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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
#1
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
#2
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
#3
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
#4
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
#5
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...
February 10, 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
#6
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
#7
Pierre Le Pogam, Mickaël 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 anti-cancer 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 8 metabolites that were most significantly changed upon a 3 h 2-DG exposure...
February 12, 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
#8
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
#9
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...
January 26, 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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28922607/antdas-automatic-data-analysis-strategy-for-uplc-qtof-based-nontargeted-metabolic-profiling-analysis
#14
Hai-Yan Fu, Xiao-Ming Guo, Yue-Ming Zhang, Jing-Jing Song, Qing-Xia Zheng, Ping-Ping Liu, Peng Lu, Qian-Si Chen, Yong-Jie Yu, Yuanbin She
High-quality data analysis methodology remains a bottleneck for metabolic profiling analysis based on ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry. The present work aims to address this problem by proposing a novel data analysis strategy wherein (1) chromatographic peaks in the UPLC-QTOF data set are automatically extracted by using an advanced multiscale Gaussian smoothing-based peak extraction strategy; (2) a peak annotation stage is used to cluster fragment ions that belong to the same compound...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28815274/a-new-metabolomics-based-strategy-for-identification-of-endogenous-markers-of-urine-adulteration-attempts-exemplified-for-potassium-nitrite
#15
Andrea E Steuer, Kim Arnold, Tom D Schneider, Michael Poetzsch, Thomas Kraemer
Urine adulteration to circumvent positive drug testing represents a problem for toxicological laboratories. While creatinine is a suitable marker for dilution, detection of chemicals is often performed by dipstick tests associated with high rates of false positives. Several methods would be necessary to check for all possible adulterants. Untargeted mass spectrometry (MS) methods used in metabolomics should theoretically allow detecting concentration changes of any endogenous urinary metabolite or presence of new biomarkers produced by chemical adulteration...
October 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28795107/mass-spectrometry-data-of-metabolomics-analysis-of-nepenthes-pitchers
#16
Muhammad Aqil Fitri Rosli, Kamalrul Azlan Azizan, Syarul Nataqain Baharum, Hoe-Han Goh
Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28752757/detailed-investigation-and-comparison-of-the-xcms-and-mzmine-2-chromatogram-construction-and-chromatographic-peak-detection-methods-for-preprocessing-mass-spectrometry-metabolomics-data
#17
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
XCMS and MZmine 2 are two widely used software packages for preprocessing untargeted LC/MS metabolomics data. Both construct extracted ion chromatograms (EICs) and detect peaks from the EICs, the first two steps in the data preprocessing workflow. While both packages have performed admirably in peak picking, they also detect a problematic number of false positive EIC peaks and can also fail to detect real EIC peaks. The former and latter translate downstream into spurious and missing compounds and present significant limitations with most existing software packages that preprocess untargeted mass spectrometry metabolomics data...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28752754/one-step-forward-for-reducing-false-positive-and-false-negative-compound-identifications-from-mass-spectrometry-metabolomics-data-new-algorithms-for-constructing-extracted-ion-chromatograms-and-detecting-chromatographic-peaks
#18
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
False positive and false negative peaks detected from extracted ion chromatograms (EIC) are an urgent problem with existing software packages that preprocess untargeted liquid or gas chromatography-mass spectrometry metabolomics data because they can translate downstream into spurious or missing compound identifications. We have developed new algorithms that carry out the sequential construction of EICs and detection of EIC peaks. We compare the new algorithms to two popular software packages XCMS and MZmine 2 and present evidence that these new algorithms detect significantly fewer false positives...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28749445/a-metabolomics-guided-exploration-of-the-phytochemical-constituents-of-vernonia-fastigiata-with-the-aid-of-pressurized-hot-water-extraction-and-liquid-chromatography-mass-spectrometry
#19
Keabetswe Masike, Bradley S Khoza, Paul A Steenkamp, Elize Smit, Ian A Dubery, Ntakadzeni E Madala
Vernonia fastigiata is a multi-purpose nutraceutical plant with interesting biological properties. However, very little is known about its phytochemical composition and, thus the need for its phytochemical characterization. In the current study, an environmentally friendly method, pressurized hot water extraction (PHWE), was used to extract metabolites from the leaves of V. fastigiata at various temperatures (50 °C, 100 °C, 150 °C and 200 °C). Ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-qTOF-MS) analysis in combination with chemometric methods, particularly principal component analysis (PCA) and liquid/gas chromatography mass spectrometry (XCMS) cloud plots, were used to descriptively visualize the data and identify significant metabolites extracted at various temperatures...
July 27, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28621925/kpic2-an-effective-framework-for-mass-spectrometry-based-metabolomics-using-pure-ion-chromatograms
#20
Hongchao Ji, Fanjuan Zeng, Yamei Xu, Hongmei Lu, Zhimin Zhang
Distilling accurate quantitation information on metabolites from liquid chromatography coupled with mass spectrometry (LC-MS) data sets is crucial for further statistical analysis and biomarker identification. However, it is still challenging due to the complexity of biological systems. The concept of pure ion chromatograms (PICs) is an effective way of extracting meaningful ions, but few toolboxes provide a full processing workflow for LC-MS data sets based on PICs. In this study, an integrated framework, KPIC2, has been developed for metabolomics studies, which can detect pure ions accurately, align PICs across samples, group PICs to identify isotope and potential adducts, fill missing peaks and do multivariate pattern recognition...
June 30, 2017: Analytical Chemistry
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