Metabolomics : Official journal of the Metabolomic Society最新文献

筛选
英文 中文
Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis. 双相情感障碍患者的代谢组学和蛋白质组学分析揭示了与止血相关的潜在分子特征。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-08-03 DOI: 10.1007/s11306-022-01924-5
Henrique Caracho Ribeiro, Partho Sen, Alex Dickens, Elisa Castañeda Santa Cruz, Matej Orešič, Alessandra Sussulini
{"title":"Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis.","authors":"Henrique Caracho Ribeiro,&nbsp;Partho Sen,&nbsp;Alex Dickens,&nbsp;Elisa Castañeda Santa Cruz,&nbsp;Matej Orešič,&nbsp;Alessandra Sussulini","doi":"10.1007/s11306-022-01924-5","DOIUrl":"https://doi.org/10.1007/s11306-022-01924-5","url":null,"abstract":"<p><strong>Introduction: </strong>Bipolar disorder (BD) is a mood disorder characterized by the occurrence of depressive episodes alternating with episodes of elevated mood (known as mania). There is also an increased risk of other medical comorbidities.</p><p><strong>Objectives: </strong>This work uses a systems biology approach to compare BD treated patients with healthy controls (HCs), integrating proteomics and metabolomics data using partial correlation analysis in order to observe the interactions between altered proteins and metabolites, as well as proposing a potential metabolic signature panel for the disease.</p><p><strong>Methods: </strong>Data integration between proteomics and metabolomics was performed using GC-MS data and label-free proteomics from the same individuals (N = 13; 5 BD, 8 HC) using generalized canonical correlation analysis and partial correlation analysis, and then building a correlation network between metabolites and proteins. Ridge-logistic regression models were developed to stratify between BD and HC groups using an extended metabolomics dataset (N = 28; 14 BD, 14 HC), applying a recursive feature elimination for the optimal selection of the metabolites.</p><p><strong>Results: </strong>Network analysis demonstrated links between proteins and metabolites, pointing to possible alterations in hemostasis of BD patients. Ridge-logistic regression model indicated a molecular signature comprising 9 metabolites, with an area under the receiver operating characteristic curve (AUROC) of 0.833 (95% CI 0.817-0.914).</p><p><strong>Conclusion: </strong>From our results, we conclude that several metabolic processes are related to BD, which can be considered as a multi-system disorder. We also demonstrate the feasibility of partial correlation analysis for integration of proteomics and metabolomics data in a case-control study setting.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"65"},"PeriodicalIF":3.6,"publicationDate":"2022-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40598039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data. 光谱分束作为一种高分辨率fe - ms代谢组指纹数据采集后处理方法。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-08-02 DOI: 10.1007/s11306-022-01923-6
Jasen P Finch, Thomas Wilson, Laura Lyons, Helen Phillips, Manfred Beckmann, John Draper
{"title":"Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data.","authors":"Jasen P Finch,&nbsp;Thomas Wilson,&nbsp;Laura Lyons,&nbsp;Helen Phillips,&nbsp;Manfred Beckmann,&nbsp;John Draper","doi":"10.1007/s11306-022-01923-6","DOIUrl":"https://doi.org/10.1007/s11306-022-01923-6","url":null,"abstract":"<p><strong>Introduction: </strong>Flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) fingerprinting produces complex, high dimensional data sets which require specialist in-silico software tools to process the data prior to analysis.</p><p><strong>Objectives: </strong>Present spectral binning as a pragmatic approach to post-acquisition procession of FIE-HRMS metabolome fingerprinting data.</p><p><strong>Methods: </strong>A spectral binning approach was developed that included the elimination of single scan m/z events, the binning of spectra and the averaging of spectra across the infusion profile. The modal accurate m/z was then extracted for each bin. This approach was assessed using four different biological matrices and a mix of 31 known chemical standards analysed by FIE-HRMS using an Exactive Orbitrap. Bin purity and centrality metrics were developed to objectively assess the distribution and position of accurate m/z within an individual bin respectively.</p><p><strong>Results: </strong>The optimal spectral binning width was found to be 0.01 amu. 80.8% of the extracted accurate m/z matched to predicted ionisation products of the chemical standards mix were found to have an error of below 3 ppm. The open-source R package binneR was developed as a user friendly implementation of the approach. This was able to process 100 data files using 4 Central Processing Units (CPU) workers in only 55 seconds with a maximum memory usage of 1.36 GB.</p><p><strong>Conclusion: </strong>Spectral binning is a fast and robust method for the post-acquisition processing of FIE-HRMS data. The open-source R package binneR allows users to efficiently process data from FIE-HRMS experiments with the resources available on a standard desktop computer.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"64"},"PeriodicalIF":3.6,"publicationDate":"2022-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9345815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40575058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Association of amino acid metabolites with osteoporosis, a metabolomic approach: Bushehr elderly health program. 氨基酸代谢物与骨质疏松症的关联,代谢组学方法:布什尔老年健康计划。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-08-01 DOI: 10.1007/s11306-022-01919-2
Nekoo Panahi, Noushin Fahimfar, Shahin Roshani, Babak Arjmand, Safoora Gharibzadeh, Gita Shafiee, Eugenia Migliavacca, Denis Breuille, Jerome N Feige, Yohan Grzywinski, John Corthesy, Farideh Razi, Ramin Heshmat, Iraj Nabipour, Farshad Farzadfar, Akbar Soltani, Bagher Larijani, Afshin Ostovar
{"title":"Association of amino acid metabolites with osteoporosis, a metabolomic approach: Bushehr elderly health program.","authors":"Nekoo Panahi,&nbsp;Noushin Fahimfar,&nbsp;Shahin Roshani,&nbsp;Babak Arjmand,&nbsp;Safoora Gharibzadeh,&nbsp;Gita Shafiee,&nbsp;Eugenia Migliavacca,&nbsp;Denis Breuille,&nbsp;Jerome N Feige,&nbsp;Yohan Grzywinski,&nbsp;John Corthesy,&nbsp;Farideh Razi,&nbsp;Ramin Heshmat,&nbsp;Iraj Nabipour,&nbsp;Farshad Farzadfar,&nbsp;Akbar Soltani,&nbsp;Bagher Larijani,&nbsp;Afshin Ostovar","doi":"10.1007/s11306-022-01919-2","DOIUrl":"https://doi.org/10.1007/s11306-022-01919-2","url":null,"abstract":"<p><strong>Introduction and objectives: </strong>Amino acids are the most frequently reported metabolites associated with low bone mineral density (BMD) in metabolomics studies. We aimed to evaluate the association between amino acid metabolic profile and bone indices in the elderly population.</p><p><strong>Methods: </strong>400 individuals were randomly selected from 2384 elderly men and women over 60 years participating in the second stage of the Bushehr elderly health (BEH) program, a population-based prospective cohort study that is being conducted in Bushehr, a southern province of Iran. Frozen plasma samples were used to measure 29 amino acid and derivatives metabolites using the UPLC-MS/MS-based targeted metabolomics platform. We conducted Elastic net regression analysis to detect the metabolites associated with BMD of different sites and lumbar spine trabecular bone score, and also to examine the ability of the measured metabolites to differentiate osteoporosis.</p><p><strong>Results: </strong>We adjusted the analysis for possible confounders (age, BMI, diabetes, smoking, physical activity, vitamin D level, and sex). Valine, leucine, isoleucine, and alanine in women and tryptophan in men were the most important amino acids inversely associated with osteoporosis (OR range from 0.77 to 0.89). Sarcosine, followed by tyrosine, asparagine, alpha aminobutyric acid, and ADMA in women and glutamine in men and when both women and men were considered together were the most discriminating amino acids detected in individuals with osteoporosis (OR range from 1.15 to 1.31).</p><p><strong>Conclusion: </strong>We found several amino acid metabolites associated with possible bone status in elderly individuals. Further studies are required to evaluate the utility of these metabolites as clinical biomarkers for osteoporosis prediction and their effect on bone health as dietary supplements.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"63"},"PeriodicalIF":3.6,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40662731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
High serum levels of L-carnitine and citric acid negatively correlated with alkaline phosphatase are detectable in Koreans before gastric cancer onset. 韩国人胃癌发病前血清中左旋肉碱和柠檬酸水平与碱性磷酸酶呈负相关。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-28 DOI: 10.1007/s11306-022-01922-7
Youngmin Han, Hye Jin Yoo, Sun Ha Jee, Jong Ho Lee
{"title":"High serum levels of L-carnitine and citric acid negatively correlated with alkaline phosphatase are detectable in Koreans before gastric cancer onset.","authors":"Youngmin Han,&nbsp;Hye Jin Yoo,&nbsp;Sun Ha Jee,&nbsp;Jong Ho Lee","doi":"10.1007/s11306-022-01922-7","DOIUrl":"https://doi.org/10.1007/s11306-022-01922-7","url":null,"abstract":"<p><strong>Introduction: </strong>Monitoring metabolic biomarkers could be utilized as an effective tool for the early detection of gastric cancer (GC) risk.</p><p><strong>Objective: </strong>We aimed to discover predictive serum biomarkers for GC and investigate biomarker-related metabolism.</p><p><strong>Methods: </strong>Subjects were randomly selected from the Korean Cancer Prevention Study-II cohort and matched by age and sex. We analyzed baseline serum samples of 160 subjects (discovery set; control and GC occurrence group, 80 each) via nontargeted screening. Identified putative biomarkers were validated in baseline serum samples of 140 subjects (validation set; control and GC occurrence group, 70 each) using targeted metabolites analysis.</p><p><strong>Results: </strong>The final analysis was conducted on the discovery set (control, n = 52 vs. GC occurrence, n = 50) and the validation set (control, n = 43 vs. GC occurrence, n = 44) applying exclusion conditions. Eighteen putative metabolite sets differed between two groups found on nontargeted metabolic screening. We focused on fatty acid-related energy metabolism. In targeted analysis, levels of decanoyl-L-carnitine (p = 0.019), L-carnitine (p = 0.033), and citric acid (p = 0.025) were significantly lower in the GC occurrence group, even after adjusting for age, sex, and smoking status. Additionally, L-carnitine and citric acid were confirmed to have an independently significant relationship to GC development. Notably, alkaline phosphatase showed a significant correlation with these two biomarkers.</p><p><strong>Conclusion: </strong>Changes in serum L-carnitine and citric acid levels that may result from alterations of fatty-acid-related energy metabolism are expected to be valuable biomarkers for the early diagnosis of GC risk.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"62"},"PeriodicalIF":3.6,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40554540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Untargeted metabolomic analysis of thoracic blood from badgers indicate changes linked to infection with bovine tuberculosis (Mycobacterium bovis): a pilot study. 一项初步研究:对来自獾的胸部血液进行的非靶向代谢组学分析表明,变化与牛结核(牛分枝杆菌)感染有关。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-27 DOI: 10.1007/s11306-022-01915-6
James Scott Bauman, Richard Pizzey, Manfred Beckmann, Bernardo Villarreal-Ramos, Jonathan King, Beverley Hopkins, David Rooke, Glyn Hewinson, Luis A J Mur
{"title":"Untargeted metabolomic analysis of thoracic blood from badgers indicate changes linked to infection with bovine tuberculosis (Mycobacterium bovis): a pilot study.","authors":"James Scott Bauman,&nbsp;Richard Pizzey,&nbsp;Manfred Beckmann,&nbsp;Bernardo Villarreal-Ramos,&nbsp;Jonathan King,&nbsp;Beverley Hopkins,&nbsp;David Rooke,&nbsp;Glyn Hewinson,&nbsp;Luis A J Mur","doi":"10.1007/s11306-022-01915-6","DOIUrl":"https://doi.org/10.1007/s11306-022-01915-6","url":null,"abstract":"<p><strong>Introduction: </strong>Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB) in cattle, represents a major disease burden to UK cattle farming, with considerable costs associated with its control. The European badger (Meles meles) is a known wildlife reservoir for bTB and better knowledge of the epidemiology of bTB through testing wildlife is required for disease control. Current tests available for the diagnosis of bTB in badgers are limited by cost, processing time or sensitivities.</p><p><strong>Materials and methods: </strong>We assessed the ability of flow infusion electrospray-high-resolution mass spectrometry (FIE-HRMS) to determine potential differences between infected and non-infected badgers based on thoracic blood samples obtained from badgers found dead in Wales. Thoracic blood samples were autoclaved for handling in a containment level 2 (CL2) hazard laboratory.</p><p><strong>Results: </strong>Here we show the major differences associated with with M. bovis infection were changes to folate, pyrimidine, histidine, glycerophospholipid and phosphonate metabolism.</p><p><strong>Conclusions: </strong>Our studies have indicated differences in the metabolomic signature of badgers found dead in relation to their infection status, suggesting metabolomics could hold potential for developing novel diagnostics for bTB in badgers. As well as highlighting a potential way to handle samples containing a highly pathogenic agent at CL2 for metabolomics studies.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"61"},"PeriodicalIF":3.6,"publicationDate":"2022-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9329164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40550037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Combining data acquisition modes in liquid-chromatography-tandem mass spectrometry for comprehensive determination of acylcarnitines in human serum. 液相色谱-串联质谱联用数据采集方式综合测定人血清中酰基肉碱。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-21 DOI: 10.1007/s11306-022-01916-5
D Luque-Córdoba, M Calderón-Santiago, F Priego-Capote
{"title":"Combining data acquisition modes in liquid-chromatography-tandem mass spectrometry for comprehensive determination of acylcarnitines in human serum.","authors":"D Luque-Córdoba,&nbsp;M Calderón-Santiago,&nbsp;F Priego-Capote","doi":"10.1007/s11306-022-01916-5","DOIUrl":"https://doi.org/10.1007/s11306-022-01916-5","url":null,"abstract":"<p><p>Acylcarnitines (ACs) are metabolites involved in fatty acid β-oxidation and organic acid metabolism. Metabolic disorders associated to these two processes can be evaluated by determining the complete profile of ACs. In this research, we present an overall strategy for identification, confirmation, and quantitative determination of acylcarnitines in human serum. By this strategy we identified the presence of 47 ACs from C2 to C24 with detection of the unsaturation degree by application of a data-independent acquisition (DIA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Complementary, quantitative determination of ACs is based on a high-throughput and fully automated method consisting of solid-phase extraction on-line coupled to LC-MS/MS in data-dependent acquisition (DDA) to improve analytical features avoiding the errors associated to sample processing. Quantitation limits were at pg mL<sup>-1</sup> level, the intra-day and between-day variability were below 15-20%, respectively; and the accuracy, expressed as bias, was always within ± 25%. The proposed method was tested with 40 human volunteers to determine the relative concentration of ACs in serum and identify predominant forms. Significant differences were detected by comparing the ACs profile of obese versus non-obese individuals.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"59"},"PeriodicalIF":3.6,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40621034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Metabolic changes associated with two endocrine abnormalities in dogs: elevated fructosamine and low thyroxine. 代谢变化与狗的两种内分泌异常有关:果糖胺升高和甲状腺素降低。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-20 DOI: 10.1007/s11306-022-01917-4
Claudia Ottka, Jenni Puurunen, Elisabeth Müller, Corinna Weber, Ruth Klein, Hannes Lohi
{"title":"Metabolic changes associated with two endocrine abnormalities in dogs: elevated fructosamine and low thyroxine.","authors":"Claudia Ottka,&nbsp;Jenni Puurunen,&nbsp;Elisabeth Müller,&nbsp;Corinna Weber,&nbsp;Ruth Klein,&nbsp;Hannes Lohi","doi":"10.1007/s11306-022-01917-4","DOIUrl":"https://doi.org/10.1007/s11306-022-01917-4","url":null,"abstract":"<p><strong>Introduction: </strong>Metabolomics studies in canine endocrine abnormalities are sparse and basic information on these abnormalities must be generated.</p><p><strong>Objectives: </strong>To characterize the metabolic changes associated with elevated fructosamine, reflecting poor glycemic control, and low thyroxine, a thyroid hormone controlling metabolism.</p><p><strong>Methods: </strong>Leftovers of clinical serum samples; 25 controls, 79 high fructosamine, and 47 low thyroxine, were analyzed using <sup>1</sup>H NMR and differences were evaluated using Firth logistic regression.</p><p><strong>Results: </strong>Both high fructosamine and low thyroxine were associated with changes in concentrations of multiple metabolites, including glycoprotein acetyls and lipids.</p><p><strong>Conclusion: </strong>These findings suggest promising makers for further research and clinical validation.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"58"},"PeriodicalIF":3.6,"publicationDate":"2022-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40524473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli. 代谢组学用于设计新的代谢工程策略,以提高大肠杆菌需氧琥珀酸的产量。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-20 DOI: 10.1007/s11306-022-01912-9
Antonio Valle, Zamira Soto, Howbeer Muhamadali, Katherine A Hollywood, Yun Xu, Jonathan R Lloyd, Royston Goodacre, Domingo Cantero, Gema Cabrera, Jorge Bolivar
{"title":"Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli.","authors":"Antonio Valle,&nbsp;Zamira Soto,&nbsp;Howbeer Muhamadali,&nbsp;Katherine A Hollywood,&nbsp;Yun Xu,&nbsp;Jonathan R Lloyd,&nbsp;Royston Goodacre,&nbsp;Domingo Cantero,&nbsp;Gema Cabrera,&nbsp;Jorge Bolivar","doi":"10.1007/s11306-022-01912-9","DOIUrl":"https://doi.org/10.1007/s11306-022-01912-9","url":null,"abstract":"<p><strong>Introduction: </strong>Glycerol is a byproduct from the biodiesel industry that can be biotransformed by Escherichia coli to high added-value products such as succinate under aerobic conditions. The main genetic engineering strategies to achieve this aim involve the mutation of succinate dehydrogenase (sdhA) gene and also those responsible for acetate synthesis including acetate kinase, phosphate acetyl transferase and pyruvate oxidase encoded by ackA, pta and pox genes respectively in the ΔsdhAΔack-ptaΔpox (M4) mutant. Other genetic manipulations to rewire the metabolism toward succinate consist on the activation of the glyoxylate shunt or blockage the pentose phosphate pathway (PPP) by deletion of isocitrate lyase repressor (iclR) or gluconate dehydrogenase (gnd) genes on M4-ΔiclR and M4-Δgnd mutants respectively.</p><p><strong>Objective: </strong>To deeply understand the effect of the blocking of the pentose phosphate pathway (PPP) or the activation of the glyoxylate shunt, metabolite profiles were analyzed on M4-Δgnd, M4-ΔiclR and M4 mutants.</p><p><strong>Methods: </strong>Metabolomics was performed by FT-IR and GC-MS for metabolite fingerprinting and HPLC for quantification of succinate and glycerol.</p><p><strong>Results: </strong>Most of the 65 identified metabolites showed lower relative levels in the M4-ΔiclR and M4-Δgnd mutants than those of the M4. However, fructose 1,6-biphosphate, trehalose, isovaleric acid and mannitol relative concentrations were increased in M4-ΔiclR and M4-Δgnd mutants. To further improve succinate production, the synthesis of mannitol was suppressed by deletion of mannitol dehydrogenase (mtlD) on M4-ΔgndΔmtlD mutant that increase ~ 20% respect to M4-Δgnd.</p><p><strong>Conclusion: </strong>Metabolomics can serve as a holistic tool to identify bottlenecks in metabolic pathways by a non-rational design. Genetic manipulation to release these restrictions could increase the production of succinate.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"56"},"PeriodicalIF":3.6,"publicationDate":"2022-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40522601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Prioritize biologically relevant ions for data-independent acquisition (BRI-DIA) in LC-MS/MS-based lipidomics analysis. 在LC-MS/MS-based脂质组学分析中,优先考虑数据独立采集(BRI-DIA)的生物学相关离子。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-16 DOI: 10.1007/s11306-022-01913-8
Likun Duan, Grace Scheidemantle, Mareca Lodge, Magdalina J Cummings, Eva Pham, Xiaoqiu Wang, Arion Kennedy, Xiaojing Liu
{"title":"Prioritize biologically relevant ions for data-independent acquisition (BRI-DIA) in LC-MS/MS-based lipidomics analysis.","authors":"Likun Duan,&nbsp;Grace Scheidemantle,&nbsp;Mareca Lodge,&nbsp;Magdalina J Cummings,&nbsp;Eva Pham,&nbsp;Xiaoqiu Wang,&nbsp;Arion Kennedy,&nbsp;Xiaojing Liu","doi":"10.1007/s11306-022-01913-8","DOIUrl":"https://doi.org/10.1007/s11306-022-01913-8","url":null,"abstract":"<p><strong>Introduction: </strong>Data-dependent acquisition (DDA) is the most commonly used MS/MS scan method for lipidomics analysis on orbitrap-based instrument. However, MS instrument associated software decide the top N precursors for fragmentation, resulting in stochasticity of precursor selection and compromised consistency and reproducibility. We introduce a novel workflow using biologically relevant lipids to construct inclusion list for data-independent acquisition (DIA), named as BRI-DIA workflow.</p><p><strong>Objectives: </strong>To ensure consistent coverage of biologically relevant lipids in LC-MS/MS-based lipidomics analysis.</p><p><strong>Methods: </strong>Biologically relevant ion list was constructed based on LIPID MAPS and lipidome atlas in MS-DIAL 4. Lipids were extracted from mouse tissues and used to assess different MS/MS scan workflow (DDA, BRI-DIA, and hybrid mode) on LC-Orbitrap Exploris 480 mass spectrometer.</p><p><strong>Results: </strong>DDA resulted in more MS/MS events, but the total number of unique lipids identified by three methods (DDA, BRI-DIA, and hybrid MS/MS scan mode) is comparable (580 unique lipids across 44 lipid subclasses in mouse liver). Major cardiolipin molecular species were identified by data generated using BRI-DIA and hybrid methods and allowed calculation of cardiolipin compositions, while identification of the most abundant cardiolipin CL72:8 was missing in data generated using DDA method, leading to wrong calculation of cardiolipin composition.</p><p><strong>Conclusion: </strong>The method of using inclusion list comprised of biologically relevant lipids in DIA MS/MS scan is as efficient as traditional DDA method in profiling lipids, but offers better consistency of lipid identification, compared to DDA method. This study was performed using Orbitrap Exploris 480, and we will further evaluate this workflow on other platforms, and if verified by future work, this biologically relevant ion fragmentation workflow could be routinely used in many studies to improve MS/MS identification capacities.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"55"},"PeriodicalIF":3.6,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40528312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Plasma nervonic acid levels were negatively associated with attention levels in community-living older adults in New Zealand. 新西兰社区生活老年人血浆神经酸水平与注意力水平呈负相关。
IF 3.6
Metabolomics : Official journal of the Metabolomic Society Pub Date : 2022-07-16 DOI: 10.1007/s11306-022-01908-5
Jamie V de Seymour, Kathryn L Beck, Cathryn A Conlon, Pamela R von Hurst, Karen D Mumme, Crystal F Haskell-Ramsay, Mary Beatrix Jones
{"title":"Plasma nervonic acid levels were negatively associated with attention levels in community-living older adults in New Zealand.","authors":"Jamie V de Seymour,&nbsp;Kathryn L Beck,&nbsp;Cathryn A Conlon,&nbsp;Pamela R von Hurst,&nbsp;Karen D Mumme,&nbsp;Crystal F Haskell-Ramsay,&nbsp;Mary Beatrix Jones","doi":"10.1007/s11306-022-01908-5","DOIUrl":"https://doi.org/10.1007/s11306-022-01908-5","url":null,"abstract":"<p><p>The global population is aging. Preserving function and independence of our aging population is paramount. A key component to maintaining independence is the preservation of cognitive function. Metabolomics can be used to identify biomarkers of cognition before noticeable deterioration. Our study investigated the plasma metabolome of 332 community-living New Zealanders between 65 and 74 years of age, using gas chromatography-mass spectrometry. Six cognitive domains were assessed. Of the 123 metabolites identified using an in-house mass spectral libraries of standards, nervonic acid had a significant, inverse association with the attention domain (P-value = 1.52E<sup>- 4</sup>; FDR = 0.019), after adjusting for covariates (apolipoprotein E -ε4 genotype, sex, body fat percentage (standardised by sex), age, education, deprivation index, physical activity, metabolic syndrome, polypharmacy, smoking status, and alcohol intake) and multiple testing. Attention is defined as the ability to concentrate on selected aspects of the environment while ignoring other stimuli. This is the first study to identify nervonic acid as a potential biomarker of attention in older adults. Future research should confirm this association in a longitudinal study.</p>","PeriodicalId":144887,"journal":{"name":"Metabolomics : Official journal of the Metabolomic Society","volume":" ","pages":"54"},"PeriodicalIF":3.6,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40596460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信