Advances in Analysis Methods for Metabolomics and Lipidomics

Topic Information

Dear Colleagues,

The increasing need for novel analytical approaches with higher selectivity, speed, and coverage is of the utmost importance in the fields of metabolomics and lipidomics. In terms of prognostics and diagnostics, the ability to quantify and identify different metabolites and lipids in biospecimes, such as biofluids, tissues and lysates, is crucial, while, the use of high-throughput techniques in clinical settings is also highly desirable. This Topic will be focused on the development, validation, and application of original methodologies based on hyphenated methods, such as UHPLC-MS, GC-MS, and CE-MS, aimed at the qualitative–quantitative analysis of metabolites and lipids in complex matrices such as cells, plasma, serum, urine, and tissue homogenates. Particular attention will be given to method optimization and validation as well as the identification and quantitation of the profiled metabolites and lipids.

Dr. Eduardo Sommella
Dr. Giulia Mazzoccanti
Dr. Emanuela Salviati
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Analytica analytica	3.6	3.7	2020	19 Days	CHF 1200	Submit
Chemosensors chemosensors	3.7	7.3	2013	19.1 Days	CHF 2000	Submit
International Journal of Molecular Sciences ijms	4.9	9.0	2000	17.8 Days	CHF 2900	Submit
Metabolites metabolites	3.7	6.9	2011	16.7 Days	CHF 2700	Submit
Molecules molecules	4.6	8.6	1996	15.1 Days	CHF 2700	Submit
Separations separations	2.7	4.5	2014	16 Days	CHF 2600	Submit
Spectroscopy Journal spectroscj	-	-	2023	23.4 Days	CHF 1000	Submit

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Published Papers (3 papers)

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All Analytica IJMS Metabolites Molecules Separations Spectroscopy Journal Chemosensors

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Supplementary material:
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20 pages, 5619 KB  

Open AccessArticle

Turnover Rate of Lipids, Metabolites and Proteins Revealed by 156-Day-Long D₂O Administration in a Guinea Pig

by Yury Kostyukevich, Anastasia Malyukova, Nikita Malyshev, Anna Vishnevskaya, Anna Levashova, Anna Kovalenko, Albert Kireev, Azat Meshcherov, Liudmila Borisova, Boris Tupertsev, Anton Bashilov and Sergey Osipenko

Int. J. Mol. Sci. 2026, 27(4), 1944; https://doi.org/10.3390/ijms27041944 - 18 Feb 2026

Viewed by 1775

Abstract

Measurement of the turnover rate of proteins, different metabolites and lipids in living organisms is important for the understanding of biochemical pathways and physiology studies. Such experiments can be performed by administering isotopically labeled substances (food or water) to the organism and measuring [...] Read more.

Measurement of the turnover rate of proteins, different metabolites and lipids in living organisms is important for the understanding of biochemical pathways and physiology studies. Such experiments can be performed by administering isotopically labeled substances (food or water) to the organism and measuring the amount of the isotopes in the endogenous compounds. Here, we administered 20% heavy water (D₂O) to a guinea pig for 156 days and regularly measured the deuterium uptake in C-H groups in the different compounds of blood, urine and feces using high-resolution mass spectrometry. We successfully measured the time required for reaching the maximum deuteration level for several classes of compounds: 10 days for blood lipids (PC, PE, TAG); 60 days for sterol derivatives, heme B and hemoglobin; and 70 days for stercobilin. Also, for those compounds, we measured the deuterium elimination time from the organism when deuterium administration was stopped. The turnover of lipids was also studied by administering deuterated oat leaves grown at 10% D₂O to the guinea pig. The analysis of blood revealed that triglycerides demonstrate the inclusion of the deuterium after 5 h. All experiments were performed on a single guinea pig that remained alive and in good health after all experiments. The current research demonstrates the possibility of using long-term D₂O administration for the investigation of metabolism. Full article

(This article belongs to the Topic Advances in Analysis Methods for Metabolomics and Lipidomics)

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25 pages, 1193 KB  

Open AccessReview

Gas Chromatography–Mass Spectrometry (GC-MS) in the Plant Metabolomics Toolbox: GC-MS in Multi-Platform Metabolomics and Integrated Multi-Omics Research

by Nadezhda Frolova, Tatiana Bilova, Svetlana Silinskaia, Anastasia Orlova, Anastasia Gurina and Andrej Frolov

Int. J. Mol. Sci. 2026, 27(3), 1343; https://doi.org/10.3390/ijms27031343 - 29 Jan 2026

Viewed by 1373

Abstract

Innovative developments of GC-MS over the last two decades made this methodology a powerful tool for profiling a broad range of volatile metabolites and non-volatile ones of non-polar, semi-polar and even polar nature after appropriate derivatization. Indeed, the high potential of GC-MS in [...] Read more.

Innovative developments of GC-MS over the last two decades made this methodology a powerful tool for profiling a broad range of volatile metabolites and non-volatile ones of non-polar, semi-polar and even polar nature after appropriate derivatization. Indeed, the high potential of GC-MS in the analysis of low molecular weight metabolites involved in essential cellular functions (energy production, metabolic adjustment, signaling) made it the method of choice for the life and plant scientists. However, despite these advances, due to their intrinsic thermal lability, multiple classes of hydrophilic low-molecule weight metabolites (like nucleotides, sugar phosphates, cofactors, CoA esters) are unsuitable under the high-temperature conditions of the split–splitless (SSL) injection and GC separation, which makes the analysis of such compounds by GC-MS challenging. Therefore, to ensure comprehensive coverage of the plant metabolome, the GC-MS-based metabolomics platform needs to be efficiently combined with other metabolomics techniques and instrumental strategies. Moreover, to get a deeper insight into dynamics of plant cell metabolism in response to endogenic and exogenic clues, integration of the metabolomics data with the output obtained from other post-genomics techniques is desired. Therefore, here, we overview different strategies for the integration of the GC-MS-based metabolite profiling output with the data, acquired by other metabolomics techniques in terms of the multi-platform metabolomics approach. Further, we comprehensively discuss the implementation of the GC-MS-based metabolomics in multi-omics strategies and the data integration strategies behind this. This approach is the promising strategy, as it gives deep and multi-level insight into physiological processes in plants in the systems biology context, with consideration of all levels of gene expression. However, multiple challenges may arise in the way of integrating data from different omics technologies, which are comprehensively discussed in this review. Full article

(This article belongs to the Topic Advances in Analysis Methods for Metabolomics and Lipidomics)

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14 pages, 960 KB  

Open AccessReview

A Comprehensive Review on Medium- and Long-Chain Fatty Acid-Derived Metabolites: From Energy Sources to Metabolic Signals

by Jin-Byung Park, Sungyun Cho and Sung-Joon Lee

Metabolites 2026, 16(1), 45; https://doi.org/10.3390/metabo16010045 - 4 Jan 2026

Cited by 3 | Viewed by 1398

Abstract

Medium- and long-chain fatty acids (MLFAs) are increasingly recognized not only as metabolic substrates but also as precursors of diverse bioactive metabolites generated through host and microbial transformations. Recent advances in analytical chemistry and microbiome research have revealed that gut microorganisms catalyze extensive [...] Read more.

Medium- and long-chain fatty acids (MLFAs) are increasingly recognized not only as metabolic substrates but also as precursors of diverse bioactive metabolites generated through host and microbial transformations. Recent advances in analytical chemistry and microbiome research have revealed that gut microorganisms catalyze extensive modifications of dietary MLFAs—producing hydroxylated, conjugated, and keto-fatty acids with enhanced potency toward host receptors. These metabolites exhibit dual activity on classical metabolic receptors, including FFAR1/4 and PPARα/γ, as well as ectopically expressed chemosensory receptors such as olfactory receptors (ORs) and bitter taste receptors (TAS2Rs). This expanded receptor landscape establishes a previously unrecognized chemosensory–metabolic axis that integrates dietary signals, microbial metabolism, and host physiology. Microbial MLFA derivatives such as 10-hydroxyoctadecenoic acid and conjugated linoleic acid regulate incretin secretion, adipogenesis, macrophage polarization, and intestinal barrier function through coordinated activation of FFARs and PPARs. Concurrently, dicarboxylic acids such as azelaic acid activate Olfr544 to modulate lipolysis, ketogenesis, GLP-1 release, and feeding behavior. TAS2Rs also sense oxidized lipids, linking lipid metabolism to immune regulation and enteroendocrine signaling. Collectively, these pathways highlight the microbiome as a metabolic transducer that converts dietary lipids into signaling molecules influencing endocrine, immune, and gut–brain circuits. Understanding the mechanisms governing MLFA bioconversion and receptor engagement provides new opportunities for therapeutic and nutritional intervention. Targeting ORs and TAS2Rs, engineering probiotics to enhance beneficial FA-derived metabolites, and developing receptor-selective synthetic analogs represent promising strategies. Future progress will require integrative approaches combining physiology, biochemistry, metabolomics, and microbial genomics to elucidate receptor specificity and host variability. Full article

(This article belongs to the Topic Advances in Analysis Methods for Metabolomics and Lipidomics)

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