MetabolitesPub Date : 2025-03-09DOI: 10.3390/metabo15030183
Young Eun Lee, Bruce A Kimball
{"title":"Examination of Intermolecular Forces Influencing Headspace Analysis of Biological Samples.","authors":"Young Eun Lee, Bruce A Kimball","doi":"10.3390/metabo15030183","DOIUrl":"10.3390/metabo15030183","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-07DOI: 10.3390/metabo15030181
Chengli Zheng, Xin Shi, Qinling Yang, Zhongkun Cai, Xiao Wang, Liuqing Yang, Xue Bai, Xiuxiang Meng, Diyan Li, Hang Jie
{"title":"Volatile Compounds in Musk and Their Anti-Stroke Mechanisms.","authors":"Chengli Zheng, Xin Shi, Qinling Yang, Zhongkun Cai, Xiao Wang, Liuqing Yang, Xue Bai, Xiuxiang Meng, Diyan Li, Hang Jie","doi":"10.3390/metabo15030181","DOIUrl":"10.3390/metabo15030181","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Musk is a widely used traditional Chinese medicine derived from musk deer that has the pharmacological effects of \"activating blood dredging collateral\" and \"consciousness-restoring resuscitation\". Its volatile compounds (VCs) play a key role in these effects, especially in the treatment of stroke. However, there have been no comprehensive studies on the differences in the VCs of these different musks. This study investigated the differences in the VCs of different musks and the potential targets and mechanisms of action for stroke. <b>Methods:</b> Different musks were studied via GC-MS, and the potential targets and mechanisms of VCs associated with stroke were investigated using network pharmacology. <b>Results:</b> A total of 99 VCs were detected in 79 musk samples. The most important VCs of different colours and forms were muscone, phenol, acetic acid, and isovaleric acid. Further study revealed that the change in organic acids and ketones was the cause of the significant difference between white musk and other types of musk. In addition, network pharmacological analyses identified 180 potential targets of the major volatile compounds of musk associated with stroke, and five key targets (<i>SRC</i>, <i>EGFR</i>, <i>ESR1</i>, <i>PTGS2</i>, and <i>DRD2</i>). Enrichment analysis showed that these key targets play an important role in neural related pathways. The molecular docking results confirmed that the key targets can effectively bind with the main VCs (muscone and phenol). <b>Conclusions:</b> These findings provide valuable insights into the distinct volatile compositions of various types of musk and underscore the significant potential of volatile compounds (VCs) in stroke treatment.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-06DOI: 10.3390/metabo15030179
Jia Li, Peng-Cheng Mei, Na An, Xiao-Xiao Fan, Yan-Qun Liu, Quan-Fei Zhu, Yu-Qi Feng
{"title":"Unraveling the Metabolic and Microbiome Signatures in Fecal Samples of Pregnant Women with Prenatal Depression.","authors":"Jia Li, Peng-Cheng Mei, Na An, Xiao-Xiao Fan, Yan-Qun Liu, Quan-Fei Zhu, Yu-Qi Feng","doi":"10.3390/metabo15030179","DOIUrl":"10.3390/metabo15030179","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Prenatal depression (PND) poses a significant threat to the health of both the mother and the developing fetus. Despite its increasing prevalence, the pathophysiology of PND is not yet fully elucidated. <b>Methods</b>: In this study, we aimed to investigate the fecal metabolites and gut microbiota in PND patients compared to healthy controls and to explore potential correlations between these factors. <b>Results</b>: Through untargeted metabolomics analysis, we identified 75 significantly altered metabolites in PND patients, of which 27 were structurally annotated and implicated key pathways, such as linoleic acid metabolism and phenylalanine, tyrosine, and tryptophan biosynthesis. Notably, two Clostridia-associated enterobacteria, <i>unclassified_c_Clostridia</i> and <i>unclassified_f_Lachnospiraceae</i>, which were enriched in the PND group, were significantly positively correlated with tyrosine and negatively correlated with multiple sulfated neurosteroids. <b>Conclusions</b>: Our findings underscore a robust association between gut microbiota dysbiosis and metabolic disturbances in PND, with specific alterations noted in tyrosine metabolism, sulfated neurosteroid homeostasis, and linoleic acid pathways. These dysregulated metabolites-tyrosine, sulfated neurosteroids, and linoleic acid-may serve as potential diagnostic biomarkers and therapeutic targets. Moreover, their interplay provides new insights into the pathophysiological mechanisms of PND, particularly highlighting the role of gut-brain axis signaling in neuroendocrine dysregulation and inflammatory responses. However, further large-scale studies and animal models are required to validate these findings and explore detailed mechanistic pathways.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Navigating Diabetes in Pregnancy: Critical Approaches to Mitigate Risks and Improve Outcomes for Mother and Child.","authors":"Zoe Paige Garvey, Abhishek Gupta, Nicole Taylor, Mahesh Thirunavukkarasu, Nilanjana Maulik","doi":"10.3390/metabo15030180","DOIUrl":"10.3390/metabo15030180","url":null,"abstract":"<p><p>With the increasing prevalence of diabetes and its growing impact on maternal and fetal health, management during pregnancy has become critical. This review describes the pathophysiology of insulin resistance during pregnancy, adverse outcomes correlated with diabetic pregnancies, and current management strategies. We investigate two leading approaches to managing pregnant patients with diabetes-lifestyle intervention and drug treatment. Lifestyle intervention, including dietary counseling, exercise regimens, patient education, and self-administered blood glucose monitoring, has demonstrated promising results in the management and prevention of gestational diabetes mellitus (GDM). Early intervention and treatment of at-risk patients have been critical for positive outcomes. Drug treatment, focusing on the utilization of insulin, insulin analogs, and antihyperglycemic agents has shown efficacy in achieving glycemic control and improving maternal and neonatal outcomes. These findings indicate that a combination of early lifestyle intervention and targeted drug treatment yields the most benefit in managing diabetes in pregnancy. To augment treatment, continuous glucose monitoring and telemedicine have become valuable tools in managing diabetes during pregnancy. Future research should aim to develop more effective antihyperglycemic agents, improve telehealth accessibility, and enhance preconception care for women at risk of developing GDM. By addressing these areas, we can significantly reduce the adverse outcomes associated with diabetes in pregnancy and improve overall maternal and fetal health.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-05DOI: 10.3390/metabo15030177
Malaika Persaud, Ainsely Lewis, Anna Kisiala, Ewart Smith, Zeynab Azimychetabi, Tamanna Sultana, Suresh S Narine, R J Neil Emery
{"title":"Untargeted Metabolomics and Targeted Phytohormone Profiling of Sweet Aloes (<i>Euphorbia neriifolia</i>) from Guyana: An Assessment of Asthma Therapy Potential in Leaf Extracts and Latex.","authors":"Malaika Persaud, Ainsely Lewis, Anna Kisiala, Ewart Smith, Zeynab Azimychetabi, Tamanna Sultana, Suresh S Narine, R J Neil Emery","doi":"10.3390/metabo15030177","DOIUrl":"10.3390/metabo15030177","url":null,"abstract":"<p><p><b>Background/Objectives:</b><i>Euphorbia neriifolia</i> is a succulent plant from the therapeutically rich family of Euphorbia comprising 2000 species globally. <i>E. neriifolia</i> is used in Indigenous Guyanese asthma therapy. <b>Methods:</b> To investigate <i>E. neriifolia's</i> therapeutic potential, traditionally heated leaf, simple leaf, and latex extracts were evaluated for phytohormones and therapeutic compounds. Full scan, data-dependent acquisition, and parallel reaction monitoring modes via liquid chromatography Orbitrap mass spectrometry were used for screening. <b>Results:</b> Pathway analysis of putative features from all extracts revealed a bias towards the phenylpropanoid, terpenoid, and flavonoid biosynthetic pathways. A total of 850 compounds were annotated using various bioinformatics tools, ranging from confidence levels 1 to 3. Lipids and lipid-like molecules (34.35%), benzenoids (10.24%), organic acids and derivatives (12%), organoheterocyclic compounds (12%), and phenylpropanoids and polyketides (10.35%) dominated the contribution of compounds among the 13 superclasses. Semi-targeted screening revealed 14 out of 16 literature-relevant therapeutic metabolites detected, with greater upregulation in traditional heated extracts. Targeted screening of 39 phytohormones resulted in 25 being detected and quantified. Simple leaf extract displayed 4.4 and 45 times greater phytohormone levels than traditional heated leaf and latex extracts, respectively. Simple leaf extracts had the greatest nucleotide and riboside cytokinin and acidic phytohormone levels. In contrast, traditional heated extracts exhibited the highest free base and glucoside cytokinin levels and uniquely contained methylthiolated and aromatic cytokinins while lacking acidic phytohormones. Latex samples had trace gibberellic acid levels, the lowest free base, riboside, and nucleotide levels, with absences of aromatic, glucoside, or methylthiolated cytokinin forms. <b>Conclusions:</b> In addition to metabolites with possible therapeutic value for asthma treatment, we present the first look at cytokinin phytohormones in the species and <i>Euphorbia</i> genus alongside metabolite screening to present a comprehensive assessment of heated leaf extract used in Indigenous Guyanese asthma therapy.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-05DOI: 10.3390/metabo15030176
Jacopo Sapienza, Giulia Agostoni, Federica Repaci, Marco Spangaro, Stefano Comai, Marta Bosia
{"title":"Metabolic Syndrome and Schizophrenia: Adding a Piece to the Interplay Between the Kynurenine Pathway and Inflammation.","authors":"Jacopo Sapienza, Giulia Agostoni, Federica Repaci, Marco Spangaro, Stefano Comai, Marta Bosia","doi":"10.3390/metabo15030176","DOIUrl":"10.3390/metabo15030176","url":null,"abstract":"<p><p>The biology of schizophrenia is highly complex and multifaceted. Numerous efforts have been made over the years to disentangle the heterogeneity of the disease, gradually leading to a more detailed understanding of its underlying pathogenic mechanisms. Two cardinal elements in the pathophysiology of schizophrenia are neuroinflammation and alterations of neurotransmission. The kynurenine (KYN) pathway (KP) is of particular importance because it is inducted by systemic low-grade inflammation in peripheral tissues, producing metabolites that are neuroactive (i.e., modulating glutamatergic and cholinergic neurotransmission), neuroprotective, or neurotoxic. Consequently, the KP is at the crossroads between two primary systems involved in the pathogenesis of schizophrenia. It bridges the central nervous system (CNS) and the periphery, as KP metabolites can cross the blood-brain barrier and modulate neuronal activity. Metabolic syndrome plays a crucial role in this context, as it frequently co-occurs with schizophrenia, contributing to a sub-inflammatory state able to activate the KP. This narrative review provides valuable insights into these complex interactions, offering a framework for developing targeted therapeutic interventions or precision psychiatry approaches of the disorder.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11944102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-05DOI: 10.3390/metabo15030178
Sofia Avnet, Emi Mizushima, Beatrice Severino, Maria Veronica Lipreri, Antonia Scognamiglio, Angela Corvino, Nicola Baldini, Margherita Cortini
{"title":"Antagonizing the S1P-S1P3 Axis as a Promising Anti-Angiogenic Strategy.","authors":"Sofia Avnet, Emi Mizushima, Beatrice Severino, Maria Veronica Lipreri, Antonia Scognamiglio, Angela Corvino, Nicola Baldini, Margherita Cortini","doi":"10.3390/metabo15030178","DOIUrl":"10.3390/metabo15030178","url":null,"abstract":"<p><strong>Background: </strong>Angiogenesis, the process of new blood vessel formation, is critically regulated by a balance of pro- and anti-angiogenic factors. This process plays a central role in tumor progression and is modulated by tumor cells. Sphingosine-1-phosphate (S1P), a bioactive lipid signaling molecule acting via G-protein-coupled receptors (S1PR1-5), has emerged as a key mediator of vascular development and pathological angiogenesis in cancer. Consequently, targeting the S1P-S1PRs axis represents a promising strategy for antiangiogenic therapies. This study explores S1PR3 as a potential therapeutic target in osteosarcoma, the most common primary bone malignancy, which we have previously demonstrated to secrete S1P within the acidic tumor microenvironment.</p><p><strong>Methods: </strong>The effects of KRX-725-II and its derivatives, Tic-4-KRX-725-II and [D-Tic]4-KRX-725-II-pepducins acting as S1PR3 antagonists as allosteric modulators of GPCR activity-were tested on metastatic osteosarcoma cells (143B) for proliferation and migration inhibition. Anti-angiogenic activity was assessed using endothelial cells (HUVEC) through proliferation and tubulogenesis assays in 2D, alongside sprouting and migration analyses in a 3D passively perfused microfluidic chip.</p><p><strong>Results: </strong>S1PR3 inhibition did not alter osteosarcoma cell growth or migration. However, it impaired endothelial cell tubulogenesis up to 75% and sprouting up to 30% in respect to controls. Conventional 2D assays revealed reduced tubule nodes and length, while 3D microfluidic models demonstrated diminished sprouting area and maximum migration distance, indicating S1PR3's role in driving endothelial cell differentiation.</p><p><strong>Conclusions: </strong>These findings highlight S1PR3 as a critical regulator of angiogenesis and posit its targeting as a novel anti-angiogenic strategy, particularly for aggressive, S1P-secreting tumors with pronounced metastatic potential and an acidic microenvironment.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11944055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-04DOI: 10.3390/metabo15030175
Liang Chen, Jiaxin Li, Chengwei Fang, Jiepeng Wang
{"title":"Metabolomics-Based Study on the Anticonvulsant Mechanism of <i>Acorus tatarinowii</i>: GABA Transaminase Inhibition Alleviates PTZ-Induced Epilepsy in Rats.","authors":"Liang Chen, Jiaxin Li, Chengwei Fang, Jiepeng Wang","doi":"10.3390/metabo15030175","DOIUrl":"10.3390/metabo15030175","url":null,"abstract":"<p><strong>Background/objectives: </strong>Epilepsy is a common chronic and recurrent neurological disorder that poses a threat to human health, and <i>Acorus tatarinowii</i> Schott (ATS), a traditional Chinese medicine, is used to treat it. This study aimed to determine its effects on plasma metabolites. Moreover, the possible mechanism of its intervention in epilepsy was preliminarily explored, combined with network pharmacology.</p><p><strong>Methods: </strong>An epileptic model of rats was established using pentylenetetrazol. The potential targets and pathways of ATS were predicted by network pharmacology. Ultra Performance Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometrynce Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometryance Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometry and statistical analyses were used to profile plasma metabolites and identify ATS's effects on epilepsy.</p><p><strong>Results: </strong>Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that ATS was involved in regulating multiple signaling pathways, mainly including the neuroactive ligand-receptor interaction and GABAerGamma-aminobutyrate transaminaseAminobutyrate Transaminaseapse signaling pathway. ATS treatment restored 19 metabolites in epiGamma-aminobutyrate transaminaseminobutyrate Transaminase rats, affecting lysine, histidine, and purine metabolism. GABA-T was found as a new key target for treating epilepsy with ATS. The IC<sub>50</sub> of ATS for inhibiting GABA-T activity was 57.9 μg/mL. Through metabolomic analysis, we detected changes in the levels of certain metabolites related to the GABAergic system. These metabolite changes can be correlated with the targets and pathways predicted by network pharmacology. One of the limitations of this study is that the correlation analysis between altered metabolites and seizure severity remains unfinished, which restricts a more in-depth exploration of the underlying biological mechanisms. In the future, our research will focus on conducting a more in-depth exploration of the correlation analysis between altered metabolites and seizure severity.</p><p><strong>Conclusions: </strong>These results improved our understanding of epilepsy and ATS treatment, potentially leading to better therapies. The identification of key metabolites and their associated pathways in this study offers potential novel therapeutic targets for epilepsy. By modulating these metabolites, future therapies could be designed to better manage the disorder. Moreover, the insights from network pharmacology can guide the development of more effective antiepileptic drugs, paving the way for improved clinical outcomes for patients.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11944195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MetabolitesPub Date : 2025-03-03DOI: 10.3390/metabo15030174
Hunter Dlugas, Seongho Kim
{"title":"A Comparative Study of Network-Based Machine Learning Approaches for Binary Classification in Metabolomics.","authors":"Hunter Dlugas, Seongho Kim","doi":"10.3390/metabo15030174","DOIUrl":"10.3390/metabo15030174","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Metabolomics has recently emerged as a key tool in the biological sciences, offering insights into metabolic pathways and processes. Over the last decade, network-based machine learning approaches have gained significant popularity and application across various fields. While several studies have utilized metabolomics profiles for sample classification, many network-based machine learning approaches remain unexplored for metabolomic-based classification tasks. This study aims to compare the performance of various network-based machine learning approaches, including recently developed methods, in metabolomics-based classification. <b>Methods</b>: A standard data preprocessing procedure was applied to 17 metabolomic datasets, and Bayesian neural network (BNN), convolutional neural network (CNN), feedforward neural network (FNN), Kolmogorov-Arnold network (KAN), and spiking neural network (SNN) were evaluated on each dataset. The datasets varied widely in size, mass spectrometry method, and response variable. <b>Results</b>: With respect to AUC on test data, BNN, CNN, FNN, KAN, and SNN were the top-performing models in 4, 1, 5, 3, and 4 of the 17 datasets, respectively. Regarding F1-score, the top-performing models were BNN (3 datasets), CNN (3 datasets), FNN (4 datasets), KAN (4 datasets), and SNN (3 datasets). For accuracy, BNN, CNN, FNN, KAN, and SNN performed best in 4, 1, 4, 4, and 4 datasets, respectively. <b>Conclusions</b>: No network-based modeling approach consistently outperformed others across the metrics of AUC, F1-score, or accuracy. Our results indicate that while no single network-based modeling approach is superior for metabolomics-based classification tasks, BNN, KAN, and SNN may be underappreciated and underutilized relative to the more commonly used CNN and FNN.</p>","PeriodicalId":18496,"journal":{"name":"Metabolites","volume":"15 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11944042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}