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Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass...
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Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 6495

Special Issue Editor

Dr. Ana Margarida Araújo

E-Mail Website
Guest Editor
Laboratory of Bromatology and Hydrology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
Interests: metabolomics; environmental sciences; toxicology; biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the intricate world of metabolic research, the techniques of Gas Chromatography–Mass Spectrometry (GC–MS) and Liquid Chromatography–Mass Spectrometry (LC–MS) have proven to be more than analytical tools; they are pivotal catalysts in our quest to decode the complex narrative of biological systems. This Special Issue, "Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry", seeks to spotlight the transformative impact these methodologies have on our ability to advance our understanding of metabolic pathways and their multifaceted implications.

GC–MS and LC–MS have revolutionized metabolic profiling, offering unparalleled specificity, sensitivity, and versatility in detecting and quantifying metabolites. These techniques stand at the forefront of metabolic research, enabling scientists to unravel the complexities of the metabolome with remarkable precision. The ability of GC–MS to separate and analyze volatile and semi-volatile compounds, coupled with the versatility of LC–MS to manage a broad spectrum of polar and nonpolar compounds, has significantly broadened the horizon of metabolic studies, facilitating comprehensive analyses that were once deemed challenging.

The relevance of these techniques extends beyond the bounds of academic curiosity; they are instrumental in addressing real-world challenges across various sectors. In healthcare, they are transforming disease diagnosis and drug development, offering insights into biomarker discovery and therapeutic interventions. In environmental science, they serve as crucial tools for monitoring pollutants and deciphering ecological dynamics. In the food industry, they ensure safety and quality, upholding the highest standards of consumer health and product integrity.

This Special Issue is a call upon researchers and innovators who are exploring the potentials of GC–MS and LC–MS to push the boundaries of metabolic research. We invite you to contribute original research articles or comprehensive review papers that not only highlight methodological advancements but also demonstrate how these techniques enhance our understanding of biological, environmental, and societal aspects. By sharing your cutting-edge research, you are contributing to a critical discourse that has the power to reshape industries, inform policymaking, and ultimately improve lives. Our aim is to compile a repository of the most innovative and impactful research in this field. Your insights and findings will be invaluable, serving as a cornerstone for future exploration and discovery.

Dr. Ana Margarida Araújo
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

  • chromatographic methods
  • mass spectrometry techniques
  • metabolic profiling
  • methodological advancements
  • biomarker discovery
  • environmental monitoring
  • food safety and quality
  • clinical diagnosis
  • drug development

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Published Papers (6 papers)

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Research

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12 pages, 1834 KiB  
Article
Examination of Intermolecular Forces Influencing Headspace Analysis of Biological Samples
by Young Eun Lee and Bruce A. Kimball
Metabolites 2025, 15(3), 183; https://doi.org/10.3390/metabo15030183 - 9 Mar 2025
Viewed by 645
Abstract
Headspace analysis is an effective method for assessing the concentrations of volatile and semi-volatile metabolites in biological samples. In particular, solid-phase microextraction (SPME) is an efficient tool for headspace analyses. Metabolites present in the sample are the typical targets of headspace analysis (rather [...] Read more.
Headspace analysis is an effective method for assessing the concentrations of volatile and semi-volatile metabolites in biological samples. In particular, solid-phase microextraction (SPME) is an efficient tool for headspace analyses. Metabolites present in the sample are the typical targets of headspace analysis (rather than the vapor phase concentration) for making measurements on sample donors (e.g., biomarkers of health or disease). Accordingly, intermolecular forces between metabolites and matrix may prevent a complete profile of the metabolite composition in the biosamples from being revealed. To assess sources of such interactions, several volatile compounds in various sample mediums were examined. Small volatile metabolites typical of human biosamples were the volatile compounds selected for this study. Test media included lipid or serum solution to simulate biological samples commonly encouraged in biomarker discovery. Headspace concentrations of volatile analytes were compared using solid-phase microextraction gas chromatography-mass spectrometry (SPME-GC-MS). Observed levels of metabolites in headspace varied among the different media, despite being fortified at equal concentrations in the samples. Overall, lower headspace responses were observed in samples containing proteins or lipids. It was found that these strong intermolecular interactions arose from irreversible chemical bonds between the volatile molecules and component of the sample matrix. However, headspace responses could be maximized when the analysis was performed at temperatures ranging from 60 to 70 °C. Furthermore, normalization of peak responses to an internal standard did not always account for these interactions. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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21 pages, 5553 KiB  
Article
Identification of Bioactive Metabolites of Capirona macrophylla by Metabolomic Analysis, Molecular Docking, and In Vitro Antiparasitic Assays
by Joseph Evaristo, Elise de Laia, Bruna Tavares, Esdras Mendonça, Larissa Grisostenes, Caroline Rodrigues, Welington do Nascimento, Carolina Garcia, Sheila Guterres, Fábio Nogueira, Fernando Zanchi and Geisa Evaristo
Metabolites 2025, 15(3), 157; https://doi.org/10.3390/metabo15030157 - 26 Feb 2025
Cited by 1 | Viewed by 755
Abstract
Capirona macrophylla is a Rubiaceae known as “mulateiro”. Ethnobotanical extracts have been used for skin treatment and in the management of leishmaniasis and malaria. Objectives: The metabolites in aqueous extracts from wood bark, leaves, and stems were identified, and their in silico docking [...] Read more.
Capirona macrophylla is a Rubiaceae known as “mulateiro”. Ethnobotanical extracts have been used for skin treatment and in the management of leishmaniasis and malaria. Objectives: The metabolites in aqueous extracts from wood bark, leaves, and stems were identified, and their in silico docking and in vitro cellular efficacy against Leishmania amazonensis and Plasmodium falciparum were evaluated. Methods: The extracts were analyzed by UHPLC/HRMSn using untargeted metabolomics approach with MSDial, MSFinder, and GNPS software for metabolite identification and spectra clustering. The most abundant metabolites underwent molecular docking using AutoDock via PyRx, targeting the dihydroorotate dehydrogenase from Leishmania and P. falciparum, and evaluated through molecular dynamics simulations using Gromacs. In vitro biological assays were conducted on 60 HPLC-fractions against these parasites. Results: Metabolomics analysis identified 5100 metabolites in ESI+ and 2839 in ESI− spectra among the “mulateiro” samples. GNPS clustering highlighted large clusters of quercetin and chlorogenic acid groups. The most abundant metabolites were isofraxidin, scopoletin, 5(S)-5-carboxystrictosidine, loliolide, quercetin, quinic acid, caffeoylquinic acid (and isomers), chlorogenic acid, neochlorogenic acid, tryptophan, N-acetyltryptophan, epicatechin, procyanidin, and kaempferol-3-O-robinoside-7-O-rhamnoside. Molecular docking pointed to 3,4-dicaffeoylquinic acid and kaempferol as promising inhibitors. The in vitro assays yielded four active HPLC-fractions against L. amazonensis with IC50 values ranging from 175.2 μg/mL to 194.8 μg/mL, and fraction G29 showed an IC50 of 119.8 μg/mL against P. falciparum. Conclusions: The ethnobotanical use of “mulateiro” wood bark tea as an antimalarial and antileishmanial agent was confirmed through in vitro assays. We speculate that these activities are attributed to linoleic acids and quinic acids. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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13 pages, 822 KiB  
Article
Chemical Informatics Combined with Kendrick Mass Analysis to Enhance Annotation and Identify Pathways in Soybean Metabolomics
by Troy D. Wood, Erin R. Tiede, Alexandra M. Izydorczak, Kevin J. Zemaitis, Heng Ye and Henry T. Nguyen
Metabolites 2025, 15(2), 73; https://doi.org/10.3390/metabo15020073 - 24 Jan 2025
Viewed by 907
Abstract
Background: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of [...] Read more.
Background: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Objectives: Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Methods: Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values were converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which were then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms. Results: In this study, more than 460 ionic formulas were identified in Pana, and more than 340 ionic formulas were identified in PI 567731, with many of these formulas reported from soybean for the first time. Conclusions: Using the SoyCyc matches, the metabolic pathways from each cultivar were compared, providing lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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15 pages, 1699 KiB  
Article
Evaluating Metabolic Profiling of Human Milk Using Biocrates MxP® QUANT 500 Assay
by Daniela Hampel, Setareh Shahab-Ferdows, Gilberto Kac and Lindsay H. Allen
Metabolites 2025, 15(1), 14; https://doi.org/10.3390/metabo15010014 - 3 Jan 2025
Viewed by 1121
Abstract
Background/Objectives: Metabolic profiling of human milk (HM) is indispensable for elucidating mother-milk-infant relationships. Methods: We evaluated the Biocrates MxP® Quant 500 assay for HM-targeted metabolomics (106 small molecules, 524 lipids) and analyzed in a feasibility test HM from apparently healthy Brazilian mothers [...] Read more.
Background/Objectives: Metabolic profiling of human milk (HM) is indispensable for elucidating mother-milk-infant relationships. Methods: We evaluated the Biocrates MxP® Quant 500 assay for HM-targeted metabolomics (106 small molecules, 524 lipids) and analyzed in a feasibility test HM from apparently healthy Brazilian mothers (A: 2–8, B: 28–50, C: 88–119 days postpartum, ntotal = 25). Results: Of the 630 possible signatures detectable with this assay, 506 were above the limits of detection in an HM-pool (10 µL) used for assay evaluation, 12 of them above the upper limit of quantitation. Analyzing five different HM-pool volumes (2–20 µL) revealed acceptable linearity for 458 metabolites. Intraday accuracy of 80–120% was attained by 469 metabolites after spiking and for 342 after a 1:2 dilution. Analyzing HM from Brazilian mothers revealed significantly lower concentrations in colostrum vs. mature milk for many flow-injection analyses (FIA) and only a few LC-MS metabolites, including triglycerides, sphingomyelins, and phosphatidylcholines. Higher concentrations at the later lactation stages were found predominantly for amino acids and related compounds. Conclusions: The MxP Quant® 500 assay is a useful tool for HM metabolic profiling, minimizing analytical bias between matrices, and enhancing our ability to study milk as a biological system. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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12 pages, 1323 KiB  
Article
Characterization and Metabolism of Drug Products Containing the Cocaine-Like New Psychoactive Substances Indatraline and Troparil
by Sascha K. Manier, Paula Mumber, Josef Zapp, Niels Eckstein and Markus R. Meyer
Metabolites 2024, 14(6), 342; https://doi.org/10.3390/metabo14060342 - 18 Jun 2024
Viewed by 1248
Abstract
With a rising demand of cocaine over the last years, it is likely that unregulated new psychoactive substances with similar effects such as indatraline ((1R,3S)-3-(3,4-dichlorophenyl)-N-methyl-2,3-dihydro-1H-inden-1-amine) and troparil (Methyl (1R,2S,3S,5 [...] Read more.
With a rising demand of cocaine over the last years, it is likely that unregulated new psychoactive substances with similar effects such as indatraline ((1R,3S)-3-(3,4-dichlorophenyl)-N-methyl-2,3-dihydro-1H-inden-1-amine) and troparil (Methyl (1R,2S,3S,5S)-8-methyl-3-phenyl-8-azabicyclo[3.2.1]octane-2-carboxylate) become popular as well. Both substances share a similar pharmacological profile as cocaine, while their potency is higher, and their duration of action is longer. This study investigated their metabolic fate in rat urine and incubations using pooled human liver S9 fraction (pHLS9). Indatraline formed two phase I and four phase II metabolites, with aromatic hydroxylation and glucuronidation being the main metabolic steps. All metabolites were detected in rat urine, while the parent compound was not detectable. Although low in abundance, indatraline metabolites were well identifiable due to their specific isotopic patterns caused by chlorine. Troparil formed four phase I and three phase II metabolites, with demethylation being the main metabolic step. Hydroxylation of the tropane ring, the phenyl ring, and combinations of these steps, as well as glucuronidation, were found. Phase I metabolites were detectable in rat urine and pHLS9, while phase II metabolites were only detectable in rat urine. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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Review

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24 pages, 906 KiB  
Review
Volatile Organic Metabolites as Potential Biomarkers for Genitourinary Cancers: Review of the Applications and Detection Methods
by Kiana L. Holbrook and Wen-Yee Lee
Metabolites 2025, 15(1), 37; https://doi.org/10.3390/metabo15010037 - 10 Jan 2025
Viewed by 1083
Abstract
Cancer is one of the leading causes of death globally, and is ranked second in the United States. Early detection is crucial for more effective treatment and a higher chance of survival rates, reducing burdens on individuals and societies. Genitourinary cancers, in particular, [...] Read more.
Cancer is one of the leading causes of death globally, and is ranked second in the United States. Early detection is crucial for more effective treatment and a higher chance of survival rates, reducing burdens on individuals and societies. Genitourinary cancers, in particular, face significant challenges in early detection. Finding new and cost-effective diagnostic methods is of clinical need. Metabolomic-based approaches, notably volatile organic compound (VOC) analysis, have shown promise in detecting cancer. VOCs are small organic metabolites involved in biological processes and disease development. They can be detected in urine, breath, and blood samples, making them potential candidates for sensitive and non-invasive alternatives for early cancer detection. However, developing robust VOC detection methods remains a hurdle. This review outlines the current landscape of major genitourinary cancers (kidney, prostate, bladder, and testicular), including epidemiology, risk factors, and current diagnostic tools. Furthermore, it explores the applications of using VOCs as cancer biomarkers, various analytical techniques, and comparisons of extraction and detection methods across different biospecimens. The potential use of VOCs in detection, monitoring disease progression, and treatment responses in the field of genitourinary oncology is examined. Full article
(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)
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