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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/28533028/optimizing-targeted-untargeted-metabolomics-by-automating-gas-chromatography-mass-spectrometry-gc-gc-ms-and-gc-ms-workflows
#1
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
#2
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
#3
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...
May 18, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28508929/untargeted-metabolomic-analysis-of-tomato-pollen-development-and-heat-stress-response
#4
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
#5
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 15, 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
#6
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...
May 23, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28497560/untargeted-metabolomic-analysis-of-capsicum-spp-by-gc-ms
#7
Bianca Camargo Aranha, Jessica Fernanda Hoffmann, Rosa Lia Barbieri, Cesar Valmor Rombaldi, Fábio Clasen Chaves
INTRODUCTION: In order to conserve the biodiversity of Capsicum species and find genotypes with potential to be utilised commercially, Embrapa Clima Temperado maintains an active germplasm collection (AGC) that requires characterisation, enabling genotype selection and support for breeding programmes. OBJECTIVE: The objective of this study was to characterise pepper accessions from the Embrapa Clima Temperado AGC and differentiate species based on their metabolic profile using an untargeted metabolomics approach...
May 11, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28484391/quantitative-evaluation-of-the-compatibility-effects-of-huangqin-decoction-on-the-treatment-of-irinotecan-induced-gastrointestinal-toxicity-using-untargeted-metabolomics
#8
Dong-Ni Cui, Xu Wang, Jia-Qing Chen, Bo Lv, Pei Zhang, Wei Zhang, Zun-Jian Zhang, Feng-Guo Xu
Huangqin decoction (HQD), a traditional Chinese medicine (TCM), has been widely used to treat gastrointestinal syndrome in China for thousands of years. Chemotherapy drug irinotecan (CPT-11) is used clinically to treat various kinds of cancers but limited by its side effects, especially delayed diarrhea. Nowadays, HQD has been proved to be effective in attenuating the intestinal toxicity induced by CPT-11. HQD consists of four medicinal herbs including Scutellaria baicalensis Georgi, Glycyrrhiza uralensis Fisch, Paeonia lactiflora Pall, and Ziziphus jujuba Mill...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28480907/metabolomic-analysis-of-the-effects-of-cadmium-and-copper-treatment-in-oryza-sativa-l-using-untargeted-liquid-chromatography-coupled-to-high-resolution-mass-spectrometry-and-all-ion-fragmentation
#9
Meritxell Navarro-Reig, Joaquim Jaumot, Benjamín Piña, Encarnación Moyano, Maria Teresa Galceran, Romà Tauler
While the knowledge of plant metabolomes has increased in the last few years, their response to the presence of toxicants is still poorly understood. Here, we analyse the metabolomic changes in Japanese rice (Oryza sativa var. Japonica) upon exposure to heavy metals (Cd(ii) and Cu(ii)) in concentrations from 10 to 1000 μM. After harvesting, rice metabolites were extracted from aerial parts of the plants and analysed by HPLC (HILIC TSK gel amide-80 column) coupled to a mass spectrometer quadrupole-Orbitrap (Q-Exactive)...
May 8, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28473744/untargeted-metabolomics-reveals-a-mild-impact-of-remote-ischemic-conditioning-on-the-plasma-metabolome-and-%C3%AE-hydroxybutyrate-as-a-possible-cardioprotective-factor-and-biomarker-of-tissue-ischemia
#10
Mia Roest Laursen, Jakob Hansen, Casper Elkjær, Ninna Stavnager, Camilla Bak Nielsen, Kasper Pryds, Jacob Johnsen, Jan Møller Nielsen, Hans Erik Bøtker, Mogens Johannsen
INTRODUCTION: Remote ischemic conditioning (RIC) is a maneuver by which short non-lethal ischemic events are applied on distant organs or limbs to reduce ischemia and reperfusion injuries caused by e.g. myocardial infarct. Although intensively investigated, the specific mechanism of this protective phenomenon remains incompletely understood and in particular, knowledge on the role of small metabolites is scarce. OBJECTIVES: In this study, we aimed to study perturbations in the plasma metabolome following RIC and gain insight into metabolic changes by the intervention as well as to identify potential novel cardio-protective metabolites...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28440083/systems-metabolomics-for-prediction-of-metabolic-syndrome
#11
Estelle Pujos-Guillot, Marion Brandolini, Mélanie Pétéra, Dhouha Grissa, Charlotte Joly, Bernard Lyan, Éléonore Herquelot, Sébastien Czernichow, Marie Zins, Marcel Goldberg, Blandine Comte
The evolution of human health is a continuum of transitions, involving multifaceted processes at multiple levels, and there is an urgent need for integrative biomarkers that can characterize and predict progression toward disease development. The objective of this work was to perform a systems metabolomics approach to predict metabolic syndrome (MetS) development. A case-control design was used within the French occupational GAZEL cohort (n = 112 males: discovery study; n = 94: replication/validation study)...
May 4, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28424615/huangqin-decoction-attenuates-cpt-11-induced-gastrointestinal-toxicity-by-regulating-bile-acids-metabolism-homeostasis
#12
Xu Wang, Dong-Ni Cui, Xiao-Min Dai, Jing Wang, Wei Zhang, Zun-Jian Zhang, Feng-Guo Xu
Irinotecan (CPT-11) is a potent chemotherapeutic agent, however, its clinical usage is often limited by the induction of severe gastrointestinal (GI) toxicity, especially late-onset diarrhea. HuangQin Decoction (HQD), commonly used for the treatment of GI ailments, has been proved could significantly ameliorate the intestinal toxicity of CPT-11. To reveal the mechanisms of CPT-11-induced toxicity and the modulation effects of HQD, a previous untargeted metabolomics study was performed and the results indicated that HQD may protect the GI tract by altering the metabolism of bile acids (BAs)...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28402628/influences-of-normalization-method-on-biomarker-discovery-in-gas-chromatography-mass-spectrometry-based-untargeted-metabolomics-what-should-be-considered
#13
Jiaqing Chen, Pei Zhang, Mengying Lv, Huimin Guo, Yin Huang, Zunjian Zhang, Fengguo Xu
Data reduction techniques in gas chromatography-mass spectrometry-based untargeted metabolomics has made the following workflow of data analysis more lucid. However, the normalization process still perplexes researchers, and its effects are always ignored. In order to reveal the influences of normalization method, five representative normalization methods (mass spectrometry total useful signal, median, probabilistic quotient normalization, remove unwanted variation-random, and systematic ratio normalization) were compared in three real data sets with different types...
April 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28401628/metabolomics-reveals-new-metabolic-perturbations-in-children-with-type-1-diabetes
#14
Alfonso Galderisi, Paola Pirillo, Vittoria Moret, Matteo Stocchero, Antonina Gucciardi, Giorgio Perilongo, Carlo Moretti, Carlamaria Monciotti, Giuseppe Giordano, Eugenio Baraldi
OBJECTIVE: Using an untargeted metabolomics approach we investigated the metabolome of children with type 1 diabetes (T1D) in comparison with healthy peers and explored the contribution of HbA1c and clinical features to the observed difference. RESEARCH DESIGN AND METHODS: We enrolled children with T1D aged 6-15 years, attending the pediatric diabetes clinic of University of Padova (Italy). Healthy controls were enrolled on voluntary basis and matched for age, sex, pubertal status, body mass index (BMI)...
April 12, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28391692/customized-consensus-spectral-library-building-for-untargeted-quantitative-metabolomics-analysis-with-data-independent-acquisition-mass-spectrometry-and-metabodia-workflow
#15
Gengbo Chen, Scott Walmsley, Gemmy C M Cheung, Liyan Chen, Ching-Yu Cheng, Roger W Beuerman, Tien Yin Wong, Lei Zhou, Hyungwon Choi
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups...
April 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28390668/strategy-for-comparative-untargeted-metabolomics-reveals-honey-markers-of-different-floral-and-geographic-origins-using-ultrahigh-performance-liquid-chromatography-hybrid-quadrupole-orbitrap-mass-spectrometry
#16
Yi Li, Yue Jin, Shupeng Yang, Wenwen Zhang, Jinzhen Zhang, Wen Zhao, Lanzhen Chen, Yaqin Wen, Yongxin Zhang, Kaizhi Lu, Yaping Zhang, Jinhui Zhou, Shuming Yang
Honey discrimination based on floral and geographic origins is limited by the ability to determine reliable markers because developing hypothetical substances in advance considerably limits the throughput of metabolomics studies. Here, we present a novel approach to screen and elucidate honey markers based on comparative untargeted metabolomics using ultrahigh-performance liquid chromatography-hybrid quadrupole-orbitrap mass spectrometry (UHPLC-Q-Orbitrap). To reduce metabolite information losses during sample preparation, the honey samples were dissolved in water and centrifuged to remove insoluble particles prior to UHPLC-Q-Orbitrap analysis in positive and negative electrospray ionization modes...
March 28, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28378853/serum-metabolomic-profiling-highlights-pathways-associated-with-liver-fat-content-in-a-general-population-sample
#17
M Koch, S Freitag-Wolf, S Schlesinger, J Borggrefe, J R Hov, M K Jensen, J Pick, M R P Markus, T Höpfner, G Jacobs, S Siegert, A Artati, G Kastenmüller, W Römisch-Margl, J Adamski, T Illig, M Nothnagel, T H Karlsen, S Schreiber, A Franke, M Krawczak, U Nöthlings, W Lieb
BACKGROUND/OBJECTIVES: Fatty liver disease (FLD) is an important intermediate trait along the cardiometabolic disease spectrum and strongly associates with type 2 diabetes. Knowledge of biological pathways implicated in FLD is limited. An untargeted metabolomic approach might unravel novel pathways related to FLD. SUBJECTS/METHODS: In a population-based sample (n=555) from Northern Germany, liver fat content was quantified as liver signal intensity using magnetic resonance imaging...
April 5, 2017: European Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28367722/feline-urine-metabolomic-signature-characterization-of-low-molecular-weight-substances-in-urine-from-domestic-cats
#18
Sol-Maiam Rivera-Vélez, Nicolas F Villarino
Objectives This aim of this study was to characterize the composition and content of the feline urine metabolome. Methods Eight healthy domestic cats were acclimated at least 10 days before starting the study. Urine samples (~2 ml) were collected by ultrasound-guided cystocentesis. Samples were centrifuged at 1000 × g for 8 mins, and the supernatant was analyzed by gas chromatography/time-of-flight mass spectrometery. The urine metabolome was characterized using an untargeted metabolomics approach. Results Three hundred and eighteen metabolites were detected in the urine of the eight cats...
March 1, 2017: Journal of Feline Medicine and Surgery
https://www.readbyqxmd.com/read/28365236/the-assessment-of-the-chronic-hepatotoxicity-induced-by-polygoni-multiflori-radix-in-rats-a-pilot-study-by-using-untargeted-metabolomics-method
#19
Xin-Hua Xia, Yuan-Yuan Yuan, Mei Liu
Polygoni Multiflori Radix is the dried root of Polygonum multiflorum Thunb officially recorded in the Chinese Pharmacopoeia as HeShouWu (HSW) in Chinese pinyin. The processed HSW are commonly used in TCM to treat liver disease and Chinese Pharmacopoeia has described the actions of it to tonify liver-kidney, replenish essence and blood, blacken beard and hair, strengthen sinew and bone, and resolve turbidity and lower lipid hence making it use not only as a herbal medicine in TCM but also as supplementary food in health care...
May 5, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28358014/untargeted-metabolomics-analysis-reveals-key-pathways-responsible-for-the-synergistic-killing-of-colistin-and-doripenem-combination-against-acinetobacter-baumannii
#20
Mohd Hafidz Mahamad Maifiah, Darren J Creek, Roger L Nation, Alan Forrest, Brian T Tsuji, Tony Velkov, Jian Li
Combination therapy is deployed for the treatment of multidrug-resistant Acinetobacter baumannii, as it can rapidly develop resistance to current antibiotics. This is the first study to investigate the synergistic effect of colistin/doripenem combination on the metabolome of A. baumannii. The metabolite levels were measured using LC-MS following treatment with colistin (2 mg/L) or doripenem (25 mg/L) alone, and their combination at 15 min, 1 hr and 4 hr (n = 4). Colistin caused early (15 min and 1 hr) disruption of the bacterial outer membrane and cell wall, as demonstrated by perturbation of glycerophospholipids and fatty acids...
March 30, 2017: Scientific Reports
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