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: 30 June 2024 | Viewed by 2136

Special Issue Editors


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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
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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

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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 (2 papers)

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Research

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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
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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 [...] 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
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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 - 03 Apr 2024
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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
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