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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/27921456/capillary-electrophoresis-mass-spectrometry-as-a-tool-for-untargeted-metabolomics
#1
Antonia García, Joanna Godzien, Ángeles López-Gonzálvez, Coral Barbas
Highly polar and ionic metabolites, such as sugars, most amino acids, organic acids or nucleotides are not retained by conventional reversed-phase LC columns and polar stationary phases and hydrophilic-interaction LC lacks of robustness, which is still limiting their applications for untargeted metabolomics where reproducibility is a must. Biological samples such as blood, urine or even tissues include many hydrophilic compounds secreted from cells, their analysis is essential for biomarker discovery, disease progression or treatment effects...
January 2017: Bioanalysis
https://www.readbyqxmd.com/read/27913891/biotransformation-of-2-4-dinitroanisole-by-a-fungal-penicillium-sp
#2
Hunter W Schroer, Kathryn L Langenfeld, Xueshu Li, Hans-Joachim Lehmler, Craig L Just
Insensitive munitions explosives are new formulations that are less prone to unintended detonation compared to traditional explosives. While these formulations have safety benefits, the individual constituents, such as 2,4-dinitroanisole (DNAN), have an unknown ecosystem fate with potentially toxic impacts to flora and fauna exposed to DNAN and/or its metabolites. Fungi may be useful in remediation and have been shown to degrade traditional nitroaromatic explosives, such as 2,4,6-trinitrotoluene and 2,4-dinitrotoluene, that are structurally similar to DNAN...
December 2, 2016: Biodegradation
https://www.readbyqxmd.com/read/27910903/prostate-cancer-patients-negative-biopsy-controls-discrimination-by-untargeted-metabolomics-analysis-of-urine-by-lc-qtof-upstream-information-on-other-omics
#3
M A Fernández-Peralbo, E Gómez-Gómez, M Calderón-Santiago, J Carrasco-Valiente, J Ruiz-García, M J Requena-Tapia, M D Luque de Castro, F Priego-Capote
The existing clinical biomarkers for prostate cancer (PCa) diagnosis are far from ideal (e.g., the prostate specific antigen (PSA) serum level suffers from lack of specificity, providing frequent false positives leading to over-diagnosis). A key step in the search for minimum invasive tests to complement or replace PSA should be supported on the changes experienced by the biochemical pathways in PCa patients as compared to negative biopsy control individuals. In this research a comprehensive global analysis by LC-QTOF was applied to urine from 62 patients with a clinically significant PCa and 42 healthy individuals, both groups confirmed by biopsy...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909055/molecular-identification-of-d-ribulokinase-in-budding-yeast-and-mammals
#4
Charandeep Singh, Enrico Glaab, Carole L Linster
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins are predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and of its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27894005/uplc-qtof-analysis-reveals-metabolomic-changes-in-the-flag-leaf-of-wheat-triticum-aestivum-l-under-low-nitrogen-stress
#5
Yang Zhang, Xin-Ming Ma, Xiao-Chun Wang, Ji-Hong Liu, Bing-Yan Huang, Xiao-Yang Guo, Shu-Ping Xiong, Gui-Xiao La
Wheat is one of the most important grain crop plants worldwide. Nitrogen (N) is an essential macronutrient for the growth and development of wheat and exerts a marked influence on its metabolites. To investigate the influence of low nitrogen stress on various metabolites of the flag leaf of wheat (Triticum aestivum L.), a metabolomic analysis of two wheat cultivars under different induced nitrogen levels was conducted during two important growth periods based on large-scale untargeted metabolomic analysis using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF)...
November 18, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27874308/microbial-metabolomic-and-immunologic-dynamics-in-a-relapsing-genetic-mouse-model-of-colitis-induced-by-t-synthase-deficiency
#6
Jonathan P Jacobs, Lin Lin, Maryam Goudarzi, Paul Ruegger, Dermot P B McGovern, Albert J Fornace, James Borneman, Lijun Xia, Jonathan Braun
Intestinal dysbiosis is thought to confer susceptibility to inflammatory bowel disease (IBD), but it is unknown whether dynamic changes in the microbiome contribute to fluctuations in disease activity. We explored this question using mice with intestine-specific deletion of C1galt1 (also known as T-synthase) (Tsyn mice). These mice develop spontaneous microbiota-dependent colitis with a remitting/relapsing course due to loss of mucin core-1 derived O-glycans. 16S rRNA sequencing and untargeted metabolomics demonstrated age-specific perturbations in the intestinal microbiome and metabolome of Tsyn mice compare with littermate controls at weeks 3 (disease onset), 5 (during remission), and 9 (after relapse)...
November 22, 2016: Gut Microbes
https://www.readbyqxmd.com/read/27871066/a-novel-amino-acid-and-metabolomics-signature-in-mice-overexpressing-muscle-uncoupling-protein-3
#7
Céline Aguer, Brian D Piccolo, Oliver Fiehn, Sean H Adams, Mary-Ellen Harper
Uncoupling protein 3 (UCP3) is highly selectively expressed in skeletal muscle and is known to lower mitochondrial reactive oxygen species and promote fatty acid oxidation; however, the global impact of UCP3 activity on skeletal muscle and whole-body metabolism have not been extensively studied. We utilized untargeted metabolomics to identify novel metabolites that distinguish mice overexpressing UCP3 in muscle, both at rest and after exercise regimens that challenged muscle metabolism, to potentially unmask subtle phenotypes...
November 10, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27856765/topic-modeling-for-untargeted-substructure-exploration-in-metabolomics
#8
Justin Johan Jozias van der Hooft, Joe Wandy, Michael P Barrett, Karl E V Burgess, Simon Rogers
The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases of known fragmented molecules...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27846849/untargeted-metabolomics-unravels-functionalities-of-phosphorylation-sites-in-saccharomyces-cerevisiae
#9
Zrinka Raguz Nakic, Gerhard Seisenbacher, Francesc Posas, Uwe Sauer
BACKGROUND: Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousands of phosphorylation sites (phosphosites) in single experiments. However, functionality of the vast majority of these sites remains unclear and we lack suitable approaches to evaluate functional relevance at a pace that matches their detection. RESULTS: Here, we assess functionality of 26 phosphosites by introducing phosphodeletion and phosphomimic mutations in 25 metabolic enzymes and regulators from the TOR and HOG signaling pathway in Saccharomyces cerevisiae by phenotypic analysis and untargeted metabolomics...
November 15, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27827887/a-conversation-on-data-mining-strategies-in-lc-ms-untargeted-metabolomics-pre-processing-and-pre-treatment-steps
#10
Fidele Tugizimana, Paul A Steenkamp, Lizelle A Piater, Ian A Dubery
Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the "exhaustive" extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter...
November 3, 2016: Metabolites
https://www.readbyqxmd.com/read/27827849/metmatch-a-semi-automated-software-tool-for-the-comparison-and-alignment-of-lc-hrms-data-from-different-metabolomics-experiments
#11
Stefan Koch, Christoph Bueschl, Maria Doppler, Alexandra Simader, Jacqueline Meng-Reiterer, Marc Lemmens, Rainer Schuhmacher
Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented...
November 2, 2016: Metabolites
https://www.readbyqxmd.com/read/27825712/untargeted-metabolomic-analysis-of-human-serum-samples-associated-with-exposure-levels-of-persistent-organic-pollutants-indicate-important-perturbations-in-sphingolipids-and-glycerophospholipids-levels
#12
Daniel Carrizo, Olivier P Chevallier, Jayne V Woodside, Sarah F Brennan, Marie M Cantwell, Geraldine Cuskelly, Christopher T Elliott
Persistent organic pollutants (POPs) are distributed globally and are associated with adverse health effects in humans. A study combining gas chromatography-mass spectrometry (GC-MS), high resolution mass spectrometry (UPLC-QTof-MS) and chemometrics for the analysis of adult human serum samples was undertaken. Levels of serum POPs found were in the low range of what has been reported in similar populations across Europe (median 33.84 p, p'-DDE, 3.02 HCB, 83.55 β-HCH, 246.62 PCBs ng/g lipids). Results indicated that compounds concentrations were significantly different between the two groups of POPs exposure (high vs low) and classes (DDE, β-HCH, HCB, PCBs)...
November 5, 2016: Chemosphere
https://www.readbyqxmd.com/read/27825627/post-acquisition-spectral-stitching-an-alternative-approach-for-data-processing-in-untargeted-metabolomics-by-uhplc-esi-hrms
#13
Eirini Baira, Eleni Siapi, Panagiotis Zoumpoulakis, Deligeorgis Stelios G, Alexios-Leandros Skaltsounis, Evagelos Gikas
INTRODUCTION: In the case of the MS-based metabolomics, the large number of false positives remains a fundamental issue. OBJECTIVE: The aim of this study was to develop a new strategy, which highlights the number of the reliable features i.e. the detected features that correspond to a consistent peak according to chromatographic and mass spectrometric criteria. METHOD: For the analysis blood samples from 20 chickens, which were administrated with naringin and 9 samples from control, were analyzed by UHPLC-HRMS (Orbitrap Velos)...
October 24, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/27822535/an-integrated-metabolomic-and-genomic-mining-workflow-to-uncover-the-biosynthetic-potential-of-bacteria
#14
Maria Maansson, Nikolaj G Vynne, Andreas Klitgaard, Jane L Nybo, Jette Melchiorsen, Don D Nguyen, Laura M Sanchez, Nadine Ziemert, Pieter C Dorrestein, Mikael R Andersen, Lone Gram
Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains...
May 2016: MSystems
https://www.readbyqxmd.com/read/27822524/from-sample-to-multi-omics-conclusions-in-under-48-hours
#15
Robert A Quinn, Jose A Navas-Molina, Embriette R Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J Minich, Alexey V Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C Dorrestein, Rob Knight
Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology...
March 2016: MSystems
https://www.readbyqxmd.com/read/27799660/toward-noninvasive-diagnosis-of-iga-nephropathy-a-pilot-urinary-metabolomic-and-proteomic-study
#16
Michaela Neprasova, Dita Maixnerova, Jan Novak, Colin Reily, Bruce A Julian, Jan Boron, Petr Novotny, Miloslav Suchanek, Vladimir Tesar, Petr Kacer
IgA nephropathy is diagnosed by renal biopsy, an invasive procedure with a risk of significant complications. Noninvasive approaches are needed for possible diagnostic purposes and especially for monitoring disease activity or responses to treatment. In this pilot project, we assessed the utility of urine samples as source of biomarkers of IgA nephropathy. We used spot urine specimens from 19 healthy controls, 11 patients with IgA nephropathy, and 8 renal-disease controls collected on day of renal biopsy. Urine samples were analyzed using untargeted metabolomic and targeted proteomic analyses by several experimental techniques: liquid chromatography coupled with mass spectrometry, immunomagnetic isolation of target proteins coupled with quantitation by mass spectrometry, and protein arrays...
2016: Disease Markers
https://www.readbyqxmd.com/read/27781435/detecting-beer-intake-by-unique-metabolite-patterns
#17
Gözde Gürdeniz, Morten Georg Jensen, Sebastian Meier, Lene Bech, Erik Lund, Lars Ove Dragsted
Evaluation of health related effects of beer intake is hampered by the lack of accurate tools for assessing intakes (biomarkers). Therefore, we identified plasma and urine metabolites associated with recent beer intake by untargeted metabolomics and established a characteristic metabolite pattern representing raw materials and beer production as a qualitative biomarker of beer intake. In a randomized, crossover, single-blinded meal study (MSt1) 18 participants were given one at a time four different test beverages: strong, regular and non-alcoholic beers and a soft drink...
October 26, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27771102/integrating-targeted-glycomics-and-untargeted-metabolomics-to-investigate-the-processing-chemistry-of-herbal-medicines-a-case-study-on-rehmanniae-radix
#18
Li Zhou, Jin-Di Xu, Shan-Shan Zhou, Qian Mao, Ming Kong, Hong Shen, Xiu-Yang Li, Su-Min Duan, Jun Xu, Song-Lin Li
It is well-recognized that multiple components, the majority of which are secondary metabolites and carbohydrates, collectively contribute to the therapeutic effects of herbal medicines. The chemical characterization of herbal medicines has focused extensively on secondary metabolites but has largely overlooked carbohydrates. Here, we proposed an integrated chromatographic technique based targeted glycomics and untargeted metabolomics strategy simultaneously determining carbohydrates and secondary metabolites for the overall chemical profiling of herbal medicines; this strategy was successfully exemplified in an investigation of processing chemistry of Rehmanniae Radix (RR), a Chinese medicinal herb...
October 17, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27768289/large-scale-prediction-of-collision-cross-section-values-for-metabolites-in-ion-mobility-mass-spectrometry
#19
Zhiwei Zhou, Xiaotao Shen, Jia Tu, Zheng-Jiang Zhu
The rapid development of metabolomics has significantly advanced health and disease related research. However, metabolite identification remains a major analytical challenge for untargeted metabolomics. While the use of collision cross-section (CCS) values obtained in ion mobility - mass spectrometry (IM-MS) effectively increases identification confidence of metabolites, it is restricted by the limited number of available CCS values for metabolites. Here, we demonstrated the use of a machine-learning algorithm called support vector regression (SVR) to develop a prediction method that utilized 14 common molecular descriptors to predict CCS values for metabolites...
October 21, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27758107/untargeted-metabolomics-analysis-of-abcc6-deficient-mice-discloses-an-altered-metabolic-liver-profile
#20
Mie Rostved Rasmussen, Kirstine Lykke Nielsen, Mia Roest Laursen, Camilla Bak Nielsen, Pia Svendsen, Henrik Dimke, Erik Ilsø Christensen, Mogens Johannsen, Søren Kragh Moestrup
Loss-of-function mutations in the transmembrane ABCC6 transport protein cause pseudoxanthoma elasticum - an ectopic, metabolic mineralization disorder affecting the skin, eye and vessels. ABCC6 is assumed to mediate efflux of one or several small molecule compounds from the liver cytosol to the circulation. Untargeted metabolomics using liquid chromatography mass spectrometry was employed to inspect liver cytosolic extracts from mice with targeted disruption of the Abcc6 gene. Absence of the ABCC6 protein induced an altered profile of metabolites in the liver causing accumulation of compounds as more features were upregulated than downregulated in ABCC6-deficient mice...
October 19, 2016: Journal of Proteome Research
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