keyword
MENU ▼
Read by QxMD icon Read
search

Xcms

keyword
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
#1
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...
February 6, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29430917/untargeted-metabolomics-reveal-lipid-alterations-upon-2-deoxyglucose-treatment-in-human-hacat-keratinocytes
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28608848/furanoterpene-diversity-and-variability-in-the-marine-sponge-spongia-officinalis-from-untargeted-lc-ms-ms-metabolomic-profiling-to-furanolactam-derivatives
#16
Cléa Bauvais, Natacha Bonneau, Alain Blond, Thierry Pérez, Marie-Lise Bourguet-Kondracki, Séverine Zirah
The Mediterranean marine sponge Spongia officinalis has been reported as a rich source of secondary metabolites and also as a bioindicator of water quality given its capacity to concentrate trace metals. In this study, we evaluated the chemical diversity within 30 S. officinalis samples collected over three years at two sites differentially impacted by anthropogenic pollutants located near Marseille (South of France). Untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling (C18 LC, ESI-Q-TOF MS) combined with XCMS Online data processing and multivariate statistical analysis revealed 297 peaks assigned to at least 86 compounds...
June 13, 2017: Metabolites
https://www.readbyqxmd.com/read/28544323/mass-spectrometric-evidence-for-the-modification-of-small-molecules-in-a-cobalt-60-irradiated-rodent-diet
#17
J K Prasain, L S Wilson, A Arabshahi, C Grubbs, S Barnes
The purpose of this study was to investigate the effect of radiation on the content of animal diet constituents using global metabolomics. Aqueous methanolic extracts of control and cobalt-60-irradiated Teklad 7001 diets were comprehensively analyzed using nano-liquid chromatography-MS/MS. Among the over 2000 ions revealed by XCMS followed by data preprocessing, 94 positive and 143 negative metabolite ions had greater than 1.5-fold changes and p-values <0.01. Use of MetaboAnalyst statistical software demonstrated complete separation of the irradiated and non-radiated diets in unsupervised principal components analysis and supervised partial least squares discriminant analysis...
August 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28497560/untargeted-metabolomic-analysis-of-capsicum-spp-by-gc-ms
#18
Bianca Camargo Aranha, Jessica Fernanda Hoffmann, Rosa Lia Barbieri, Cesar Valmor Rombaldi, Fábio Clasen Chaves
INTRODUCTION: In order to conserve the biodiversity of Capsicum species and find genotypes with potential to be utilised commercially, Embrapa Clima Temperado maintains an active germplasm collection (AGC) that requires characterisation, enabling genotype selection and support for breeding programmes. OBJECTIVE: The objective of this study was to characterise pepper accessions from the Embrapa Clima Temperado AGC and differentiate species based on their metabolic profile using an untargeted metabolomics approach...
May 11, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28448069/systems-biology-guided-by-xcms-online-metabolomics
#19
Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson, Julijana Ivanisevic, H Paul Benton, Mingliang Fang, Aries Aisporna, Brian Hilmers, Farris L Poole, Michael P Thorgersen, Michael W W Adams, Gregory Krantz, Matthew W Fields, Paul D Robbins, Laura J Niedernhofer, Trey Ideker, Erica L Majumder, Judy D Wall, Nicholas J W Rattray, Royston Goodacre, Luke L Lairson, Gary Siuzdak
No abstract text is available yet for this article.
April 27, 2017: Nature Methods
https://www.readbyqxmd.com/read/28436590/identification-of-small-molecules-using-accurate-mass-ms-ms-search
#20
REVIEW
Tobias Kind, Hiroshi Tsugawa, Tomas Cajka, Yan Ma, Zijuan Lai, Sajjan S Mehta, Gert Wohlgemuth, Dinesh Kumar Barupal, Megan R Showalter, Masanori Arita, Oliver Fiehn
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-based annotation of chemical structures is impacted by instrumental settings and requirements, data acquisition modes including data-dependent and data-independent methods, library scoring algorithms, as well as post-curation steps. We critically discuss parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed...
April 24, 2017: Mass Spectrometry Reviews
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"