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Correction: Metabolic response of Klebsiella oxytoca to ciprofloxacin exposure: a metabolomics approach. 更正:催产克雷伯菌对环丙沙星暴露的代谢反应:代谢组学方法。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-03-06 DOI: 10.1007/s11306-025-02234-2
Shwan Ahmed, Sahand Shams, Dakshat Trivedi, Cassio Lima, Rachel McGalliard, Christopher M Parry, Enitan D Carrol, Howbeer Muhamadali, Royston Goodacre
{"title":"Correction: Metabolic response of Klebsiella oxytoca to ciprofloxacin exposure: a metabolomics approach.","authors":"Shwan Ahmed, Sahand Shams, Dakshat Trivedi, Cassio Lima, Rachel McGalliard, Christopher M Parry, Enitan D Carrol, Howbeer Muhamadali, Royston Goodacre","doi":"10.1007/s11306-025-02234-2","DOIUrl":"10.1007/s11306-025-02234-2","url":null,"abstract":"","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"38"},"PeriodicalIF":3.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolomic analysis to study the effect of foliar copper supplementation on sulfur-containing compounds of garlic bulb by LC-MS. 利用LC-MS代谢组学分析研究叶片补铜对大蒜鳞茎含硫化合物的影响。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-03-05 DOI: 10.1007/s11306-025-02237-z
Natália Reis de Almeida, Brena Rodrigues Mota Ikehara, Camila Cristina Calácio, Thaísa Fernanda Oliveira, Frederico Garcia Pinto
{"title":"Metabolomic analysis to study the effect of foliar copper supplementation on sulfur-containing compounds of garlic bulb by LC-MS.","authors":"Natália Reis de Almeida, Brena Rodrigues Mota Ikehara, Camila Cristina Calácio, Thaísa Fernanda Oliveira, Frederico Garcia Pinto","doi":"10.1007/s11306-025-02237-z","DOIUrl":"10.1007/s11306-025-02237-z","url":null,"abstract":"<p><strong>Introduction: </strong>Garlic (Allium sativum L.) is renowned for its health-promoting properties, largely due to its sulfur-rich compounds. While copper is essential for plant growth and metabolism, excessive levels can disrupt cellular processes and lead to oxidative stress.</p><p><strong>Objectives: </strong>This study aims to investigate the impact of copper supplementation on the metabolic profile of garlic, with a particular focus on changes in sulfur metabolism.</p><p><strong>Methods: </strong>Ito garlic cloves were harvested in 2020 on Red-Yellow Latosol soil. Copper chelate fertilizer was applied foliarly at 300 mL/ha, 30, 20, and 10 days before harvest. After harvesting, cloves were refrigerated and analyzed. Using LC-MS metabolomics, the metabolic profile of garlic was analyzed after copper supplementation to assess changes, specifically in sulfur-containing compounds.</p><p><strong>Results: </strong>Copper supplementation led to a significant reduction in key sulfur-containing metabolites critical for the health-promoting properties of garlic, including allicin (FC = 0.0947), alliin (FC = 0.0147), and γ-glutamyl-S-allylcysteine (FC = 0.0076). Enrichment analysis identified alterations in pathways related to glutamine, glutamate, alanine, and aspartate metabolism. Additionally, precursors of glutathione (GSH) were depleted, likely as a result of GSH sparing efforts to counteract copper-induced oxidative stress. This redirection may increase susceptibility to ferroptosis, a form of cell death linked to oxidative damage.</p><p><strong>Conclusion: </strong>The metabolomic analysis of copper-supplemented Ito garlic cloves showed a significant reduction in sulfur compounds allicin, alliin, and γ-glutamyl-S-allylcysteine, important for organoleptic and medicinal properties. This decrease indicates a metabolic shift towards antioxidant defenses, with glutathione being redirected to defense pathways rather than secondary metabolites. Future studies should explore oxidative stress and ferroptosis markers, and lipidomics for a deeper understanding of garlic response to copper exposure.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"36"},"PeriodicalIF":3.5,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of gangliosides and ceramides as biomarkers for mucopolysaccharidosis type II (hunter syndrome) through untargeted lipidomic analysis. 通过非靶向脂质组学分析鉴定神经节苷和神经酰胺作为II型粘多糖病(猎人综合征)的生物标志物。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-03-01 DOI: 10.1007/s11306-025-02233-3
Asma Farjallah, Bruno Maranda, Roberto Giugliani, Christiane Auray-Blais
{"title":"Identification of gangliosides and ceramides as biomarkers for mucopolysaccharidosis type II (hunter syndrome) through untargeted lipidomic analysis.","authors":"Asma Farjallah, Bruno Maranda, Roberto Giugliani, Christiane Auray-Blais","doi":"10.1007/s11306-025-02233-3","DOIUrl":"10.1007/s11306-025-02233-3","url":null,"abstract":"<p><strong>Introduction: </strong>Mucopolysaccharidosis type II (Hunter syndrome) is an X-linked recessive disorder caused by iduronate-2-sulfatase deficiency, affecting mainly male patients. The lack of its enzyme activity causes the accumulation of the glycosaminoglycans heparan sulfate and dermatan sulfate in all body tissues and leads to a secondary accumulation of gangliosides and ceramides.</p><p><strong>Objective and methods: </strong>We conducted a lipidomic study to investigate the dysregulation of lipid pathways in neuronopathic MPS type II. A modified liquid extraction was performed for untargeted lipid analysis. A reverse phase ultraperformance liquid chromatography coupled to quadrupole time-of-flight (UPLC-QTOF) mass spectrometry allowed the identification of upregulated ganglioside and ceramide biomarkers in the plasma and urine of a MPS II patient group compared to a healthy control group.</p><p><strong>Results: </strong>The altered pathways, including those related to glycerophospholipid metabolism and fatty acid oxidation, highlight the essential role of lipid metabolism in the progression of the disease.</p><p><strong>Conclusion: </strong>The accumulation of gangliosides and ceramides could be associated with the neuropathology in various lysosomal storage diseases including MPS II.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"35"},"PeriodicalIF":3.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolomic profiling of plasma from glioma and meningioma patients based on two complementary mass spectrometry techniques. 基于两种互补质谱技术的脑胶质瘤和脑膜瘤患者血浆代谢组学分析。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-22 DOI: 10.1007/s11306-025-02231-5
Adrian Godlewski, Patrycja Mojsak, Tomasz Pienkowski, Tomasz Lyson, Zenon Mariak, Joanna Reszec, Karol Kaminski, Marcin Moniuszko, Adam Kretowski, Michal Ciborowski
{"title":"Metabolomic profiling of plasma from glioma and meningioma patients based on two complementary mass spectrometry techniques.","authors":"Adrian Godlewski, Patrycja Mojsak, Tomasz Pienkowski, Tomasz Lyson, Zenon Mariak, Joanna Reszec, Karol Kaminski, Marcin Moniuszko, Adam Kretowski, Michal Ciborowski","doi":"10.1007/s11306-025-02231-5","DOIUrl":"10.1007/s11306-025-02231-5","url":null,"abstract":"<p><strong>Introduction: </strong>Extracranial and intracranial tumors are a diverse group of malignant and benign neoplasms, influenced by multiple factors. Given the complex nature of these tumors and usually late or accidental diagnosis, minimally invasive, rapid, early, and accurate diagnostic methods are urgently required. Metabolomics offers promising insights into central nervous system tumors by uncovering distinctive metabolic changes linked to tumor development.</p><p><strong>Objectives: </strong>This study aimed to elucidate the role of altered metabolites and the associated biological pathways implicated in the development of gliomas and meningiomas.</p><p><strong>Methods: </strong>The study was conducted on 95 patients with gliomas, 68 patients with meningiomas, and 71 subjects as a control group. The metabolic profiling of gliomas and meningiomas achieved by integrating untargeted metabolomic analysis based on GC-MS and targeted analysis performed using LC-MS/MS represents the first comprehensive study. Three comparisons (gliomas or meningiomas vs. controls as well as gliomas vs. meningiomas) were performed to reveal statistically significant metabolites.</p><p><strong>Results: </strong>Comparative analysis revealed 97, 56, and 27 significant metabolites for gliomas vs. controls, meningiomas vs. controls and gliomas vs. meningiomas comparison, respectively. Moreover, among above mentioned comparisons unique metabolites involved in arginine biosynthesis and metabolism, the Krebs cycle, and lysine degradation pathways were found. Notably, 2-aminoadipic acid has been identified as a metabolite that can be used in distinguishing two tumor types.</p><p><strong>Conclusions: </strong>Our results provide a deeper understanding of the metabolic changes associated with brain tumor development and progression.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"33"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolic and proteomic analysis of a medicinal morel (Morchella elata) from Western Himalayas, Kashmir. 喀什米尔喜马拉雅山脉西部药用羊肚菌的代谢和蛋白质组学分析。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-22 DOI: 10.1007/s11306-025-02222-6
Tariq Saiff Ullah, Syeda Sadiqa Firdous, Hamayun Shaheen, Muhamamd Manzoor, Syed Waseem Gillani, Wayne Thomas Shier, Baber Ali, Tabarak Malik, Sezai Ercisli, Reem M Aljowaie, Mohamed S Elshikh
{"title":"Metabolic and proteomic analysis of a medicinal morel (Morchella elata) from Western Himalayas, Kashmir.","authors":"Tariq Saiff Ullah, Syeda Sadiqa Firdous, Hamayun Shaheen, Muhamamd Manzoor, Syed Waseem Gillani, Wayne Thomas Shier, Baber Ali, Tabarak Malik, Sezai Ercisli, Reem M Aljowaie, Mohamed S Elshikh","doi":"10.1007/s11306-025-02222-6","DOIUrl":"10.1007/s11306-025-02222-6","url":null,"abstract":"<p><p>Morels are edible fungi growing naturally in the wild and cultivated for food and medicines worldwide. They have been collected and consumed by people since ancient times. In the present study, fruiting bodies of Morchella elata were collected from the field during the years 2020-22 through consecutive field visits. Identification was carried out through a morpho-anatomical and phylogenetic study that confirmed the collected morel species as Morchella elata. The metabolic analysis was conducted using Ultra High-Performance Liquid Chromatography/Mass Spectrometry (UHPLC/MS) and FTICR/orbitrap techniques. The study revealed the presence of 159 organic compounds and 435 peptide sequences in the ascocarp. Different bioactive and significant compounds have been identified in the fruiting bodies of M. elata. This mushroom is highly nutritious, and the presence of these bioactive compounds contributes to its health benefits, making it a potential functional food in nutraceuticals. From the current study, it is concluded that M. elata is an edible, highly nutritive fungus and contains many bioactive contents. It could be used in the screening of bioactive substances useful in the preparation of anticancer drugs.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"34"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of metabolite-disease associations based on knowledge graph. 基于知识图谱的代谢物-疾病关联识别。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-22 DOI: 10.1007/s11306-025-02227-1
Fuheng Xiao, Canling Huang, Ali Chen, Wei Xiao, Zhanchao Li
{"title":"Identification of metabolite-disease associations based on knowledge graph.","authors":"Fuheng Xiao, Canling Huang, Ali Chen, Wei Xiao, Zhanchao Li","doi":"10.1007/s11306-025-02227-1","DOIUrl":"10.1007/s11306-025-02227-1","url":null,"abstract":"<p><strong>Background: </strong>Despite the insights that metabolite analysis can provide into the onset, development, and progression of diseases-thus offering new concepts and methodologies for prevention, diagnosis, and treatment-traditional wet lab experiments are often time-consuming and labor-intensive. Consequently, this study aimed to develop a machine learning model named COM-RAN, which is based on a knowledge graph and random forest algorithm, to identify potential associations between metabolites and diseases.</p><p><strong>Methods: </strong>Firstly, we integrated the known associations between diseases and metabolites. Secondly, we provided a synthesis of the extant data regarding diseases and metabolites, accompanied by supplementary information pertinent to these entities. Thirdly, knowledge graph-based embedded features were used to characterize disease-metabolite associations. Finally, a random forest algorithm was employed to construct a model for identifying potential disease-metabolite associations.</p><p><strong>Results: </strong>The experimental results demonstrated that the proposed model achieved an Area Under the Receiver Operating Characteristic Curve (AUC) of 0.968 in 5-fold cross-validations, while the Area Under the Precision-Recall Curve (AUPR) was 0.901, outperforming the vast majority of existing prediction methods. The case studies corroborated the majority of the novel associations identified by COM-RAN, thereby further demonstrating the reliability of the current method in predicting the potential relationship between metabolites and diseases.</p><p><strong>Conclusion: </strong>The COM-RAN model demonstrated promise in predicting associations between diseases and metabolites, suggesting that integrating knowledge graphs with machine learning methodologies can significantly improve the accuracy and reliability of predictions related to disease-associated metabolites.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"32"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evaluation of solutions for stabilizing feces in metabolomics studies using GC × GC-TOFMS. 用GC × GC- tofms评价代谢组学研究中稳定粪便的溶液。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-21 DOI: 10.1007/s11306-025-02232-4
Seo Lin Nam, Kieran S Tarazona Carrillo, A Paulina de la Mata, Ryland T Giebelhaus, Olle M de Bruin, Evgueni Doukhanine, James J Harynuk
{"title":"Evaluation of solutions for stabilizing feces in metabolomics studies using GC × GC-TOFMS.","authors":"Seo Lin Nam, Kieran S Tarazona Carrillo, A Paulina de la Mata, Ryland T Giebelhaus, Olle M de Bruin, Evgueni Doukhanine, James J Harynuk","doi":"10.1007/s11306-025-02232-4","DOIUrl":"10.1007/s11306-025-02232-4","url":null,"abstract":"<p><strong>Introduction: </strong>Fecal metabolomics studies have garnered interest in recent years due to the potential for these samples to provide unique information about an individual. Stool is a dynamic mixture of human excrement, microbiota, and enzymes that yields a constantly changing metabolite profile. The main challenge in a fecal metabolomics study is ensuring that the metabolite profile changes as little as possible between sample collection and sample processing/analysis.</p><p><strong>Objectives: </strong>This study aimed to evaluate the efficacy of five solutions in preserving human fecal metabolites over a seven-day storage period at ambient temperature, enabling at-home collection, cost-effective ambient transport and sample storage.</p><p><strong>Method: </strong>Five solutions with varying chemical compositions were evaluated for their ability to stabilize fecal metabolites. Samples were stored at ambient temperature for seven days, and metabolites were analyzed using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS). The stabilizing efficacy of the solutions was assessed using total useful peak area (TUPA), absolute relative change (ARC) and compound class-based analyses, comparing the initial, stabilized, and unstabilized samples.</p><p><strong>Results: </strong>Different solutions demonstrated varied efficiencies for different compound classes. Overall, the results indicated that the use of stabilization solutions significantly minimized changes in the fecal metabolite profile compared to unstabilized samples left at room temperature for one week.</p><p><strong>Conclusion: </strong>This study demonstrates that stabilization solutions are effective in preserving fecal metabolites during storage at ambient temperature, supporting the feasibility of at-home sample collection.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"31"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Harnessing NMR technology for enhancing field crop improvement: applications, challenges, and future perspectives. 利用核磁共振技术促进大田作物改良:应用、挑战和未来展望。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-20 DOI: 10.1007/s11306-025-02229-z
Vedant Gautam, Vibhootee Garg, Nitesh Meena, Sunidhi Kumari, Shubham Patel, Mukesh, Himanshu Singh, Shreyashi Singh, R K Singh
{"title":"Harnessing NMR technology for enhancing field crop improvement: applications, challenges, and future perspectives.","authors":"Vedant Gautam, Vibhootee Garg, Nitesh Meena, Sunidhi Kumari, Shubham Patel, Mukesh, Himanshu Singh, Shreyashi Singh, R K Singh","doi":"10.1007/s11306-025-02229-z","DOIUrl":"10.1007/s11306-025-02229-z","url":null,"abstract":"<p><strong>Introduction: </strong>Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as a transformative technology in agricultural research, offering powerful analytical capabilities for field crop improvement. With global challenges such as food security and climate change intensifying, there is an urgent need for innovative methodologies to enhance our understanding of plant health, metabolic pathways, and crop-environment interactions. NMR's ability to provide nondestructive, real-time analysis of plant metabolites and soil chemistry positions it as a critical tool for addressing these pressing concerns.</p><p><strong>Objective: </strong>This review aims to elucidate the potential of NMR spectroscopy in advancing field crop improvement by highlighting its applications, challenges, and future perspectives in agricultural methodologies. The focus is on the evolution and application of NMR in agricultural research, particularly in metabolomics, phenotyping, and quality assessment.</p><p><strong>Method: </strong>A comprehensive literature review was conducted to analyze recent advancements in NMR applications in agriculture. Particular emphasis was given to high-resolution magic angle spinning (HR-MAS) and time-domain NMR techniques, which have been instrumental in elucidating plant metabolites and soil chemistry. Studies showcasing the integration of NMR with complementary technologies for enhanced metabolic profiling and genetic marker identification were reviewed.</p><p><strong>Results: </strong>Findings indicate that NMR spectroscopy is an indispensable tool in agriculture due to its ability to identify biomarkers indicative of crop resilience, monitor soil composition, and contribute to food safety and quality assessments. The integration of NMR with other technologies has accelerated metabolic profiling, aiding in the breeding of high-yielding and stress-resistant crop varieties. However, challenges such as sensitivity limitations and the need for standardization remain.</p><p><strong>Conclusion: </strong>NMR spectroscopy holds immense potential for revolutionizing agricultural research and crop improvement. Overcoming existing challenges, such as sensitivity and standardization, is crucial for its broader application in practical agricultural settings. Collaborative efforts among researchers, agronomists, and policymakers will be essential for leveraging NMR technology to address global food security challenges and promote sustainable agricultural practices.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"27"},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes. 在秀丽隐杆线虫脂质体中常检测到磷酸化鞘糖脂。
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-20 DOI: 10.1007/s11306-024-02216-w
Michael Witting, Liesa Salzer, Sven W Meyer, Aiko Barsch
{"title":"Phosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes.","authors":"Michael Witting, Liesa Salzer, Sven W Meyer, Aiko Barsch","doi":"10.1007/s11306-024-02216-w","DOIUrl":"10.1007/s11306-024-02216-w","url":null,"abstract":"<p><strong>Introduction: </strong>The identification of lipids is a cornerstone of lipidomics, and due to the specific characteristics of lipids, it requires dedicated analysis workflows. Identifying novel lipids and lipid species for which no reference spectra are available is tedious and often involves a lot of manual work. Integrating high-resolution mass spectrometry with enhancements from chromatographic and ion mobility separation enables the in-depth investigation of intact lipids.</p><p><strong>Objectives: </strong>We investigated phosphorylated glycosphingolipids from the nematode Caenorhabditis elegans, a biomedical model organism, and aimed to identify different species from this class of lipids, which have been described in one particular publication only. We checked if these lipids can be detected in lipid extracts of C. elegans.</p><p><strong>Methods: </strong>We used UHPLC-UHR-TOF-MS and UHPLC-TIMS-TOF-MS in combination with dedicated data analysis to check for the presence of phosphorylated glycosphingolipids. Specifically, candidate features were identified in two datasets using Mass Spec Query Language (MassQL) to search fragmentation data. The additional use of retention time (RT) and collisional cross section (CCS) information allowed to filter false positive annotations.</p><p><strong>Results: </strong>As a result, we detected all previously described phosphorylated glycosphingolipids and novel species as well as their biosynthetic precursors in two different lipidomics datasets. MassQL significantly speeds up the process by saving time that would otherwise be spent on manual data investigations. In total over 20 sphingolipids could be described.</p><p><strong>Conclusion: </strong>MassQL allowed us to search for phosphorylated glycosphingolipids and their potential biosynthetic precursors systematically. Using orthogonal information such as RT and CCS helped filter false positive results. With the detection in two different datasets, we demonstrate that these sphingolipids are a general part of the C. elegans lipidome.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"29"},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An untargeted metabolome-wide association study of maternal perinatal tobacco smoking in newborn blood spots. 新生儿血斑中孕产妇围产期吸烟的非靶向代谢组关联研究
IF 3.5 3区 医学
Metabolomics Pub Date : 2025-02-20 DOI: 10.1007/s11306-025-02225-3
Di He, Qi Yan, Karan Uppal, Douglas I Walker, Dean P Jones, Beate Ritz, Julia E Heck
{"title":"An untargeted metabolome-wide association study of maternal perinatal tobacco smoking in newborn blood spots.","authors":"Di He, Qi Yan, Karan Uppal, Douglas I Walker, Dean P Jones, Beate Ritz, Julia E Heck","doi":"10.1007/s11306-025-02225-3","DOIUrl":"10.1007/s11306-025-02225-3","url":null,"abstract":"<p><strong>Introduction: </strong>Maternal tobacco smoking in the perinatal period increases the risk for adverse outcomes in offspring.</p><p><strong>Objective: </strong>To better understand the biological pathways through which maternal tobacco use may have long-term impacts on child metabolism, we performed a high-resolution metabolomics (HRM) analysis in newborns, following an untargeted metabolome-wide association study workflow.</p><p><strong>Methods: </strong>The study population included 899 children without cancer diagnosis before age 6 and born between 1983 and 2011 in California. Newborn dried blood spots were collected by the California Genetic Disease Screening Program between 12 and 48 h after birth and stored for later research use. Based on HRM, we considered mothers to be active smokers if they were self- or provider-reported smokers on birth certificates or if we detected any cotinine or high hydroxycotinine intensities in newborn blood. We used partial least squares discriminant analysis and Mummichog pathway analysis to identify metabolites and metabolic pathways associated with maternal tobacco smoking.</p><p><strong>Results: </strong>A total of 26,183 features were detected with HRM, including 1003 that were found to be associated with maternal smoking late in pregnancy and early postpartum (Variable Importance in Projection (VIP) scores > = 2). Smoking affected metabolites and metabolic pathways in neonatal blood including vitamin A (retinol) metabolism, the kynurenine pathway, and tryptophan and arachidonic acid metabolism.</p><p><strong>Conclusion: </strong>The smoking-associated metabolites and pathway perturbations that we identified suggested inflammatory responses and have also been implicated in chronic diseases of the central nervous system and the lung. Our results suggest that infant metabolism in the early postnatal period reflects smoking specific physiologic responses to maternal smoking with strong biologic plausibility.</p>","PeriodicalId":18506,"journal":{"name":"Metabolomics","volume":"21 2","pages":"30"},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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