keyword
MENU ▼
Read by QxMD icon Read
search

Xcms

keyword
https://www.readbyqxmd.com/read/27836228/avoiding-hard-chromatographic-segmentation-a-moving-window-approach-for-the-automated-resolution-of-gas-chromatography-mass-spectrometry-based-metabolomics-signals-by-multivariate-methods
#1
Xavier Domingo-Almenara, Alexandre Perera, Jesus Brezmes
Gas chromatography-mass spectrometry (GC-MS) produces large and complex datasets characterized by co-eluted compounds and at trace levels, and with a distinct compound ion-redundancy as a result of the high fragmentation by the electron impact ionization. Compounds in GC-MS can be resolved by taking advantage of the multivariate nature of GC-MS data by applying multivariate resolution methods. However, multivariate methods have to be applied in small regions of the chromatogram, and therefore chromatograms are segmented prior to the application of the algorithms...
October 29, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27809493/influence-of-mass-resolving-power-in-orbital-ion-trap-mass-spectrometry-based-metabolomics
#2
Lukáš Najdekr, David Friedecký, Ralf Tautenhahn, Tomáš Pluskal, Junhua Wang, Yingying Huang, Tomas Adam
Modern separation methods in conjunction with high resolution accurate mass (HRAM) spectrometry can provide an enormous number of features characterized by exact mass and chromatographic behavior. Higher mass resolving power usually requires longer scanning times, and thus fewer data points are acquired across the target peak. This could cause difficulties for quantification, feature detection and deconvolution. The aim of this work was to describe the influence of mass spectrometry resolving power on profiling metabolomics experiments...
November 3, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27802026/magnetic-microbead-affinity-selection-screening-magmass-of-botanical-extracts-for-inhibitors-of-15-lipoxygenase
#3
Michael D Rush, Elisabeth M Walker, Tristesse Burton, Richard B van Breemen
To expedite the identification of active natural products in complex mixtures such as botanical extracts, a magnetic microbead affinity selection screening (MagMASS) procedure was developed. This technique utilizes target proteins immobilized on magnetic beads for rapid bioaffinity isolation of ligands from complex mixtures. A MagMASS method was developed and validated for 15-lipoxygenase. As a proof of concept, several North American prairie plants used medicinally by Native Americans were extracted with MeOH and screened...
November 1, 2016: Journal of Natural Products
https://www.readbyqxmd.com/read/27775610/prediction-detection-and-validation-of-isotope-clusters-in-mass-spectrometry-data
#4
Hendrik Treutler, Steffen Neumann
Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92 % of the cases...
October 20, 2016: Metabolites
https://www.readbyqxmd.com/read/27639145/urinary-exposure-marker-discovery-for-toxicants-using-ultra-high-pressure-liquid-chromatography-coupled-with-orbitrap-high-resolution-mass-spectrometry-and-three-untargeted-metabolomics-approaches
#5
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
https://www.readbyqxmd.com/read/27620381/assessing-the-similarity-of-ligand-binding-conformations-with-the-contact-mode-score
#6
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
https://www.readbyqxmd.com/read/27584017/an-untargeted-metabolomics-approach-to-characterize-short-term-and-long-term-metabolic-changes-after-bariatric-surgery
#7
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
https://www.readbyqxmd.com/read/27584001/erah-a-computational-tool-integrating-spectral-deconvolution-and-alignment-with-quantification-and-identification-of-metabolites-in-gc-ms-based-metabolomics
#8
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
https://www.readbyqxmd.com/read/27566348/screening-halogenated-environmental-contaminants-in-biota-based-on-isotopic-pattern-and-mass-defect-provided-by-high-resolution-mass-spectrometry-profiling
#9
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
https://www.readbyqxmd.com/read/27560777/smartphone-analytics-mobilizing-the-lab-into-the-cloud-for-omic-scale-analyses
#10
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
https://www.readbyqxmd.com/read/27525358/metabonomic-analysis-of-biochemical-changes-in-the-plasma-and-urine-of-carrageenan-induced-rats-after-treatment-with-yi-guan-jian-decoction
#11
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
https://www.readbyqxmd.com/read/27344456/evaluation-of-chromatographic-conditions-in-reversed-phase-liquid-chromatography-mass-spectrometry-systems-for-fingerprinting-of-polar-and-amphiphilic-plant-metabolites
#12
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
https://www.readbyqxmd.com/read/27342796/identification-of-absorbed-components-and-metabolites-of-zhi-zi-hou-po-decoction-in-rat-plasma-after-oral-administration-by-an-untargeted-metabolomics-driven-strategy-based-on-lc-ms
#13
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
https://www.readbyqxmd.com/read/27110228/annotation-of-the-human-cerebrospinal-fluid-lipidome-using-high-resolution-mass-spectrometry-and-a-dedicated-data-processing-workflow
#14
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
https://www.readbyqxmd.com/read/27013931/a-novel-metabolomic-approach-used-for-the-comparison-of-staphylococcus-aureus-planktonic-cells-and-biofilm-samples
#15
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
https://www.readbyqxmd.com/read/26842580/analysis-of-human-plasma-metabolites-across-different-liquid-chromatography-mass-spectrometry-platforms-cross-platform-transferable-chemical-signatures
#16
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
https://www.readbyqxmd.com/read/26784691/imet-q-a-user-friendly-tool-for-label-free-metabolomics-quantitation-using-dynamic-peak-width-determination
#17
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
https://www.readbyqxmd.com/read/26760048/lc-ms-based-metabolomics-discovers-purine-endogenous-associations-with-low-dose-salbutamol-in-urine-collected-for-antidoping-tests
#18
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
https://www.readbyqxmd.com/read/26673825/a-roadmap-for-the-xcms-family-of-software-solutions-in-metabolomics
#19
REVIEW
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
https://www.readbyqxmd.com/read/26639619/george-a-computational-tool-to-detect-the-presence-of-stable-isotope-labeling-in-lc-ms-based-untargeted-metabolomics
#20
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
keyword
keyword
39980
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"