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https://www.readbyqxmd.com/read/29915347/comparative-evaluation-of-ms-based-metabolomics-software-and-its-application-to-preclinical-alzheimer-s-disease
#1
Ling Hao, Jingxin Wang, David Page, Sanjay Asthana, Henrik Zetterberg, Cynthia Carlsson, Ozioma C Okonkwo, Lingjun Li
Mass spectrometry-based metabolomics has undergone significant progresses in the past decade, with a variety of software packages being developed for data analysis. However, systematic comparison of different metabolomics software tools has rarely been conducted. In this study, several representative software packages were comparatively evaluated throughout the entire pipeline of metabolomics data analysis, including data processing, statistical analysis, feature selection, metabolite identification, pathway analysis, and classification model construction...
June 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907290/comprehensive-evaluation-of-untargeted-metabolomics-data-processing-software-in-feature-detection-quantification-and-discriminating-marker-selection
#2
Zhucui Li, Yan Lu, Yufeng Guo, Haijie Cao, Qinhong Wang, Wenqing Shui
Data analysis represents a key challenge for untargeted metabolomics studies and it commonly requires extensive processing of more than thousands of metabolite peaks included in raw high-resolution MS data. Although a number of software packages have been developed to facilitate untargeted data processing, they have not been comprehensively scrutinized in the capability of feature detection, quantification and marker selection using a well-defined benchmark sample set. In this study, we acquired a benchmark dataset from standard mixtures consisting of 1100 compounds with specified concentration ratios including 130 compounds with significant variation of concentrations...
October 31, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29893550/autonomous-multi-modal-metabolomics-data-integration-for-comprehensive-pathway-analysis
#3
Tao Huan, Amelia Palermo, Julijana Ivanisevic, Duane Rinehart, David Edler, Thiery Phommavongsay, H Paul Benton, Carlos Guijas, Xavier Domingo-Almenara, Benedikt Warth, Gary Siuzdak
Comprehensive metabolomic data can be achieved using multiple orthogonal separation and mass spectrometry (MS) analytical techniques. However, drawing biologically relevant conclusions from this data and combining it with additional layers of data collected by other omic technologies present a significant bioinformatic challenge. To address this, a data processing approach was designed to automate the comprehensive prediction of dysregulated metabolic pathways/networks from multiple data sources. The platform autonomously integrates multiple MS-based metabolomics data types without constraints due to different sample preparation/extraction, chromatographic separation, or MS detection method...
June 12, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29846054/dataset-dependent-acquisition-enables-comprehensive-tandem-mass-spectrometry-coverage-of-complex-samples
#4
Corey David Broeckling, Emmy Hoyes, Keith Richardson, Jeffery M Brown, Jessica E Prenni
Tandem mass spectrometry (MS/MS) is an invaluable experimental tool for providing analytical data supporting the identification of small molecules and peptides in mass spectrometry based 'omics' experiments. Data dependent MS/MS (DDA) is an MS/MS acquisition strategy which is responsive to the signals detected in a given sample. However, in analysis of even moderately complex samples with state of the art instrumentation, the speed of MS/MS acquisition is insufficient to offer comprehensive MS/MS coverage of all detected molecules...
May 30, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29808994/the-metabonomic-profiling-of-chicken-eggs-during-storage-using-high-performance-liquid-chromatography-quadrupole-time-of-flight-mass-spectrometry
#5
Amy Elizabeth Johnson, Kate Louise Sidwick, Vasil R Pirgozliev, Anthony Edge, David Frederick Thompson
Metabonomic techniques have been used to discover subtle differences in the small molecule profiles of chicken eggs, which could help to combat fraud within the egg industry. High Performance Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (HPLC-Q-ToF-MS) was used to obtain profiles of the small molecules present in the yolks of chicken eggs stored for different lengths of time. Statistical analysis, including the use of XCMS Online and further exploratory statistics, was able to uncover differences in the abundances of several of the small molecules found in these egg yolks...
May 29, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29790936/simextargid-a-comprehensive-package-for-real-time-lc-ms-data-acquisition-and-analysis
#6
William M B Edmands, Josie Hayes, Stephen M Rappaport
Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29742587/exploratory-application-of-neuropharmacometabolomics-in-severe-childhood-traumatic-brain-injury
#7
Fanuel T Hagos, Philip E Empey, Pengcheng Wang, Xiaochao Ma, Samuel M Poloyac, Hülya Bayır, Patrick M Kochanek, Michael J Bell, Robert S B Clark
OBJECTIVES: To employ metabolomics-based pathway and network analyses to evaluate the cerebrospinal fluid metabolome after severe traumatic brain injury in children and the capacity of combination therapy with probenecid and N-acetylcysteine to impact glutathione-related and other pathways and networks, relative to placebo treatment. DESIGN: Analysis of cerebrospinal fluid obtained from children enrolled in an Institutional Review Board-approved, randomized, placebo-controlled trial of a combination of probenecid and N-acetylcysteine after severe traumatic brain injury (Trial Registration NCT01322009)...
May 7, 2018: Critical Care Medicine
https://www.readbyqxmd.com/read/29606472/application-of-an-advanced-and-wide-scope-non-target-screening-workflow-with-lc-esi-qtof-ms-and-chemometrics-for-the-classification-of-the-greek-olive-oil-varieties
#8
Natasa P Kalogiouri, Reza Aalizadeh, Nikolaos S Thomaidis
An optimized and validated LC-ESI-QTOF-MS method with an integrated non-target screening workflow was applied in the investigation of the metabolomic profile of 51 Greek monovarietal extra virgin olive oils (EVOOs) from the varieties: Manaki, Ladoelia, Koroneiki, Amfissis, Chalkidikis and Kolovi. Data processing was carried out with the R language and XCMS package. A local database consisting of 1608 compounds naturally occurring in different organs of Olea Europa L. was compiled in order to accelerate the identification workflow...
August 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29516137/elucidation-of-non-intentionally-added-substances-migrating-from-polyester-polyurethane-lacquers-using-automated-lc-hrms-data-processing
#9
Elsa Omer, Ronan Cariou, Gérald Remaud, Yann Guitton, Hélène Germon, Paul Hill, Gaud Dervilly-Pinel, Bruno Le Bizec
An untargeted strategy aiming at identifying non-intentionally added substances (NIAS) migrating from coatings was developed. This innovative approach was applied to two polyester-polyurethane lacquers, for which suppliers previously provided the identity of the monomers involved. Lacquers were extracted with acetonitrile and analyzed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Data, acquired in the full scan mode, were processed using an open-source R-environment (xcms and CAMERA packages) to list the detected features and deconvolute them in groups related to individual compounds...
March 8, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29494574/data-processing-multi-omic-pathway-mapping-and-metabolite-activity-analysis-using-xcms-online
#10
Erica M Forsberg, Tao Huan, Duane Rinehart, H Paul Benton, Benedikt Warth, Brian Hilmers, Gary Siuzdak
Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes...
April 2018: Nature Protocols
https://www.readbyqxmd.com/read/29453510/next-generation-metabolic-screening-targeted-and-untargeted-metabolomics-for-the-diagnosis-of-inborn-errors-of-metabolism-in-individual-patients
#11
Karlien L M Coene, Leo A J Kluijtmans, Ed van der Heeft, Udo F H Engelke, Siebolt de Boer, Brechtje Hoegen, Hanneke J T Kwast, Maartje van de Vorst, Marleen C D G Huigen, Irene M L W Keularts, Michiel F Schreuder, Clara D M van Karnebeek, Saskia B Wortmann, Maaike C de Vries, Mirian C H Janssen, Christian Gilissen, Jasper Engel, Ron A Wevers
The implementation of whole-exome sequencing in clinical diagnostics has generated a need for functional evaluation of genetic variants. In the field of inborn errors of metabolism (IEM), a diverse spectrum of targeted biochemical assays is employed to analyze a limited amount of metabolites. We now present a single-platform, high-resolution liquid chromatography quadrupole time of flight (LC-QTOF) method that can be applied for holistic metabolic profiling in plasma of individual IEM-suspected patients. This method, which we termed "next-generation metabolic screening" (NGMS), can detect >10,000 features in each sample...
February 16, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29448994/automatic-untargeted-metabolic-profiling-analysis-coupled-with-chemometrics-for-improving-metabolite-identification-quality-to-enhance-geographical-origin-discrimination-capability
#12
Lu Han, Yue-Ming Zhang, Jing-Jing Song, Mei-Juan Fan, Yong-Jie Yu, Ping-Ping Liu, Qing-Xia Zheng, Qian-Si Chen, Chang-Cai Bai, Tao Sun, Yuan-Bin She
Untargeted metabolic profiling analysis is employed to screen metabolites for specific purposes, such as geographical origin discrimination. However, the data analysis remains a challenging task. In this work, a new automatic untargeted metabolic profiling analysis coupled with a chemometric strategy was developed to improve the metabolite identification results and to enhance the geographical origin discrimination capability. Automatic untargeted metabolic profiling analysis with chemometrics (AuMPAC) was used to screen the total ion chromatographic (TIC) peaks that showed significant differences among the various geographical regions...
March 16, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29433821/a-method-for-screening-active-components-from-chinese-herbs-by-cell-membrane-chromatography-offline-high-performance-liquid-chromatography-mass-spectrometry-and-an-online-statistical-tool-for-data-processing
#13
Yan Cao, Shaozhan Wang, Yinghua Li, Xiaofei Chen, Langdong Chen, Dongyao Wang, Zhenyu Zhu, Yongfang Yuan, Diya Lv
Cell membrane chromatography (CMC) has been successfully applied to screen bioactive compounds from Chinese herbs for many years, and some offline and online two-dimensional (2D) CMC-high performance liquid chromatography (HPLC) hyphenated systems have been established to perform screening assays. However, the requirement of sample preparation steps for the second-dimensional analysis in offline systems and the need for an interface device and technical expertise in the online system limit their extensive use...
March 9, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29430917/untargeted-metabolomics-reveal-lipid-alterations-upon-2-deoxyglucose-treatment-in-human-hacat-keratinocytes
#14
Pierre Le Pogam, Mickael Doué, Yann Le Page, Denis Habauzit, Maxim Zhadobov, Ronan Sauleau, Yves Le Dréan, David Rondeau
The glucose analogue 2-deoxyglucose (2-DG) impedes cancer progression in animal models and is currently being assessed as an anticancer therapy, yet the mode of action of this drug of high clinical significance has not been fully delineated. In an attempt to better characterize its pharmacodynamics, an integrative UPLC-Q-Exactive-based joint metabolomic and lipidomic approach was undertaken to evaluate the metabolic perturbations induced by this drug in human HaCaT keratinocyte cells. R-XCMS data processing and subsequent multivariate pattern recognition, metabolites identification, and pathway analyses identified eight metabolites that were most significantly changed upon a 3 h 2-DG exposure...
March 2, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29415459/chemometric-analysis-of-the-volatile-compounds-generated-by-aspergillus-carbonarius-strains-isolated-from-grapes-and-dried-vine-fruits
#15
Zhan Cheng, Menghua Li, Philip J Marriott, Xiaoxu Zhang, Shiping Wang, Jiangui Li, Liyan Ma
Ochratoxin A (OTA) contamination in grape production is an important problem worldwide. Microbial volatile organic compounds (MVOCs) have been demonstrated as useful tools to identify different toxigenic strains. In this study, Aspergillus carbonarius strains were classified into two groups, moderate toxigenic strains (MT) and high toxigenic strains (HT), according to OTA-forming ability. The MVOCs were analyzed by GC-MS and the data processing was based on untargeted profiling using XCMS Online software. Orthogonal projection to latent structures discriminant analysis (OPLS-DA) was performed using extract ion chromatogram GC-MS datasets...
February 6, 2018: Toxins
https://www.readbyqxmd.com/read/29413978/metabolomics-analysis-of-serum-reveals-the-effect-of-danggui-buxue-tang-on-fatigued-mice-induced-by-exhausting-physical-exercise
#16
Xiaoyao Miao, Bingkun Xiao, Sufang Shui, Jianyun Yang, Rongqing Huang, Junxing Dong
Danggui Buxue Tang (DBT), believed to invigorate 'Qi' (vital energy) and nourish 'Blood' (body circulation), is a traditional Chinese medicine formula. In this study, a metabolomics approach with gas chromatography coupled to mass spectrometry combined with pattern recognition was adopted to investigate the underlying mechanism of the antifatigue effect of DBT on fatigue of mice induced by weight-loaded forced swimming. Fourteen endogenous metabolites, up-regulated or down-regulated, were identified in the model mice by analysis tools of partial least-squares discriminant analysis (PLS-DA) and XCMS online software...
March 20, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29412933/assessment-of-protected-designation-of-origin-for-colombian-coffees-based-on-hrms-based-metabolomics
#17
Duvan E Hoyos Ossa, Rubén Gil-Solsona, Gustavo A Peñuela, Juan Vicente Sancho, Felix J Hernández
An untargeted metabolomics approach based on HRMS has been applied to Colombian green coffee to develop a discrimination model to highlight the most differential compounds. For this purpose, 41 green coffee samples of different genotypes collected from 5 regions were analysed. Samples were extracted with aqueous and organic solvents to cover a wide range of compounds. Sample extracts were randomly injected and data were pre-processed with XCMS software. PCA was used to verify quality control samples behaviour, and PLS-DA and DD-SIMCA were employed to create models for discrimination using VIP variable selection method...
June 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29068675/use-of-liquid-chromatography-quadrupole-time-of-flight-mass-spectrometry-and-metabonomic-profiling-to-differentiate-between-normally-slaughtered-and-dead-on-arrival-poultry-meat
#18
Kate L Sidwick, Amy E Johnson, Craig D Adam, Luisa Pereira, David F Thompson
Metabonomic profiling techniques, with established quality control methods, have been used to detect subtle metabolic differences in tissue that could aid in the discovery of fraud within the food industry. Liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) was utilized to acquire metabolic profiles of muscle, heart, and liver tissue from normally slaughtered and dead on arrival chickens. A workflow including XCMS Online for data processing and robust confirmatory statistics was used in order to differentiate between the two sample types...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28959852/-subacute-toxicity-metabonomics-of-jinlingzi-powder-based-on-lc-ms
#19
Shu-Jie Shen, Su-Fang Shui, Bing-Kun Xiao, Jian-Yun Yang, Rong-Qing Huang
To further understand the metabolic characteristics of Jinlingzi powder toxicity effect in rats and explore the effect of Jinlingzi powder on unknown biological pathways in the treatment process. In this experiment, the effect of three doses of Jinlingzi powder decoction on rat liver and kidney was investigated to explore the characteristics and rules of Jinlingzi powder on in vivo metabonomic changes in rats. First, urine and serum samples of the rats were used for LC-MS analysis. Under the XCMS online analysis, 44 differential substances were found in the identification of metabolites...
February 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28945073/exposome-scale-investigations-guided-by-global-metabolomics-pathway-analysis-and-cognitive-computing
#20
Benedikt Warth, Scott Spangler, Mingliang Fang, Caroline H Johnson, Erica M Forsberg, Ana Granados, Richard L Martin, Xavier Domingo-Almenara, Tao Huan, Duane Rinehart, J Rafael Montenegro-Burke, Brian Hilmers, Aries Aisporna, Linh T Hoang, Winnie Uritboonthai, H Paul Benton, Susan D Richardson, Antony J Williams, Gary Siuzdak
Concurrent exposure to a wide variety of xenobiotics and their combined toxic effects can play a pivotal role in health and disease, yet are largely unexplored. Investigating the totality of these exposures, i.e., the "exposome", and their specific biological effects constitutes a new paradigm for environmental health but still lacks high-throughput, user-friendly technology. We demonstrate the utility of mass spectrometry-based global exposure metabolomics combined with tailored database queries and cognitive computing for comprehensive exposure assessment and the straightforward elucidation of biological effects...
November 7, 2017: Analytical Chemistry
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