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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/28642031/clustering-of-ms-2-spectra-using-unsupervised-methods-to-aid-the-identification-of-secondary-metabolites-from-pseudomonas-aeruginosa
#1
Tobias Depke, Raimo Franke, Mark Brönstrup
Pseudomonas aeruginosa is an important opportunistic pathogen that produces a large arsenal of small molecule virulence factors and quorum sensing signal molecules. The annotation of these secondary metabolites in untargeted, mass spectrometry-based metabolomics is difficult, as many of them cannot be found in common metabolite databases, and as manual annotation is tedious. We therefore developed an algorithm named CluMSID that uses cosine similarities of product ion spectra and neutral loss patterns in combination with unsupervised clustering methods such as multidimensional scaling, density based clustering and hierarchical clustering to group structurally similar compounds and hence facilitate their annotation...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28635678/evaluation-of-classifier-performance-for-multiclass-phenotype-discrimination-in-untargeted-metabolomics
#2
Patrick J Trainor, Andrew P DeFilippis, Shesh N Rai
Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes. Despite this, a comprehensive and rigorous evaluation of the accuracy of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics datasets, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines (SVM), Artificial Neural Network, k-Nearest Neighbors (k-NN), and Naïve Bayes classification techniques for discrimination...
June 21, 2017: Metabolites
https://www.readbyqxmd.com/read/28631923/influence-of-ingesting-a-flavonoid-rich-supplement-on-the-metabolome-and-concentration-of-urine-phenolics-in-overweight-obese-women
#3
David C Nieman, Sivapriya Ramamoorthy, Colin D Kay, Courtney L Goodman, Christopher R Capps, Zach L Shue, Nicole Heyl, Mary H Grace
This study evaluated the effect of ingesting a flavonoid-rich supplement (329 mg/d) on total urine phenolics and shifts in plasma metabolites in overweight/obese female adults using untargeted metabolomics procedures. Participants (N=103, 18-65 y, BMI ≥ 25 kg/m2) were randomized to flavonoid (F) or placebo (P) groups for 12 weeks, with blood and 24-h urine samples collected pre-study, 4- and 12-weeks in a parallel design. Supplements were prepared as chewable tablets, and included vitamin C, wild bilberry fruit extract, green tea leaf extract, quercetin, caffeine, and omega 3 fatty acids...
June 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#4
Alexey V Melnik, Pieter C Dorrestein, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28627685/metabolomic-analysis-based-on-1h-nuclear-magnetic-resonance-spectroscopy-metabolic-profiles-in-tuberculous-malignant-and-transudative-pleural-effusion
#5
Cheng Wang, Jingjin Peng, Yanling Kuang, Jiaqiang Zhang, Luming Dai
Pleural effusion is a common clinical manifestation with various causes. Current diagnostic and therapeutic methods have exhibited numerous limitations. By involving the analysis of dynamic changes in low molecular weight catabolites, metabolomics has been widely applied in various types of disease and have provided platforms to distinguish many novel biomarkers. However, to the best of our knowledge, there are few studies regarding the metabolic profiling for pleural effusion. In the current study, 58 pleural effusion samples were collected, among which 20 were malignant pleural effusions, 20 were tuberculous pleural effusions and 18 were transudative pleural effusions...
June 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28621528/unsupervised-discovery-and-comparison-of-structural-families-across-multiple-samples-in-untargeted-metabolomics
#6
Justin Johan Jozias van der Hooft, Joe Wandy, Francesca Young, Sandosh Padmanabhan, Konstantinos Gerasimidis, Karl E V Burgess, Michael P Barrett, Simon Rogers
In untargeted metabolomics approaches, the inability to structurally annotate relevant features and map them to biochemical pathways is hampering the full exploitation of many metabolomics experiments. Furthermore, variable metabolic content across samples result in sparse feature matrices that are statistically hard to handle. Here, we introduce MS2LDA+ that tackles both above-mentioned problems. Previously, we presented MS2LDA, which extracts biochemically-relevant molecular substructures ('Mass2Motifs') from a collection of fragmentation spectra as sets of co-occurring molecular fragments and neutral losses, thereby recognizing building blocks of metabolomics...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28615704/the-early-metabolomic-response-of-adipose-tissue-during-acute-cold-exposure-in-mice
#7
Xiyuan Lu, Ashley Solmonson, Alessia Lodi, Sara M Nowinski, Enrique Sentandreu, Christopher L Riley, Edward M Mills, Stefano Tiziani
To maintain core body temperature in cold conditions, mammals activate a complex multi-organ metabolic response for heat production. White adipose tissue (WAT) primarily functions as an energy reservoir, while brown adipose tissue (BAT) is activated during cold exposure to generate heat from nutrients. Both BAT and WAT undergo specific metabolic changes during acute cold exposure. Here, we use an untargeted metabolomics approach to characterize the initial metabolic response to cold exposure in multiple adipose tissue depots in mice...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28613827/tuning-metabolome-coverage-in-reversed-phase-lc-ms-metabolomics-of-meoh-extracted-samples-using-the-reconstitution-solvent-composition
#8
Anna Lindahl, Siv Sääf, Janne Lehtiö, Anders Nordström
Considering the physicochemical diversity of the metabolome, untargeted metabolomics will inevitably discriminate against certain compound classes. Efforts are nevertheless made to maximize the metabolome coverage. Contrary to the main steps of a typical liquid chromatography-mass spectrometry (LC-MS) metabolomics workflow, such as metabolite extraction, the sample reconstitution step has not been optimized for maximal metabolome coverage. This sample concentration step typically occurs after metabolite extraction, when dried samples are reconstituted in a solvent for injection on column...
June 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28599708/quantification-of-metabolites-in-dried-blood-spots-by-direct-infusion-high-resolution-mass-spectrometry
#9
Monique G M de Sain-van der Velden, Maria van der Ham, Johan Gerrits, Hubertus C M T Prinsen, Marcel Willemsen, Mia L Pras-Raves, Judith J Jans, Nanda M Verhoeven-Duif
Diagnosis and treatment of inborn errors of metabolism (IEM) require the analysis of a variety of metabolites. These compounds are usually quantified by targeted platforms. High resolution mass spectrometry (HRMS) has the potential to detect hundreds to thousands of metabolites simultaneously. A chip-based nanoelectrospray source (chip-based nanoESI) enables the direct infusion of biological samples. Major advantages of this system include high sample throughput, no sample carryover, and low sample consumption...
August 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28597074/early-metabolic-markers-identify-potential-targets-for-the-prevention-of-type-2-diabetes
#10
Gopal Peddinti, Jeff Cobb, Loic Yengo, Philippe Froguel, Jasmina Kravić, Beverley Balkau, Tiinamaija Tuomi, Tero Aittokallio, Leif Groop
AIMS/HYPOTHESIS: The aims of this study were to evaluate systematically the predictive power of comprehensive metabolomics profiles in predicting the future risk of type 2 diabetes, and to identify a panel of the most predictive metabolic markers. METHODS: We applied an unbiased systems medicine approach to mine metabolite combinations that provide added value in predicting the future incidence of type 2 diabetes beyond known risk factors. We performed mass spectrometry-based targeted, as well as global untargeted, metabolomics, measuring a total of 568 metabolites, in a Finnish cohort of 543 non-diabetic individuals from the Botnia Prospective Study, which included 146 individuals who progressed to type 2 diabetes by the end of a 10 year follow-up period...
June 8, 2017: Diabetologia
https://www.readbyqxmd.com/read/28595722/knowledge-integration-strategies-for-untargeted-metabolomics-based-on-mcr-als-analysis-of-ce-ms-and-lc-ms-data
#11
Elena Ortiz-Villanueva, Fernando Benavente, Benjamín Piña, Victoria Sanz-Nebot, Romà Tauler, Joaquim Jaumot
In this work, two knowledge integration strategies based on multivariate curve resolution alternating least squares (MCR-ALS) were used for the simultaneous analysis of data from two metabolomic platforms. The benefits and the suitability of these integration strategies were demonstrated in a comparative study of the metabolite profiles from yeast (Saccharomyces cerevisiae) samples grown in non-fermentable (acetate) and fermentable (glucose) carbon source. Untargeted metabolomics data acquired by capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography-mass spectrometry (LC-MS) were jointly analysed...
July 25, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28580151/transcriptomic-and-metabolomic-analyses-of-cucumber-fruit-peels-reveal-a-developmental-increase-in-terpenoid-glycosides-associated-with-age-related-resistance-to-phytophthora-capsici
#12
Ben N Mansfeld, Marivi Colle, Yunyan Kang, A Daniel Jones, Rebecca Grumet
The oomycete, Phytophthora capsici, infects cucumber (Cucumis sativus L.) fruit. An age-related resistance (ARR) to this pathogen was previously observed in fruit of cultivar 'Vlaspik' and shown to be associated with the peel. Young fruits are highly susceptible, but develop resistance at ~10-12 days post pollination (dpp). Peels from resistant (16 dpp) versus susceptible (8 dpp) age fruit are enriched with genes associated with defense, and methanolic extracts from resistant age peels inhibit pathogen growth...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28575008/plasma-metabolome-and-skin-proteins-in-charcot-marie-tooth-1a-patients
#13
Beatriz Soldevilla, Carmen Cuevas-Martín, Clara Ibáñez, Fulvio Santacatterina, María A Alberti, Carolina Simó, Carlos Casasnovas, Celedonio Márquez-Infante, Teresa Sevilla, Samuel I Pascual, María Sánchez-Aragó, Carmen Espinos, Francesc Palau, José M Cuezva
OBJECTIVE: Charcot-Marie-Tooth 1A (CMT1A) disease is the most common inherited neuropathy that lacks of therapy and of molecular markers to assess disease severity. Herein, we have pursued the identification of potential biomarkers in plasma samples and skin biopsies that could define the phenotype of CMT1A patients at mild (Mi), moderate (Mo) and severe (Se) stages of disease as assessed by the CMT neuropathy score to contribute to the understanding of CMT pathophysiology and eventually inform of the severity of the disease...
2017: PloS One
https://www.readbyqxmd.com/read/28560878/serial-metabolome-changes-in-a-prospective-cohort-of-subjects-with-influenza-viral-infection-and-comparison-with-dengue-fever
#14
Liang Cui, Jinling Fang, Eng Eong Ooi, Yie Hou Lee
Influenza virus infection (IVI) and dengue virus infection (DVI) are major public health threats. Between IVI and DVI, clinical symptoms can be overlapping yet infection-specific, but host metabolome changes are not well-described. Untargeted metabolomics and targeted oxylipinomic analyses were performed on sera serially collected at three phases of infection from a prospective cohort study of adult subjects with either H3N2 influenza infection or dengue fever. Untargeted metabolomics identified 26 differential metabolites and major perturbed pathways included purine metabolism, fatty acid biosynthesis and β-oxidation, tryptophan metabolism, phospholipid catabolism and steroid hormone pathway...
May 31, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28533028/optimizing-targeted-untargeted-metabolomics-by-automating-gas-chromatography-mass-spectrometry-gc-gc-ms-and-gc-ms-workflows
#15
Albert Robbat, Nicole Kfoury, Eugene Baydakov, Yuriy Gankin
New database building and MS subtraction algorithms have been developed for automated, sequential two-dimensional gas chromatography/mass spectrometry (GC-GC/MS). This paper reports the first use of a database building tool, with full mass spectrum subtraction, that does not rely on high resolution MS data. The software was used to automatically inspect GC-GC/MS data of high elevation tea from Yunnan, China, to build a database of 350 target compounds. The database was then used with spectral deconvolution to identify 285 compounds by GC/MS of the same tea...
May 8, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28520403/integrated-strategy-for-unknown-ei-ms-identification-using-quality-control-calibration-curve-multivariate-analysis-ei-ms-spectral-database-and-retention-index-prediction
#16
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900 000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a "four-step" strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28518204/integrated-metabolomics-and-metallomics-analyses-in-acute-coronary-syndrome-patients
#17
Xuejiao Yin, Leonardo Pinto de Carvalho, Mark Y Chan, Sam Fong Yau Li
Acute coronary syndrome (ACS) is the leading cause of morbidity and mortality. Accurate risk prediction in ACS patients is critically important for helping clinicians make therapeutic decisions, such as recommending a more aggressive intervention and intensive follow-up. However, risk stratification in ACS patients remains challenging, and the identification of novel predictors is necessary for improving the prognostic prediction in ACS patients. We employed metallomics and untargeted metabolomics approaches to discover new biomarkers from the plasma samples of 20 ACS patients and 20 non-ACS patients...
June 21, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28508929/untargeted-metabolomic-analysis-of-tomato-pollen-development-and-heat-stress-response
#18
Marine J Paupière, Florian Müller, Hanjing Li, Ivo Rieu, Yury M Tikunov, Richard G F Visser, Arnaud G Bovy
Pollen development metabolomics. Developing pollen is among the plant structures most sensitive to high temperatures, and a decrease in pollen viability is often associated with an alteration of metabolite content. Most of the metabolic studies of pollen have focused on a specific group of compounds, which limits the identification of physiologically important metabolites. To get a better insight into pollen development and the pollen heat stress response, we used a liquid chromatography-mass spectrometry platform to detect secondary metabolites in pollen of tomato (Solanum lycopersicum L...
May 16, 2017: Plant Reproduction
https://www.readbyqxmd.com/read/28507131/involvement-of-a-gut-retina-axis-in-protection-against-dietary-glycemia-induced-age-related-macular-degeneration
#19
Sheldon Rowan, Shuhong Jiang, Tal Korem, Jedrzej Szymanski, Min-Lee Chang, Jason Szelog, Christa Cassalman, Kalavathi Dasuri, Christina McGuire, Ryoji Nagai, Xue-Liang Du, Michael Brownlee, Naila Rabbani, Paul J Thornalley, James D Baleja, Amy A Deik, Kerry A Pierce, Justin M Scott, Clary B Clish, Donald E Smith, Adina Weinberger, Tali Avnit-Sagi, Maya Lotan-Pompan, Eran Segal, Allen Taylor
Age-related macular degeneration (AMD) is the major cause of blindness in developed nations. AMD is characterized by retinal pigmented epithelial (RPE) cell dysfunction and loss of photoreceptor cells. Epidemiologic studies indicate important contributions of dietary patterns to the risk for AMD, but the mechanisms relating diet to disease remain unclear. Here we investigate the effect on AMD of isocaloric diets that differ only in the type of dietary carbohydrate in a wild-type aged-mouse model. The consumption of a high-glycemia (HG) diet resulted in many AMD features (AMDf), including RPE hypopigmentation and atrophy, lipofuscin accumulation, and photoreceptor degeneration, whereas consumption of the lower-glycemia (LG) diet did not...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28506062/lc-ms-untargeted-metabolomics-to-explain-the-signal-metabolites-inducing-browning-in-fresh-cut-lettuce
#20
Carlos J García, Rocío García-Villalba, María I Gil, Francisco A Tomas-Barberan
Enzymatic browning is one of the main causes of quality loss in lettuce as a prepared and ready-to-eat cut salad. An untargeted metabolomics approach using UPLC-ESI-QTOF-MS was performed to explain the wound response of lettuce after cutting and to identify the metabolites responsible of browning. Two cultivars of Romaine lettuce with different browning susceptibilities were studied at short time intervals after cutting. From the total 5975 entities obtained from the raw data after alignment, filtration reduced the number of features to 2959, and the statistical analysis found that only 1132 entities were significantly different...
June 7, 2017: Journal of Agricultural and Food Chemistry
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