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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/28213207/epimetabolites-discovering-metabolism-beyond-building-and-burning
#1
REVIEW
Megan R Showalter, Tomas Cajka, Oliver Fiehn
Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism...
February 14, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28211494/hepatocyte-secreted-extracellular-vesicles-modify-blood-metabolome-and-endothelial-function-by-an-arginase-dependent-mechanism
#2
Felix Royo, Laura Moreno, Justyna Mleczko, Laura Palomo, Esperanza Gonzalez, Diana Cabrera, Angel Cogolludo, Francisco Perez Vizcaino, Sebastiaan van-Liempd, Juan M Falcon-Perez
Hepatocytes release extracellular vesicles (EVs) loaded with signaling molecules and enzymes into the bloodstream. Although the importance of EVs in the intercellular communication is already recognized, the metabolic impact of the enzymes carried by these vesicles is still unclear. We evaluated the global effect of the enzymatic activities of EVs by performing untargeted metabolomic profiling of serum samples after their exposure to EVs. This approach revealed a significant change in the abundance of 94 serum metabolic signals...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208263/visualization-quantification-and-alignment-of-spectral-drift-in-population-scale-untargeted-metabolomics-data
#3
Jeramie D Watrous, Mir Henglin, Brian Claggett, Kim A Lehmann, Martin G Larson, Susan Cheng, Mohit Jain
Untargeted liquid-chromatography-mass spectrometry (LC-MS)-based metabolomics analysis of human biospecimens has become among the most promising strategies for probing the underpinnings of human health and disease. Analysis of spectral data across population scale cohorts, however, is precluded by day-to-day nonlinear signal drifts in LC retention time or batch effects that complicate comparison of thousands of untargeted peaks. To date, there exists no efficient means of visualization and quantitative assessment of signal drift, correction of drift when present, and automated filtering of unstable spectral features, particularly across thousands of data files in population scale experiments...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28195169/untargeted-metabolomics-of-colonic-digests-reveals-kynurenine-pathway-metabolites-dityrosine-and-3-dehydroxycarnitine-as-red-versus-white-meat-discriminating-metabolites
#4
Caroline Rombouts, Lieselot Y Hemeryck, Thomas Van Hecke, Stefaan De Smet, Winnok H De Vos, Lynn Vanhaecke
Epidemiological research has demonstrated that the consumption of red meat is an important risk factor for the development of colorectal cancer (CRC), diabetes mellitus and cardiovascular diseases. However, there is no holistic insight in the (by-) products of meat digestion that may contribute to disease development. To address this hiatus, an untargeted mass spectrometry (MS)-based metabolomics approach was used to create red versus white meat associated metabolic fingerprints following in vitro colonic digestion using the fecal inocula of ten healthy volunteers...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185342/untargeted-metabolomics-analysis-of-adipogenic-transformation-in-op9-dl1-cells-using-liquid-chromatography-mass-spectrometry-implications-for-thymic-adipogenesis
#5
Jianxin Tan, Yajun Wang, Siliang Wang, Nannan Zhang, Simeng Wu, Zhe Yuan, Xike Zhu
Adipocyte deposition is a key feature of age-related thymic involution, but the underlying mechanisms responsible for thymic adiposity remain to be elucidated. In the present study, we utilized rosiglitazone, a potent peroxisome proliferator-activated receptor γ agonist, to induce adipogenic differentiation of OP9-DL1 cells, and detected the metabolomics alterations during adipogenic differentiation by using liquid chromatography-mass spectrometry. The obtained metabolites were further processed by multivariate statistical analysis, including principal component analysis, partial least squares discriminant analysis, and orthogonal projection on latent-structures discriminant analysis...
February 9, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28169076/metabolites-as-biomarkers-of-adverse-reactions-following-vaccination-a-pilot-study-using-nuclear-magnetic-resonance-metabolomics
#6
Bruce M McClenathan, Delisha A Stewart, Christina E Spooner, Wimal W Pathmasiri, Jason P Burgess, Susan L McRitchie, Y Sammy Choi, Susan C J Sumner
An Adverse Event Following Immunization (AEFI) is an adverse reaction to a vaccination that goes above and beyond the usual side effects associated with vaccinations. One serious AEFI related to the smallpox vaccine is myopericarditis. Metabolomics involves the study of the low molecular weight metabolite profile of cells, tissues, and biological fluids, and provides a functional readout of the phenotype. Metabolomics may help identify a particular metabolic signature in serum of subjects who are predisposed to developing AEFIs...
March 1, 2017: Vaccine
https://www.readbyqxmd.com/read/28168878/network-marker-selection-for-untargeted-lc-ms-metabolomics-data
#7
Qingpo Cai, Jessica A Alvarez, Jian Kang, Tianwei Yu
Untargeted metabolomics using high-resolution liquid chromatography - mass spectrometry (LC-MS) is becoming one of the major areas of high-throughput biology. Functional analysis, i.e. analyzing the data based on metabolic pathways or the genome-scale metabolic network, is critical in feature selection and interpretation of metabolomics data. One of the main challenges in the functional analyses is the lack of the feature identity in the LC-MS data itself. By matching mass-to-charge ratio (m/z) values of the features to theoretical values derived from known metabolites, some features can be matched to one or more known metabolites...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28168106/untargeted-metabolomics-approach-for-unraveling-robust-biomarkers-of-nutritional-status-in-fasted-gilthead-sea-bream-sparus-aurata
#8
Ruben Gil-Solsona, Jaime Nácher-Mestre, Leticia Lacalle-Bergeron, Juan Vicente Sancho, Josep Alvar Calduch-Giner, Félix Hernández, Jaume Pérez-Sánchez
A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares-Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components...
2017: PeerJ
https://www.readbyqxmd.com/read/28166731/metabolomic-analysis-of-pathways-related-to-rice-grain-chalkiness-by-a-notched-belly-mutant-with-high-occurrence-of-white-belly-grains
#9
Zhaomiao Lin, Xincheng Zhang, Zunxin Wang, Yutong Jiang, Zhenghui Liu, Danny Alexander, Ganghua Li, Shaohua Wang, Yanfeng Ding
BACKGROUND: Grain chalkiness is a highly undesirable trait deleterious to rice appearance and milling quality. The physiological and molecular foundation of chalkiness formation is still partially understood, because of the complex interactions between multiple genes and growing environments. RESULTS: We report the untargeted metabolomic analysis of grains from a notched-belly mutant (DY1102) with high percentage of white-belly, which predominantly occurs in the bottom part proximal to the embryo...
February 7, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28166632/metabolomics-based-elucidation-of-active-metabolic-pathways-in-erythrocytes-and-hsc-derived-reticulocytes
#10
Anubhav Srivastava, Krystal J Evans, Anna Elizabeth Sexton, Louis Schofield, Darren John Creek
A detailed analysis of the metabolic state of human stem cell derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high resolution LC-MS based, untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable isotope-labelled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28159289/untargeted-metabolomics-based-on-ultra-high-performance-liquid-chromatography-high-resolution-mass-spectrometry-merged-with-chemometrics-a-new-predictable-tool-for-an-early-detection-of-mycotoxins
#11
Josep Rubert, Laura Righetti, Milena Stranska-Zachariasova, Zbynek Dzuman, Jana Chrpova, Chiara Dall'Asta, Jana Hajslova
In order to explore the early detection of mycotoxins in wheat three standardized approaches (Fusarium disease severity, PCR assays for Fusarium spp. identification and mycotoxin quantification) and a novel untargeted metabolomics strategy were jointly assessed. In the first phase of this research, standardized approaches were able to quantify mycotoxins and identify Fusarium spp. Then, an UHPLC-QTOF metabolic fingerprinting method was developed to investigate plant-pathogen cross-talk. At the same time, chemometrics analysis demonstrated to be a powerful tool in order to distinguish low and strong infection levels...
June 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28133682/uhplc-q-tof-ms-based-plasma-metabolomics-reveals-the-metabolic-perturbations-by-manganese-exposure-in-rat-models
#12
Hui Wang, Zhiqi Liu, Shengyi Wang, Dongan Cui, Xinke Zhang, Yongming Liu, Yihua Zhang
Although manganese (Mn) is an essential metal ion biological cofactor, high concentrations could potentially induce an accumulation in the brain and lead to manganism. However, there is no "gold standard" for manganism assessment due to a lack of objective biomarkers. We hypothesized that Mn-induced alterations are associated with metabolic responses to manganism. Here we use an untargeted metabolomics approach by performing ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) on control and Mn-treated rat plasma, to identify metabolic disruptions under high Mn exposure conditions...
January 30, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28132861/global-and-untargeted-metabolomics-evidence-of-the-protective-effect-of-different-extracts-of-dipsacus-asper-wall-ex-c-b-clarke-on-estrogen-deficiency-after-ovariectomia-in-rats
#13
Yi Tao, Xi Chen, Weidong Li, Baochang Cai, Liuqing Di, Liyun Shi, Lihong Hu
ETHNOPHARMACOLOGICAL RELEVANCE: Dipsacus asper Wall. ex C.B. Clarke (DA) is an effectively traditional Chinese medicine for treating osteoporosis and bone fracture. Until now, studies on pharmacological mechanism of DA mostly centered on cell and gene level, little is known about its metabolic signatures. The aim of this study is to investigate the anti-osteoporosis effects of crude and wine-processed DA by global and untargeted metabolic profiling of rats serum, liver and kidney derived from sham, model and treated groups...
January 26, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28132177/metabolomic-strategies-involving-mass-spectrometry-combined-with-liquid-and-gas-chromatography
#14
Aline Soriano Lopes, Elisa Castañeda Santa Cruz, Alessandra Sussulini, Aline Klassen
Amongst all omics sciences, there is no doubt that metabolomics is undergoing the most important growth in the last decade. The advances in analytical techniques and data analysis tools are the main factors that make possible the development and establishment of metabolomics as a significant research field in systems biology. As metabolomic analysis demands high sensitivity for detecting metabolites present in low concentrations in biological samples, high-resolution power for identifying the metabolites and wide dynamic range to detect metabolites with variable concentrations in complex matrices, mass spectrometry is being the most extensively used analytical technique for fulfilling these requirements...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28112165/loss-of-merlin-induces-metabolomic-adaptation-that-engages-dependence-on-hedgehog-signaling
#15
Shamik Das, William P Jackson, Jeevan K Prasain, Ann Hanna, Sarah K Bailey, J Allan Tucker, Sejong Bae, Landon S Wilson, Rajeev S Samant, Stephen Barnes, Lalita A Shevde
The tumor suppressor protein Merlin is proteasomally degraded in breast cancer. We undertook an untargeted metabolomics approach to discern the global metabolomics profile impacted by Merlin in breast cancer cells. We discerned specific changes in glutathione metabolites that uncovered novel facets of Merlin in impacting the cancer cell metabolome. Concordantly, Merlin loss increased oxidative stress causing aberrant activation of Hedgehog signaling. Abrogation of GLI-mediated transcription activity compromised the aggressive phenotype of Merlin-deficient cells indicating a clear dependence of cells on Hedgehog signaling...
January 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28107906/development-of-data-independent-acquisition-workflows-for-metabolomic-analysis-on-a-quadrupole-orbitrap-platform
#16
Juntuo Zhou, Yuhua Li, Xi Chen, Lijun Zhong, Yuxin Yin
Untargeted metabolomic profiling has been widely used in recent years. However, the low reproducibility of the data-dependent acquisition (DDA) strategy presents a major bottleneck that considerably limits the reliability of metabolomic studies in biological and clinical research. The data-independent acquisition (DIA) strategy is proposed to solve the above-mentioned problem, and it is gaining popularity. This paper presents a novel approach for performing metabolomic analysis using an untargeted, liquid chromatography-data independent-mass spectrometry (LC-DIA-MS) strategy on a quadrupole-Orbitrap platform...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28097070/sponge-exhalent-seawater-contains-a-unique-chemical-profile-of-dissolved-organic-matter
#17
Cara L Fiore, Christopher J Freeman, Elizabeth B Kujawinski
Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater)...
2017: PeerJ
https://www.readbyqxmd.com/read/28093124/the-co-feature-ratio-a-novel-method-for-the-measurement-of-chromatographic-and-signal-selectivity-in-lc-ms-based-metabolomics
#18
Albert Elmsjö, Jakob Haglöf, Mikael K R Engskog, Marika Nestor, Torbjörn Arvidsson, Curt Pettersson
Evaluation of analytical procedures, especially in regards to measuring chromatographic and signal selectivity, is highly challenging in untargeted metabolomics. The aim of this study was to suggest a new straightforward approach for a systematic examination of chromatographic and signal selectivity in LC-MS-based metabolomics. By calculating the ratio between each feature and its co-eluting features (the co-features), a measurement of the chromatographic selectivity (i.e. extent of co-elution) as well as the signal selectivity (e...
March 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28090435/-13-c-metabolomics-nmr-and-iroa-for-unknown-identification
#19
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
#20
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 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
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