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"Untargeted metabolomics"

Luisa Matos Do Canto, Catalin Marian, Rency S Varghese, Jaeil Ahn, Patricia A Da Cunha, Shawna Willey, Mary Sidawy, Janice D Rone, Amrita K Cheema, George Luta, Mohammad R Nezami Ranjbar, Habtom W Ressom, Bassem R Haddad
Identification of new biomarkers for breast cancer remains critical in order to enhance early detection of the disease and improve its prognosis. Towards this end, we performed an untargeted metabolomic analysis of breast ductal fluid using an ultra-performance liquid chromatography coupled with a quadrupole time-of-light (UPLC-QTOF) mass spectrometer. We investigated the metabolomic profiles of breast tumors using ductal fluid samples collected by ductal lavage (DL). We studied fluid from both the affected breasts and the unaffected contralateral breasts (as controls) from 43 women with confirmed unilateral breast cancer...
October 13, 2016: International Journal of Oncology
Carl Brunius, Lin Shi, Rikard Landberg
INTRODUCTION: Liquid chromatography-mass spectrometry (LC-MS) is a commonly used technique in untargeted metabolomics owing to broad coverage of metabolites, high sensitivity and simple sample preparation. However, data generated from multiple batches are affected by measurement errors inherent to alterations in signal intensity, drift in mass accuracy and retention times between samples both within and between batches. These measurement errors reduce repeatability and reproducibility and may thus decrease the power to detect biological responses and obscure interpretation...
2016: Metabolomics: Official Journal of the Metabolomic Society
Juntuo Zhou, Yuxin Yin
Advances in liquid chromatography-mass spectrometry (LC-MS) instruments and analytical strategies have brought about great progress in targeted metabolomics analysis. This methodology is now capable of performing precise targeted measurement of dozens or hundreds of metabolites in complex biological samples. Classic targeted quantification assay using the multiple reaction monitoring (MRM) mode has been the foundation of high-quality metabolite quantitation. However, utilization of this strategy in biological studies has been limited by its relatively low metabolite coverage and throughput capacity...
October 10, 2016: Analyst
Jordyn M Wolfand, Gregory H LeFevre, Richard G Luthy
Fipronil is a recalcitrant phenylpyrazole-based pesticide used for flea/tick treatment and termite control that is distributed in urban aquatic environments via stormwater and contributes to stream toxicity. We discovered that fipronil is rapidly metabolized (t1/2 = 4.2 d) by the white rot fungus Trametes versicolor to fipronil sulfone and multiple previously unknown fipronil transformation products, lowering fipronil concentration by 96.5%. Using an LC-QTOF-MS untargeted metabolomics approach, we identified four novel fipronil fungal transformation products: hydroxylated fipronil sulfone, glycosylated fipronil sulfone, and two compounds with unresolved structures...
October 12, 2016: Environmental Science. Processes & Impacts
Ruijun Li, Fengyu Li, Qiang Feng, Zhipeng Liu, Zhuye Jie, Bo Wen, Xun Xu, Shilong Zhong, Guanglei Li, Kunlun He
This study performed untargeted metabolomics for plasma samples from 40 coronary heart disease patients and 43 healthy controls by high-performance liquid chromatography coupled with mass spectrometry technology to find a set of effective biomarkers for CHD diagnosis and prognosis. The discriminating metabolites were extracted and analyzed by univariate and multivariate analysis methods. We found five metabolites (1-naphthol, 2-naphthol, methylitaconate, N-acetyl-d-glucosamine 6-phosphate and l-carnitine) contributing to the separation of CHD patients from healthy controls, and a subset of two metabolites in these five were identified as potential plasma biomarkers for CHD diagnosis...
September 22, 2016: Molecular BioSystems
Henrike Knacke, Maik Pietzner, Kieu Trinh Do, Werner Römisch-Margl, Gabi Kastenmüller, Uwe Völker, Henry Völzke, Jan Krumsiek, Anna Artati, Henri Wallaschofski, Matthias Nauck, Karsten Suhre, Jerzy Adamski, Nele Friedrich
OBJECTIVE: Insulin-like Growth Factor (IGF-I) is known for its various physiological and severe pathophysiological effects on human metabolism, however underlying molecular mechanisms still remain unsolved. To reveal possible molecular mechanisms mediating these effects, for the first time we associated serum IGF-I levels with multi-fluid untargeted metabolomics data. METHODS: Plasma/urine samples of 995 non-diabetic participants of the Study of Health in Pomerania (SHIP-TREND) were characterized by mass spectrometry...
October 6, 2016: Journal of Clinical Endocrinology and Metabolism
Oscar D Rangel-Huerta, Concepcion M Aguilera, Antonio Perez-de-la-Cruz, Fernando Vallejo, Francisco Tomas-Barberan, Angel Gil, Maria D Mesa
SCOPE: To identify biomarkers of orange juice (OJ) consumption containing different doses of polyphenols and to determine its impact on oxidative stress and inflammation using an untargeted metabolomics analysis. METHODS AND RESULTS: Thirty subjects aged 22-63 years from the BIONAOS study consumed a normal-polyphenol OJ (NPJ) or a high-polyphenol OJ (HPJ) (299 or 745 mg/l, respectively) for 12 weeks in a randomized, parallel, double-blind study. UHPLC-MS, univariate and multivariate statistical analysis and ROC curves were used to design biomarkers of consumption in serum...
September 30, 2016: Molecular Nutrition & Food Research
Amanda L Peterson, Adam K Walker, Erica K Sloan, Darren J Creek
Cancer cells often have dysregulated metabolism, which is largely characterized by the Warburg effect-an increase in glycolytic activity at the expense of oxidative phosphorylation-and increased glutamine utilization. Modern metabolomics tools offer an efficient means to investigate metabolism in cancer cells. Currently, a number of protocols have been described for harvesting adherent cells for metabolomics analysis, but the techniques vary greatly and they lack specificity to particular cancer cell lines with diverse metabolic and structural features...
2016: Metabolites
Jen-Yi Hsu, Jing-Fang Hsu, Yet-Ran Chen, Chia-Lang Shih, Yi-Sheng Hsu, Yi-Jen Chen, Shu-Han Tsai, Pao-Chi Liao
Human biomonitoring is the assessment of actual internal contamination of chemicals by measuring exposure markers, chemicals or their metabolites, in human urine, blood, serum, and other body fluids. However, the metabolism of chemicals within an organism is extremely complex. Therefore, the identification of metabolites is often difficult and laborious. Several untargeted metabolomics methods have been developed to perform objective searching/filtering of accurate-mass-based LC-MS data to facilitate metabolite identification...
October 5, 2016: Analytica Chimica Acta
Ferheen Baig, Raimund Pechlaner, Manuel Mayr
No abstract text is available yet for this article.
September 20, 2016: Journal of the American College of Cardiology
Alexandra C Schrimpe-Rutledge, Simona G Codreanu, Stacy D Sherrod, John A McLean
Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches...
September 13, 2016: Journal of the American Society for Mass Spectrometry
Matthew S P Boyles, Christina Ranninger, Roland Reischl, Marc Rurik, Richard Tessadri, Oliver Kohlbacher, Albert Duschl, Christian G Huber
BACKGROUND: The rapidly increasing number of engineered nanoparticles (NPs), and products containing NPs, raises concerns for human exposure and safety. With this increasing, and ever changing, catalogue of NPs it is becoming more difficult to adequately assess the toxic potential of new materials in a timely fashion. It is therefore important to develop methods which can provide high-throughput screening of biological responses. The use of omics technologies, including metabolomics, can play a vital role in this process by providing relatively fast, comprehensive, and cost-effective assessment of cellular responses...
2016: Particle and Fibre Toxicology
A McMillan, J B Renaud, G B Gloor, G Reid, M W Sumarah
Liquid chromatography-high resolution mass spectrometry (LC-MS) has emerged as one of the most widely used platforms for untargeted metabolomics due to its unparalleled sensitivity and metabolite coverage. Despite its prevalence of use, the proportion of true metabolites identified in a given experiment compared to background contaminants and ionization-generated artefacts remains poorly understood. Salt clusters are well documented artefacts of electrospray ionization MS, recognized by their characteristically high mass defects (for this work simply generalized as the decimal numbers after the nominal mass)...
2016: Journal of Cheminformatics
Azam Yazdani, Akram Yazdani, Ahmad Samiei, Eric Boerwinkle
Untargeted metabolomics, measurement of large numbers of metabolites irrespective of their chemical or biologic characteristics, has proven useful for identifying novel biomarkers of health and disease. Of particular importance is the analysis of networks of metabolites, as opposed to the level of an individual metabolite. The aim of this study is to achieve causal inference among serum metabolites in an observational setting. A metabolomics causal network is identified using the genome granularity directed acyclic graph (GDAG) algorithm where information across the genome in a deeper level of granularity is extracted to create strong instrumental variables and identify causal relationships among metabolites in an upper level of granularity...
August 31, 2016: Journal of Biomedical Informatics
Sophie H Narath, Selma I Mautner, Eva Svehlikova, Bernd Schultes, Thomas R Pieber, Frank M Sinner, Edgar Gander, Gunnar Libiseller, Michael G Schimek, Harald Sourij, Christoph Magnes
Bariatric surgery is currently one of the most effective treatments for obesity and leads to significant weight reduction, improved cardiovascular risk factors and overall survival in treated patients. To date, most studies focused on short-term effects of bariatric surgery on the metabolic profile and found high variation in the individual responses to surgery. The aim of this study was to identify relevant metabolic changes not only shortly after bariatric surgery (Roux-en-Y gastric bypass) but also up to one year after the intervention by using untargeted metabolomics...
2016: PloS One
Xavier Domingo-Almenara, Jesus Brezmes, Maria Vinaixa, Sara Samino, Noelia Ramirez, Marta Ramon-Krauel, Carles Lerin, Marta Díaz, Lourdes Ibáñez, Xavier Correig, Alexandre Perera-Lluna, Oscar Yanes
Gas chromatography coupled to mass spectrometry (GC/MS) has been a long-standing approach used for identifying small molecules due to the highly reproducible ionization process of electron impact ionization (EI). However, the use of GC-EI MS in untargeted metabolomics produces large and complex data sets characterized by coeluting compounds and extensive fragmentation of molecular ions caused by the hard electron ionization. In order to identify and extract quantitative information on metabolites across multiple biological samples, integrated computational workflows for data processing are needed...
October 4, 2016: Analytical Chemistry
Zijuan Lai, Oliver Fiehn
Mass spectrometry-based untargeted metabolomics detects many peaks that cannot be identified. While advances have been made for automatic structure annotations in LC-electrospray-MS/MS, no open source solutions are available for hard electron ionization used in GC-MS. In metabolomics, most compounds bear moieties with acidic protons, for example, amino, hydroxyl, or carboxyl groups. Such functional groups increase the boiling points of metabolites too much for use in GC-MS. Hence, in GC-MS-focused metabolomics, derivatization of these groups is essential and has been employed since the 1960s...
August 31, 2016: Mass Spectrometry Reviews
Darren J Creek, Hwa H Chua, Simon A Cobbold, Brunda Nijagal, James I Macrae, Benjamin K Dickerman, Paul R Gilson, Stuart A Ralph, Malcolm J McConville
High-throughput phenotypic screening of chemical libraries has resulted in the identification of thousands of compounds with potent antimalarial activity, although in most cases, the mechanism(s) of action of these compounds remain unknown. Here we have investigated the mode of action of 90 antimalarial compounds derived from the Malaria Box collection using high-coverage, untargeted metabolomics analysis. Approximately half of the tested compounds induced significant metabolic perturbations in in vitro cultures of P...
August 29, 2016: Antimicrobial Agents and Chemotherapy
Aude Habran, Mauro Commisso, Pierre Helwi, Ghislaine Hilbert, Stefano Negri, Nathalie Ollat, Eric Gomès, Cornelis van Leeuwen, Flavia Guzzo, Serge Delrot
The present work investigates the interactions between soil content, rootstock, and scion by focusing on the effects of roostocks and nitrogen supply on grape berry content. Scions of Cabernet Sauvignon (CS) and Pinot Noir (PN) varieties were grafted either on Riparia Gloire de Montpellier (RGM) or 110 Richter (110R) rootstock. The 4 rooststock/scion combinations were fertilized with 3 different levels of nitrogen after fruit set. Both in 2013 and 2014, N supply increased N uptake by the plants, and N content both in vegetative and reproductory organs...
2016: Frontiers in Plant Science
Andrew J Chetwynd, Amanda Samarawickrama, Jaime H Vera, Stephen A Bremner, Alaa Abdul-Sada, Yvonne Gilleece, Stephen G Holt, Elizabeth M Hill
BACKGROUND: The use of combination antiretroviral therapy (cART) has substantially improved the outlook for patients with HIV infection. However, lifelong exposure to cART is also associated with adverse metabolic changes and an enhanced risk of renal, hepatic and cardiovascular dysfunction. This study investigated disruptions of the urinary metabolome of cART-exposed patients, thereby furthering our understanding of some of the side effects of pharmaceutical intervention. METHODS: HIV-positive patients were recruited from an HIV clinic and divided into cART-naïve and cART-exposed groups...
August 16, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
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