be supplemented by data-driven outlier detection in assessing spectral outputs, which is demonstrated here using a novel machine learning approach based on support vector machine regression combined with leave-one-out cross-validation. These steps are essential to reduce the frequency of false positive identifications and close the reproducibility gap, including between software platforms, which, for downstream users such as bioinformaticians and clinicians, can be an underappreciated source of biomarker identification errors. 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, 4907 KiB  
Article
Metabolomics Analysis of Rabbit Plasma after Ocular Exposure to Vapors of Sulfur Mustard
by Jihéne Bouhlel, Fanny Caffin, Fanny Gros-Désormeaux, Thierry Douki, Jean-François Benoist, Florence A. Castelli, Emeline Chu-Van, Christophe Piérard, Christophe Junot and François Fenaille
Metabolites 2024, 14(7), 349; https://doi.org/10.3390/metabo14070349 - 21 Jun 2024
Cited by 1 | Viewed by 863
Abstract
Sulfur mustard (SM) is a highly potent alkylating vesicant agent and remains a relevant threat to both civilians and military personnel. The eyes are the most sensitive organ after airborne SM exposure, causing ocular injuries with no antidote or specific therapeutics available. In [...] Read more.
Sulfur mustard (SM) is a highly potent alkylating vesicant agent and remains a relevant threat to both civilians and military personnel. The eyes are the most sensitive organ after airborne SM exposure, causing ocular injuries with no antidote or specific therapeutics available. In order to identify relevant biomarkers and to obtain a deeper understanding of the underlying biochemical events, we performed an untargeted metabolomics analysis using liquid chromatography coupled to high-resolution mass spectrometry of plasma samples from New Zealand white rabbits ocularly exposed to vapors of SM. Metabolic profiles (332 unique metabolites) from SM-exposed (n = 16) and unexposed rabbits (n = 8) were compared at different time intervals from 1 to 28 days. The observed time-dependent changes in metabolic profiles highlighted the profound dysregulation of the sulfur amino acids, the phenylalanine, the tyrosine and tryptophan pathway, and the polyamine and purine biosynthesis, which could reflect antioxidant and anti-inflammatory activities. Taurine and 3,4-dihydroxy-phenylalanine (Dopa) seem to be specifically related to SM exposure and correspond well with the different phases of ocular damage, while the dysregulation of adenosine, polyamines, and acylcarnitines might be related to ocular neovascularization. Additionally, neither cysteine, N-acetylcysteine, or guanine SM adducts were detected in the plasma of exposed rabbits at any time point. Overall, our study provides an unprecedented view of the plasma metabolic changes post-SM ocular exposure, which may open up the development of potential new treatment strategies. 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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14 pages, 4142 KiB  
Article
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
Viewed by 1375
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 [...] Read more.
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  
Article
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
Cited by 2 | Viewed by 2040
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 [...] Read more.
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  
Review
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 - 3 Apr 2024
Cited by 2 | Viewed by 1680
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 [...] Read more.
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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