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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
Yun Ding, Ye Fang, Juana Moreno, J Ramanujam, Mark Jarrell, Michal Brylinski
Structural and computational biologists often need to measure the similarity of ligand binding conformations. The commonly used root-mean-square deviation (RMSD) is not only ligand-size dependent, but also may fail to capture biologically meaningful binding features. To address these issues, we developed the Contact Mode Score (CMS), a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. The CMS is less dependent on the ligand size and has the ability to include flexible receptors...
September 6, 2016: Computational Biology and Chemistry
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
Ronan Cariou, Elsa Omer, Alexis Léon, Gaud Dervilly-Pinel, Bruno Le Bizec
In the present work, we addressed the question of global seeking/screening organohalogenated compounds in a large panel of complex biological matrices, with a particular focus on unknown chemicals that may be considered as potential emerging hazards. A fishing strategy was developed based on untargeted profiling among full scan acquisition datasets provided by high resolution mass spectrometry. Since large datasets arise from such profiling, filtering useful information stands as a central question. In this way, we took advantage of the exact mass differences between Cl and Br isotopes...
September 14, 2016: Analytica Chimica Acta
J Rafael Montenegro-Burke, Thiery Phommavongsay, Aries E Aisporna, Tao Huan, Duane Rinehart, Erica Forsberg, Farris L Poole, Michael P Thorgersen, Michael W W Adams, Gregory Krantz, Matthew W Fields, Trent R Northen, Paul D Robbins, Laura J Niedernhofer, Luke Lairson, H Paul Benton, Gary Siuzdak
Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms...
October 4, 2016: Analytical Chemistry
Sufang Shui, Shujie Shen, Rongqing Huang, Bingkun Xiao, Jianyun Yang
The urinary and plasma metabonomics method based on a Agilent-1200 LC system coupled to an Agilent-6410 mass spectrometry (HPLC-MS/MS) had been established to investigate the anti-inflammatory activity of Yi-Guan-Jian (YGJ) decoction and explore its potential anti-inflammatory mechanism. Rat acute inflammation was induced by subcutaneous injection of carrageenan in hind paws. Multivariate statistical approaches, such as principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA) and XCMS online software were used to distinguish normal control group (NG), model group (MG), aspirin-treated group (AG) and Yi-Guan-Jian decoction group (YGJ), aimed at finding out the potential biomarkers...
October 15, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Nikoline J Nielsen, Giorgio Tomasi, Jan H Christensen
Metabolic fingerprinting is a relatively young scientific discipline requiring robust, yet flexible and fit-for-purpose analytical methods. Here, we introduce a simple approach to select reversed phase LC systems with electrospray MS detection for fingerprinting of polar and amphiphilic plant metabolites. The approach does not rely on isotopic labeling or biological origin of sample constituent and can also be used for non-biological matrices (e.g., oil or sewage sludge) or for other optimization purposes (e...
August 2016: Analytical and Bioanalytical Chemistry
Kaiwen Luo, Fang Feng
In this study, a novel untargeted metabolomics-driven strategy based on LC-MS was used to rapidly screen and identify the absorbed components and metabolites of Zhi-Zi-Hou-Po decoction (ZZHPD) in rat plasma. The plasma sample was obtained from orbital venous of rats after oral administration and pretreated by protein precipitation before analysis. All sample data from total ion chromatograms (TICs) of LC-TOF/MS were aligned and peak picked by XCMS and MetAlign combined to extract three-dimensional datasets (peak code, t R -m/z pairs and ion intensity)...
August 2016: Analytical and Bioanalytical Chemistry
Alexandre Seyer, Samia Boudah, Simon Broudin, Christophe Junot, Benoit Colsch
INTRODUCTION: Due to its proximity with the brain, cerebrospinal fluid (CSF) could be a medium of choice for the discovery of biomarkers of neurological and psychiatric diseases using untargeted analytical approaches. OBJECTIVES: This study explored the CSF lipidome in order to generate a robust mass spectral database using an untargeted lipidomic approach. METHODS: Cerebrospinal fluid samples from 45 individuals were analyzed by liquid chromatography coupled to high-resolution mass spectrometry method (LC-HRMS)...
2016: Metabolomics: Official Journal of the Metabolomic Society
Laurence H Stipetic, Matthew J Dalby, Robert L Davies, Fraser R Morton, Gordon Ramage, Karl E V Burgess
INTRODUCTION: Bacterial cell characteristics change significantly during differentiation between planktonic and biofilm states. While established methods exist to detect and identify transcriptional and proteomic changes, metabolic fluctuations that distinguish these developmental stages have been less amenable to investigation. OBJECTIVES: The objectives of the study were to develop a robust reproducible sample preparation methodology for high throughput biofilm analysis and to determine differences between Staphylococcus aureus in planktonic and biofilm states...
2016: Metabolomics: Official Journal of the Metabolomic Society
Kelly H Telu, Xinjian Yan, William E Wallace, Stephen E Stein, Yamil Simón-Manso
RATIONALE: The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures...
March 15, 2016: Rapid Communications in Mass Spectrometry: RCM
Hui-Yin Chang, Ching-Tai Chen, T Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, Ting-Yi Sung
Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification...
2016: PloS One
Yaoyao Wang, Richard Caldwell, David A Cowan, Cristina Legido-Quigley
Current antidoping analytical methods are tailored mainly to the targeting of known drugs and endogenous molecules. This causes difficulties in rapidly reacting to emerging threats, such as designer drugs, biological therapeutic agents, and technologies. Biomarkers are considered as a promising approach for the fight against these threats to sport. The main purpose of this study was to find surrogate biomarkers induced by the intake of small amounts of the model compound salbutamol and explore a sensitive approach to help screen for possible drug misuse...
February 16, 2016: Analytical Chemistry
Nathaniel G Mahieu, Jessica Lloyd Genenbacher, Gary J Patti
Global profiling of metabolites in biological samples by liquid chromatography/mass spectrometry results in datasets too large to evaluate manually. Fortunately, a variety of software programs are now available to automate the data analysis. Selection of the appropriate processing solution is dependent upon experimental design. Most metabolomic studies a decade ago had a relatively simple experimental design in which the intensities of compounds were compared between only two sample groups. More recently, however, increasingly sophisticated applications have been pursued...
February 2016: Current Opinion in Chemical Biology
Jordi Capellades, Miriam Navarro, Sara Samino, Marta Garcia-Ramirez, Cristina Hernandez, Rafael Simo, Maria Vinaixa, Oscar Yanes
Studying the flow of chemical moieties through the complex set of metabolic reactions that happen in the cell is essential to understanding the alterations in homeostasis that occur in disease. Recently, LC/MS-based untargeted metabolomics and isotopically labeled metabolites have been used to facilitate the unbiased mapping of labeled moieties through metabolic pathways. However, due to the complexity of the resulting experimental data sets few computational tools are available for data analysis. Here we introduce geoRge, a novel computational approach capable of analyzing untargeted LC/MS data from stable isotope-labeling experiments...
January 5, 2016: Analytical Chemistry
Robert Winkler
In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as 'workflow decay', can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis...
2015: PeerJ
Pedro A Segura, Karim Saadi, Alexandra Clair, Marc-André Lecours, Viviane Yargeau
We studied the nature and antimicrobial activity of ozonolysis transformation products (OTPs) of levofloxacin (LEV), a frequently detected fluoroquinolone antimicrobial in environmental waters. Two bioassays, the Kirby-Bauer test and the broth microdilution assay, were used to measure changes in the antimicrobial activity of solutions at low LEV to O3 molar ratios (2:1, 2:3 and 1:3) compared to solutions without added O3 (LEV:O3 1:0). The Kirby-Bauer test was not sensitive enough to detect significant differences in the growth inhibition zones in samples LEV:O3 2:1 and LEV:O3 1:0; however, the broth microdilution assay showed that bacterial growth inhibition was significantly lower (P<0...
2015: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Mingliang Fang, Julijana Ivanisevic, H Paul Benton, Caroline H Johnson, Gary J Patti, Linh T Hoang, Winnie Uritboonthai, Michael E Kurczy, Gary Siuzdak
Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s)...
November 3, 2015: Analytical Chemistry
Nathaniel G Mahieu, Jonathan L Spalding, Gary J Patti
MOTIVATION: Current informatic techniques for processing raw chromatography/mass spectrometry data break down under several common, non-ideal conditions. Importantly, hydrophilic liquid interaction chromatography (a key separation technology for metabolomics) produces data which are especially challenging to process. We identify three critical points of failure in current informatic workflows: compound specific drift, integration region variance, and naive missing value imputation. We implement the Warpgroup algorithm to address these challenges...
January 15, 2016: Bioinformatics
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