keyword
MENU ▼
Read by QxMD icon Read
search

Xcms

keyword
https://www.readbyqxmd.com/read/28621925/kpic2-an-effective-framework-for-mass-spectrometry-based-metabolomics-using-pure-ion-chromatograms
#1
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
#2
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
#3
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 NIH 7001 diets were comprehensively analyzed using nanoLC-MS/MS. Among the over two thousand 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...
May 24, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28497560/untargeted-metabolomic-analysis-of-capsicum-spp-by-gc-ms
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27809493/influence-of-mass-resolving-power-in-orbital-ion-trap-mass-spectrometry-based-metabolomics
#13
Lukáš Najdekr, David Friedecký, Ralf Tautenhahn, Tomáš Pluskal, Junhua Wang, Yingying Huang, Tomáš 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...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27802026/magnetic-microbead-affinity-selection-screening-magmass-of-botanical-extracts-for-inhibitors-of-15-lipoxygenase
#14
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 23, 2016: Journal of Natural Products
https://www.readbyqxmd.com/read/27775610/prediction-detection-and-validation-of-isotope-clusters-in-mass-spectrometry-data
#15
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
#16
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
#17
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...
October 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
#18
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
#19
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
#20
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
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"