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https://www.readbyqxmd.com/read/28959852/-subacute-toxicity-metabonomics-of-jinlingzi-powder-based-on-lc-ms
#1
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
#2
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 E 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...
September 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28922607/antdas-automatic-data-analysis-strategy-for-uplc-qtof-based-nontargeted-metabolic-profiling-analysis
#3
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
#4
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...
August 16, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28795107/mass-spectrometry-data-of-metabolomics-analysis-of-nepenthes-pitchers
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/28243334/metabolomic-analysis-of-human-oral-cancer-cells-with-adenylate-kinase-2-or-phosphorylate-glycerol-kinase-1-inhibition
#15
Eoon Hye Ji, Li Cui, Xiaoqing Yuan, Siliangyu Cheng, Diana Messadi, Xinmin Yan, Shen Hu
The purpose of this study was to use liquid chromatography-mass spectrometry (LC-MS) with XCMS for a quantitative metabolomic analysis of UM1 and UM2 oral cancer cells after knockdown of metabolic enzyme adenylate kinase 2 (AK2) or phosphorylate glycerol kinase 1 (PGK1). UM1 and UM2 cells were initially transfected with AK2 siRNA, PGK1 siRNA or scrambled control siRNA, and then analyzed with LC-MS for metabolic profiles. XCMS analysis of the untargeted metabolomics data revealed a total of 3200-4700 metabolite features from the transfected UM1 or UM2 cancer cells and 369-585 significantly changed metabolites due to AK2 or PGK1 suppression...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28225594/mass-spectral-feature-list-optimizer-ms-flo-a-tool-to-minimize-false-positive-peak-reports-in-untargeted-liquid-chromatography-mass-spectroscopy-lc-ms-data-processing
#16
Brian C DeFelice, Sajjan Singh Mehta, Stephanie Samra, Tomáš Čajka, Benjamin Wancewicz, Johannes F Fahrmann, Oliver Fiehn
Untargeted metabolomics by liquid chromatography-mass spectrometry generates data-rich chromatograms in the form of m/z-retention time features. Managing such datasets is a bottleneck. Many popular data processing tools, including XCMS-online and MZmine2, yield numerous false-positive peak detections. Flagging and removing such false peaks manually is a time-consuming task and prone to human error. We present a web application, Mass Spectral Feature List Optimizer (MS-FLO), to improve the quality of feature lists after initial processing to expedite the process of data curation...
March 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194963/mspurity-automated-evaluation-of-precursor-ion-purity-for-mass-spectrometry-based-fragmentation-in-metabolomics
#17
Thomas N Lawson, Ralf J M Weber, Martin R Jones, Andrew J Chetwynd, Giovanny Rodrı Guez-Blanco, Riccardo Di Guida, Mark R Viant, Warwick B Dunn
Tandem mass spectrometry (MS/MS or MS(2)) is a widely used approach for structural annotation and identification of metabolites in complex biological samples. The importance of assessing the contribution of the precursor ion within an isolation window for MS(2) experiments has been previously detailed in proteomics, where precursor ion purity influences the quality and accuracy of matching to mass spectral libraries, but to date, there has been little attention to this data-processing technique in metabolomics...
February 8, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/27991859/breath-mass-ion-biomarkers-of-breast-cancer
#18
Michael Phillips, Renee Cataneo, Cassie Lebauer, Mayur Mundada, Christobel Saunders
BACKGROUND: Breath volatile organic compounds (VOCs) contain biomarkers of breast cancer that are detectable with gas chromatography mass spectrometry (GC MS). However, chemical identification of breath VOC biomarkers may be erroneous because spectral matching can misidentify their structure. Breath mass ions detected with GC MS have been proposed as intrinsically robust biomarkers because they can be identified without spectral matching. We investigated whether breath mass ion biomarkers could identify breast cancer...
December 19, 2016: Journal of Breath Research
https://www.readbyqxmd.com/read/27983788/data-streaming-for-metabolomics-accelerating-data-processing-and-analysis-from-days-to-minutes
#19
J Rafael Montenegro-Burke, Aries E Aisporna, H Paul Benton, Duane Rinehart, Mingliang Fang, Tao Huan, Benedikt Warth, Erica M Forsberg, Brian T Abe, Julijana Ivanisevic, Luc Teyton, Luke L Lairson, Gary Siuzdak
The speed and throughput of analytical platforms has been a driving force in recent years in the "omics" technologies and while great strides have been accomplished in both chromatography and mass spectrometry, data analysis times have not benefited at the same pace. Even though personal computers have become more powerful, data transfer times still represent a bottleneck in data processing due to the increasingly complex data files and studies with a greater number of samples. To meet the demand of analyzing hundreds to thousands of samples within a given experiment, we have developed a data streaming platform, XCMS Stream, which capitalizes on the acquisition time to compress and stream recently acquired data files to data processing servers, mimicking just-in-time production strategies from the manufacturing industry...
December 16, 2016: Analytical Chemistry
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
#20
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...
November 25, 2016: Journal of Chromatography. A
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