Application of Analytical Technology in Metabolomics

Abstract submission deadline

31 August 2025

Manuscript submission deadline

31 October 2025

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Topic Information

Dear Colleagues,

Metabolomics, as an important part of systems biology, is concerned with both targeted and untargeted analysis of endogenous and exogenous small molecule metabolites found within a biological sample. Metabolomics is a powerful approach for biomarker discovery with the technological advancement in the Analytical and identification of small molecules for early diagnosis, monitoring therapeutic response, and establishing disease pathogenesis. These cutting-edge technologies, which include accurate measurement of HPLC/UPLC, CE, HRMS, and NMR technology, can perform the detection of metabolites within minutes. The metabolomics field is gaining popularity due to the development of new Analytical methods and innovative sample processing techniques. In the light of the impressive past and ongoing development in the area of metabolomics by the use of modern analytical methods in conjunction with Analytical techniques, we believe that this Topic will bring together original research papers as well as review articles that highlight recent advances in innovative sample processing, current Analytical, and targeted & untargeted methods for bioanalysis/preclinical and clinical analysis in the field of metabolomics. Additionally, miniaturization of sample processing methods for metabolomics analysis is also welcome.

Dr. Preeti Chandra
Dr. Raúl G. Enríquez
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Analytica analytica	-	1.8	2020	17.9 Days	CHF 1000	Submit
Metabolites metabolites	3.5	5.7	2011	16.1 Days	CHF 2700	Submit
Toxins toxins	3.9	7.5	2009	20.3 Days	CHF 2700	Submit
Molecules molecules	4.2	7.4	1996	15.1 Days	CHF 2700	Submit
Cells cells	5.1	9.9	2012	17 Days	CHF 2700	Submit
Chemosensors chemosensors	3.7	5.0	2013	20.1 Days	CHF 2700	Submit

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Published Papers (6 papers)

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All Analytica Metabolites Toxins Molecules Cells Chemosensors

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15 pages, 2552 KiB  

Open AccessArticle

Mapping Thrombosis Serum Markers by ¹H-NMR Allied with Machine Learning Tools

by Lucas G. Martins, Bruna M. Manzini, Silmara Montalvão, Millene A. Honorato, Marina P. Colella, Gabriela G. Y. Hayakawa, Erich V. de Paula, Fernanda A. Orsi, Erik S. Braga, Nataša Avramović, Folurunsho Bright Omage, Ljubica Tasic and Joyce M. Annichino-Bizzacchi

Molecules 2024, 29(24), 5895; https://doi.org/10.3390/molecules29245895 - 13 Dec 2024

Viewed by 905

Abstract

Machine learning and artificial intelligence tools were used to investigate the discriminatory potential of blood serum metabolites for thromboembolism and antiphospholipid syndrome (APS). ¹H-NMR-based metabonomics data of the serum samples of patients with arterial or venous thromboembolism (VTE) without APS (n = [...] Read more.

Machine learning and artificial intelligence tools were used to investigate the discriminatory potential of blood serum metabolites for thromboembolism and antiphospholipid syndrome (APS). ¹H-NMR-based metabonomics data of the serum samples of patients with arterial or venous thromboembolism (VTE) without APS (n = 32), thrombotic primary APS patients (APS, n = 32), and healthy controls (HCs) (n = 32) were investigated. Unique metabolic profiles between VTE and HCs, APS and HCs, and between VTE and triple-positive APS groups were indicative of the significant alterations in the metabolic pathways of glycolysis, the TCA cycle, lipid metabolism, and branched-chain amino acid (BCAA) metabolism, and pointed to the complex pathogenesis mechanisms of APS and VTE. Histidine, 3-hydroxybutyrate, and threonine were shown to be the top three metabolites with the most substantial impact on model predictions, suggesting that these metabolites play a pivotal role in distinguishing among APS, VTE, and HCs. These metabolites might be potential biomarkers to differentiate APS and VTE patients. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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13 pages, 4863 KiB  

Open AccessArticle

Application of ATR-FTIR Spectroscopy for Analysis of Salt Stress in Brussels Sprouts

by Su-Min Yun, Cheol-Soo Kim, Jeung-Joo Lee and Jung-Sung Chung

Metabolites 2024, 14(9), 470; https://doi.org/10.3390/metabo14090470 - 26 Aug 2024

Viewed by 1422

Abstract

Salt stress is one of the environmental stresses that significantly reduces crop productivity and quality worldwide. Methods to overcome salt stress include developing salt-resistant crops by inserting various resistance genes or to diagnosing and responding to the effects of salt stress at an [...] Read more.

Salt stress is one of the environmental stresses that significantly reduces crop productivity and quality worldwide. Methods to overcome salt stress include developing salt-resistant crops by inserting various resistance genes or to diagnosing and responding to the effects of salt stress at an early stage. In this study, we investigate the effects of salinity stress on growth, photosynthetic efficiency, and metabolic changes in Brussels sprouts (Brassica oleracea var. gemmifera). Fresh weight and leaf area decreased significantly with increasing NaCl concentration, indicating that salinity stress has a detrimental effect on plant growth. However, chlorophyll fluorescence parameters did not show significant changes, suggesting that photosynthetic efficiency was not significantly affected over 10 days. Fourier transform infrared (FTIR) spectroscopy revealed notable metabolic adjustments, especially in lipids, plastids, proteins, and carbohydrates, indicating biosynthesis of protective compounds such as anthocyanins and proline in response to salinity stress. Pearson correlation analysis confirmed a strong relationship between NaCl concentration and the observed physiological and metabolic changes. The findings highlight the potential of FTIR spectroscopy as a non-destructive tool for early detection of salinity stress and timely intervention to improve crop resilience and yield. This study highlights the widespread application of FTIR spectroscopy in agricultural research to manage abiotic stresses in crops. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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16 pages, 8494 KiB  

Open AccessArticle

Identification of a Chimera Mass Spectrum of Isomeric Lipid A Species Using Negative Ion Tandem Mass Spectrometry

by Ágnes Dörnyei, Anikó Kilár and Viktor Sándor

Toxins 2024, 16(7), 322; https://doi.org/10.3390/toxins16070322 - 18 Jul 2024

Viewed by 1320

Abstract

The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation [...] Read more.

The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation of lipid A, used independently or in combination with separation techniques. However, it is challenging to accurately characterize constitutional isomers of lipid A extracts by direct mass spectrometry, as the elemental composition and molecular mass of these molecules are identical. Thus, their simultaneous fragmentation leads to a composite, so-called chimera mass spectrum. The present study focuses on the phosphopositional isomers of the classical monophosphorylated, hexaacylated Escherichia coli-type lipid A. Collision-induced dissociation (CID) was performed in an HPLC-ESI-QTOF system. Energy-resolved mass spectrometry (ERMS) was applied to uncover the distinct fragmentation profiles of the phosphorylation isomers. A fragmentation strategy applying multi-levels of collision energy has been proposed and applied to reveal sample complexity, whether it contains only a 4′-phosphorylated species or a mixture of 1- and 4′-phosphorylated variants. This comparative fragmentation study of isomeric lipid A species demonstrates the high potential of ERMS-derived information for the successful discrimination of co-ionized phosphorylation isomers of hexaacylated lipid A. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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14 pages, 1561 KiB  

Open AccessArticle

Selected Ion Monitoring for Orbitrap-Based Metabolomics

by Wenyun Lu, Matthew J. McBride, Won Dong Lee, Xi Xing, Xincheng Xu, Xi Li, Anna M. Oschmann, Yihui Shen, Caroline Bartman and Joshua D. Rabinowitz

Metabolites 2024, 14(4), 184; https://doi.org/10.3390/metabo14040184 - 25 Mar 2024

Cited by 1 | Viewed by 6235

Abstract

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion [...] Read more.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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11 pages, 1990 KiB  

Open AccessArticle

Identification of Sanguinarine Metabolites in Rats Using UPLC-Q-TOF-MS/MS

by Mengting Liu, Zhiqin Liu, Zhuang Dong, Xianglin Zou, Jianguo Zeng and Zihui Yang

Molecules 2023, 28(22), 7641; https://doi.org/10.3390/molecules28227641 - 17 Nov 2023

Cited by 4 | Viewed by 1771

Abstract

Sanguinarine (SAN), as the main active component of a traditional Chinese veterinary medicine, has been widely used in the animal husbandry and breeding industry. However, the metabolites of SA are still uncertain. Therefore, this research aimed to investigate the metabolites of SA based [...] Read more.

Sanguinarine (SAN), as the main active component of a traditional Chinese veterinary medicine, has been widely used in the animal husbandry and breeding industry. However, the metabolites of SA are still uncertain. Therefore, this research aimed to investigate the metabolites of SA based on rats in vivo. The blood, feces, and urine of rats were collected after the oral administration of 40 mg/kg SAN. Ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) was employed to identify the metabolites of SAN. The elemental composition of sanguinarine metabolites was inferred by analyzing their exact molecular weight, and the structures of the metabolites were predicted based on their fragment ions and cleavage pathways. A total of 12 metabolites were identified, including three metabolites in the plasma, four in the urine, and nine in the feces. According to the possible metabolic pathways deduced in this study, SAN was mainly metabolized through reduction, oxidation, demethylation, hydroxylation, and glucuronidation. This present research has summarized the metabolism of SAN in rats, which is helpful for further studying the metabolic mechanism of SAN in vivo and in vitro. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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10 pages, 1843 KiB  

Open AccessArticle

The Synthesis of Biphasic Metabolites of Carfentanil

by Junchang Wang, Jianwen Hu, Pingyong Liao, Shang Xue, Shan He, Ruijia Chen, Xuejun Zhao and Wenbin Liu

Molecules 2023, 28(22), 7625; https://doi.org/10.3390/molecules28227625 - 16 Nov 2023

Viewed by 1878

Abstract

Carfentanil is an ultra-potent synthetic opioid. The Russian police force used both carfentanil and remifentanil to resolve a hostage incident in Moscow. This reported use sparked an interest in the pharmacology and toxicology of carfentanil in the human body, and data on its [...] Read more.

Carfentanil is an ultra-potent synthetic opioid. The Russian police force used both carfentanil and remifentanil to resolve a hostage incident in Moscow. This reported use sparked an interest in the pharmacology and toxicology of carfentanil in the human body, and data on its metabolites were later published. However, there have been few studies on the synthesis of carfentanil metabolites, and biological extraction has also put forward large uncertainty in subsequent studies. The aim of the present study is to investigate the synthesis of biphasic metabolites that are unique to carfentanil. The purpose was to produce corresponding metabolites conveniently, quickly, and at low cost that can be used for comparison with published structures and to confirm the administration of carfentanil. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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