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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/28090435/-13-c-metabolomics-nmr-and-iroa-for-unknown-identification
#1
Chaevien S Clendinen, Gregory S Stupp, Bing Wang, Timothy J Garrett, Arthur S Edison
ABSTRACT BACKGROUND: Isotopic Ratio Outlier Analysis (IROA) is an untargeted metabolomics method that uses stable isotopic labeling and LC-HRMS for identification and relative quantification of metabolites in a biological sample under varying experimental conditions. OBJECTIVE: We demonstrate a method using high-sensitivity (13)C NMR to identify an unknown metabolite isolated from fractionated material from an IROA LC-HRMS experiment. METHODS: IROA samples from the nematode Caenorhabditis elegans were fractionated using LC-HRMS using 5 repeated injections and collecting 30 sec fractions...
August 2016: Current Metabolomics
https://www.readbyqxmd.com/read/28074041/transcription-factor-xpp1-is-a-switch-between-primary-and-secondary-fungal-metabolism
#2
Christian Derntl, Bernhard Kluger, Christoph Bueschl, Rainer Schuhmacher, Robert L Mach, Astrid R Mach-Aigner
Fungi can produce a wide range of chemical compounds via secondary metabolism. These compounds are of major interest because of their (potential) application in medicine and biotechnology and as a potential source for new therapeutic agents and drug leads. However, under laboratory conditions, most secondary metabolism genes remain silent. This circumstance is an obstacle for the production of known metabolites and the discovery of new secondary metabolites. In this study, we describe the dual role of the transcription factor Xylanase promoter binding protein 1 (Xpp1) in the regulation of both primary and secondary metabolism of Trichoderma reesei Xpp1 was previously described as a repressor of xylanases...
January 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28069401/analytes-related-to-erythrocyte-metabolism-are-reliable-biomarkers-for-preanalytical-error-due-to-delayed-plasma-processing-in-metabolomics-studies
#3
Mahim Jain, Adam D Kennedy, Sarah H Elsea, Marcus J Miller
INTRODUCTION: Delaying plasma separation after phlebotomy (processing delay) can cause perturbations of numerous small molecule analytes. This poses a major challenge to the clinical application of metabolomics analyses. We define the analyte changes that occur during processing delays and generate a model for the post hoc detection of this preanalytical error. METHODS: Using an untargeted metabolomics platform we analyzed EDTA-preserved plasma specimens harvested after processing delays lasting from minutes to days...
January 6, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28058728/untargeted-metabolomic-profiling-of-seminal-plasma-in-non-obstructive-azoospermia-men-a-non-invasive-detection-of-spermatogenesis
#4
Kambiz Gilany, Ahmad Mani-Varnosfaderani, Arash Minai-Tehrani, Fateme Mirzajani, Alireza Ghassempour, Mohammed Reza Sadeghi, Mehdi Amini, Hassan Rezadoost
Male factor infertility is involved in almost half of all infertile couples. Lack of the ejaculated sperm due to testicular malfunction has been reported in 6-10% of infertile, a condition named non-obstructive azoospermia (NOA). In this study, we investigated untargeted metabolomic profiling of the seminal plasma in NOA men using gas chromatography-mass spectrometry (GC-MS) and advance chemometrics. In this regard, the seminal plasma fluids of 11 NOA men with TESE-negative (AZN), 9 NOA men with TESE-positive (AZP) and 10 fertile (F) healthy men (as a control group) were collected...
January 6, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28049773/crosstalk-between-alternatively-spliced-ugt1a-isoforms-and-colon-cancer-cell-metabolism
#5
Yannick Audet-Delage, Michele Rouleau, Melanie Rouleau, Joannie Roberge, Stephanie Miard, Frederic Picard, Bernard Tetu, Chantal Guillemette
Alternative splicing at the human glucuronosyltransferase 1 gene locus (UGT1) produces alternate isoforms UGT1A_i2s that control glucuronidation activity through protein-protein interactions. Here, we hypothesized that UGT1A_i2s function into a complex protein network connecting other metabolic pathways with influence on cancer cell metabolism. This is based on a pathway enrichment analysis of proteomic data that identified several high-confidence candidate interaction proteins of UGT1A_i2 proteins in human tissues, namely the rate-limiting enzyme of glycolysis pyruvate kinase (PKM), which plays a critical role in cancer cell metabolism and tumor growth...
January 3, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28039739/what-computational-non-targeted-mass-spectrometry-based-metabolomics-can-gain-from-shotgun-proteomics
#6
REVIEW
Hamid Hamzeiy, Jürgen Cox
Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs...
December 28, 2016: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28025165/searching-molecular-structure-databases-using-tandem-ms-data-are-we-there-yet
#7
REVIEW
Sebastian Böcker
Untargeted metabolomics experiments usually rely on tandem mass spectrometry (MS/MS) to identify the thousands of compounds in a complex sample. Spectral libraries used for identification are incomplete, and many metabolites remain unknown. There has been a recent development to replace spectral libraries by molecular structure databases when searching the MS/MS data of the unknown compound. Several tools have been developed for this task, including CFM-ID, MetFrag, MAGMa(+), FingerID and CSI:FingerID. These methods are already helpful for everyday metabolomics; with further advances, these methods can become indispensable tools for tomorrow's metabolomics...
December 22, 2016: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28018221/metabolomic-study-on-idiosyncratic-liver-injury-induced-by-different-extracts-of-polygonum-multiflorum-in-rats-integrated-with-pattern-recognition-and-enriched-pathways-analysis
#8
Chun-Yu Li, Can Tu, Dan Gao, Rui-Lin Wang, Hai-Zhu Zhang, Ming Niu, Rui-Yu Li, Cong-En Zhang, Rui-Sheng Li, Xiao-He Xiao, Mei-Hua Yang, Jia-Bo Wang
Currently, numerous liver injury cases related to a famous Chinese herb- Polygonum Multiflorum (Heshouwu in Chinese) have attracted great attention in many countries. Our previous work showed that Heshouwu-induced hepatotoxicity belonged to idiosyncratic drug-induced liver injury (IDILI). Unfortunately, the components and mechanisms attributed to IDILI of Heshouwu are difficult to determine and thus remain unknown. Attempts to explore puzzles, we prepared the chloroform (CH)-, ethyl acetate (EA)-, and residue (RE) extracts of Heshouwu to investigate IDILI constituents and underlying mechanisms, using biochemistry, histopathology, and metabolomics examinations...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28012379/the-lc-ms-based-metabolomics-of-hydroxytyrosol-administration-in-rats-reveals-amelioration-of-the-metabolic-syndrome
#9
Nikolaos Lemonakis, Hemant Poudyal, Maria Halabalaki, Lindsay Brown, Anthony Tsarbopoulos, Alexios-Leandros Skaltsounis, Evagelos Gikas
Hydroxytyrosol (HT), an important component of olive fruit and olive oil, improves the signs of metabolic syndrome in rats following chronic treatment. At a dose of 20mg/kg/day, HT decreased adiposity and improved cardiovascular and liver structure and function in rats fed with a high-carbohydrate, high-fat diet. An untargeted metabolomics approach has been employed using both UPLC-Orbitrap and -QqTOF methods to identify the changes induced by chronic HT administration on the plasma metabolome. 31 metabolites have been found to be differentially expressed between the examined groups...
January 15, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28009452/metabolic-profiles-revealed-synergistically-antidepressant-effects-of-lilies-and-rhizoma-anemarrhenae-in-a-rat-model-of-depression
#10
Hongli Du, Hongxia Zhao, Xueli Lai, Qishan Lin, Zhenyu Zhu, Yifeng Chai, Ziyang Lou
Depression is the predominant cause of illness and disability. We applied untargeted metabolomics using mass spectrometry to identify metabolic signatures associated with depression in serum and explored the antidepressant effects of Lilies and Rhizoma Anemarrhenae on an experimental model of chronic unpredictable mild stress (CUMS). Meanwhile metabolomics based on UHPLC-Q-TOF-MS, was used to study the change in metabolites in CUMS rat serum and to evaluate the effects of Anemarrhena Rhizoma, Lilies (alone and in combination)...
December 23, 2016: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28003796/a-novel-targeted-untargeted-gc-orbitrap-metabolomics-methodology-applied-to-candida-albicans-and-staphylococcus-aureus-biofilms
#11
Stefan Weidt, Jennifer Haggarty, Ryan Kean, Cristian I Cojocariu, Paul J Silcock, Ranjith Rajendran, Gordon Ramage, Karl E V Burgess
INTRODUCTION: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus-hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality...
2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27991533/distinct-urine-metabolome-after-asian-ginseng-and-american-ginseng-intervention-based-on-gc-ms-metabolomics-approach
#12
Liu Yang, Qing-Tao Yu, Ya-Zhong Ge, Wen-Song Zhang, Yong Fan, Chung-Wah Ma, Qun Liu, Lian-Wen Qi
Ginseng occupies a prominent position in the list of best-selling natural products worldwide. Asian ginseng (Panax ginseng) and American ginseng (Panax quinquefolius) show different properties and medicinal applications in pharmacology, even though the main active constituents of them are both thought to be ginsenosides. Metabolomics is a promising method to profile entire endogenous metabolites and monitor their fluctuations related to exogenous stimulus. Herein, an untargeted metabolomics approach was applied to study the overall urine metabolic differences between Asian ginseng and American ginseng in mice...
December 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27988319/unsaturated-plasma-phospholipids-are-consistently-lower-in-the-patients-diagnosed-with-gestational-diabetes-mellitus-throughout-pregnancy-a-longitudinal-metabolomics-study-of-chinese-pregnant-women-part-1
#13
Kai P Law, Xun Mao, Ting-Li Han, Hua Zhang
BACKGROUND: Gestational diabetes mellitus (GDM) is a milder degree of hyperglycaemia diagnosed during pregnancy that can lead to serious, long-term consequences for both mother and foetus. The pathophysiology of GDM is not fully understood. The number of pregnant women diagnosed with GDM has been steadily increasing, but effective screening tools for early risk stratification are still missing. The emerging field of metabolomics has the potential to provide new insights and as a result is increasingly being used in studies of GDM...
December 14, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27984853/butia-spp-arecaceae-lc-ms-based-metabolomics-for-species-and-geographical-origin-discrimination
#14
Jessica Fernanda Hoffmann, Ivan Ricardo Carvalho, Rosa Lia Barbieri, Cesar Valmor Rombaldi, Fabio Clasen Chaves
The metabolic variability of fruit from Butia spp. (Arecaceae) genotypes from different geographical locations was characterized using untargeted metabolomics by liquid chromatography-mass spectrometry (LC-MS) followed by multivariate data analyses. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) from LC-MS data sets showed a clear distinction among Butia catarinensis, Butia odorata, Butia paraguayensis, and Butia yatay. The major metabolites that contributed to species discrimination were primary metabolites including sugars and organic acids and specialized metabolites such as tetrahydroxy-trans-stilbene and rutin...
January 3, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27979300/a-new-exploration-of-licorice-metabolome
#15
Giovanni Rizzato, Elisa Scalabrin, Marta Radaelli, Gabriele Capodaglio, Oreste Piccolo
The roots and rhizomes of licorice plants (genus Glycyrrhiza L.) are commercially employed, after processing, in confectionery production or as sweetening and flavouring agents in the food, tobacco and beer industries. G. glabra, G. inflata and G. uralensis are the most significant licorice species, often indistinctly used for different productions. Licorice properties are directly related to its chemical composition, which determines the commercial values and the quality of the derived products. In order to better understand the characteristics and properties of each species, a chemical characterization of three species of licorice (G...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27979195/untargeted-metabolomic-analysis-of-human-serum-samples-associated-with-different-levels-of-red-meat-consumption-a-possible-indicator-of-type-2-diabetes
#16
Daniel Carrizo, Olivier P Chevallier, Jayne V Woodside, Sarah F Brennan, Marie M Cantwell, Geraldine Cuskelly, Christopher T Elliott
Red meat consumption has been associated with negative health effects. A study to identify biomarkers of meat consumption was undertaken using serum samples collected from combining high resolution mass spectrometry (UPLC-QTof-MS) and chemometrics. Using orthogonal partial last-squares discriminant analysis (OPLS-DA), multivariate models were created for both modes of acquisition (ESI-/ESI+) and red meat intake classes (YES/NO). In the serum samples, a total 3280 and 3225 ions of interest were detected in positive and negative modes, respectively...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27977166/xmsannotator-an-r-package-for-network-based-annotation-of-high-resolution-metabolomics-data
#17
Karan Uppal, Douglas I Walker, Dean P Jones
Improved analytical technologies and data extraction algorithms enable detection of >10,000 reproducible signals by liquid chromatography high-resolution mass spectrometry, creating a bottleneck in chemical identification. In principle, measurement of more than one million chemicals would be possible if algorithms were available to facilitate utilization of the raw mass spectrometry data, especially low abundance metabolites. Here we describe an automated computational framework to annotate ions for possible chemical identity using a multistage clustering algorithm in which metabolic pathway associations are used along with intensity profiles, retention time characteristics, mass defect, and isotope/adduct patterns...
December 15, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27976333/large-scale-discovery-and-deorphanization-of-natural-products-using-fungal-artificial-chromosomes-and-untargeted-metabolomics-fac-ms
#18
K D Clevenger, J W Bok, R Ye, G P Miley, T Velk, C Chen, K Yang, P Gao, M Lamprecht, P M Thomas, M N Islam, C C Wu, N P Keller, N L Kelleher
No abstract text is available yet for this article.
December 2016: Planta Medica
https://www.readbyqxmd.com/read/27975918/co-cultivation-approach-and-untargeted-metabolomics-in-the-search-for-new-secondary-metabolites-from-endophytic-fungi
#19
F Barakat, M Vansteelandt, A Triastuti, L Rieusset, B Cabanillas, M Haddad, N Fabre
No abstract text is available yet for this article.
December 2016: Planta Medica
https://www.readbyqxmd.com/read/27958387/performance-evaluation-and-online-realization-of-data-driven-normalization-methods-used-in-lc-ms-based-untargeted-metabolomics-analysis
#20
Bo Li, Jing Tang, Qingxia Yang, Xuejiao Cui, Shuang Li, Sijie Chen, Quanxing Cao, Weiwei Xue, Na Chen, Feng Zhu
In untargeted metabolomics analysis, several factors (e.g., unwanted experimental &biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided...
December 13, 2016: Scientific Reports
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