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https://www.readbyqxmd.com/read/29098829/-difference-of-chemical-constituents-in-eucommiae-cortex-from-different-habitats-by-lc-qtof-ms-ms
#1
Ying Yan, Hui Zhao, Li-Si Zou, Xun-Hong Liu, Chuan Chai, Sheng-Nan Wang, Yu-Jiao Hua
In order to study the influence of ecological environment regarding the synthesis and accumulation of metabolites in Eucommiae Cortex, LC-QTOF MS/MS method combined with multivariate statistical analysis was used to analyze the differences of chemical constituents in Eucommiae Cortex from different habitats. Through the analysis of the multistage tandem mass spectrometry, the characteristic peaks were extracted with mass spectrometry data peak matching, peak alignment, and noise filtering. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) were used for data processing...
July 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29054151/enhanced-ms-ms-coverage-for-metabolite-identification-in-lc-ms-based-untargeted-metabolomics-by-target-directed-data-dependent-acquisition-with-time-staggered-precursor-ion-list
#2
Yang Wang, Ruibing Feng, Ruibing Wang, Fengqing Yang, Peng Li, Jian-Bo Wan
Metabolite identification is one of the major bottlenecks in liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics owing to the difficulty of acquiring MS/MS information of most metabolites detected. Data dependent acquisition (DDA) has been currently used to acquire MS/MS data in untargeted metabolomics. When dealing with the complex biological samples, top-n-based DDA method selects only a small fraction of the ions for fragmentation, leading to low MS/MS coverage of metabolites in untargeted metabolomics...
November 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29029747/an-alignment-algorithm-for-lc-ms-based-metabolomics-dataset-assisted-by-ms-ms-information
#3
Lili Li, Weijie Ren, Hongwei Kong, Chunxia Zhao, Xinjie Zhao, Xiaohui Lin, Xin Lu, Guowang Xu
Liquid chromatography-mass spectrometry (LC-MS) is an important analytical platform for metabolomics study. Peak alignment of metabolomics dataset is one of the keys for a successful metabolomics study. In this work, a MS/MS-based peak alignment method for LC-MS metabolomics data was developed. A rigorous strategy for screening endogenous reference variables was proposed. Firstly, candidate endogenous reference variables were selected based on MS, MS/MS and retention time in all samples. Multiple robust endogenous reference variables were obtained through further evaluation and confirmation...
October 16, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28985049/themis-batch-preprocessing-for-ultrahigh-resolution-mass-spectra-of-complex-mixtures
#4
Remy Gavard, David Rossell, Simon E F Spencer, Mark P Barrow
Fourier transform ion cyclotron resonance mass spectrometry affords the resolving power to determine an unprecedented number of components in complex mixtures, such as petroleum. The software tools required to also analyze these data struggle to keep pace with advancing instrument capabilities and increasing quantities of data, particularly in terms of combining information efficiently across multiple replicates. Improved confidence in data and the use of replicates is particularly important where strategic decisions will be based upon the analysis...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28922607/antdas-automatic-data-analysis-strategy-for-uplc-qtof-based-nontargeted-metabolic-profiling-analysis
#5
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/28755905/mass-spectra-based-peak-alignment-for-automatic-nontargeted-metabolic-profiling-analysis-for-biomarker-screening-in-plant-samples
#6
Hai-Yan Fu, Ou Hu, Yue-Ming Zhang, Li Zhang, Jing-Jing Song, Peang Lu, Qing-Xia Zheng, Ping-Ping Liu, Qian-Si Chen, Bing Wang, Xiao-Yu Wang, Lu Han, Yong-Jie Yu
Nontargeted metabolic profiling analysis is a difficult task in a routine investigation because hundreds of chromatographic peaks are eluted within a short time, and the time shift problem is severe across samples. To address these problems, the present work developed an automatic nontargeted metabolic profiling analysis (anTMPA) method. First, peaks from the total ion chromatogram were extracted using modified multiscale Gaussian smoothing method. Then, a novel peak alignment strategy was employed based on the mass spectra and retention times of the peaks in which the maximum mass spectral correlation coefficient path was extracted using a modified dynamic programming method...
September 1, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28573461/automatic-frequency-and-phase-alignment-of-in-vivo-j-difference-edited-mr-spectra-by-frequency-domain-correlation
#7
Evita C Wiegers, Bart W J Philips, Arend Heerschap, Marinette van der Graaf
OBJECTIVE: J-difference editing is often used to select resonances of compounds with coupled spins in (1)H-MR spectra. Accurate phase and frequency alignment prior to subtracting J-difference-edited MR spectra is important to avoid artefactual contributions to the edited resonance. MATERIALS AND METHODS: In-vivo J-difference-edited MR spectra were aligned by maximizing the normalized scalar product between two spectra (i.e., the correlation over a spectral region)...
June 1, 2017: Magma
https://www.readbyqxmd.com/read/28520864/from-chromatogram-to-analyte-to-metabolite-how-to-pick-horses-for-courses-from-the-massive-web-resources-for-mass-spectral-plant-metabolomics
#8
Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R Fernie
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification...
July 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28357402/copar-a-chip-seq-optimal-peak-analyzer
#9
Binhua Tang, Xihan Wang, Victor X Jin
Sequencing data quality and peak alignment efficiency of ChIP-sequencing profiles are directly related to the reliability and reproducibility of NGS experiments. Till now, there is no tool specifically designed for optimal peak alignment estimation and quality-related genomic feature extraction for ChIP-sequencing profiles. We developed open-sourced COPAR, a user-friendly package, to statistically investigate, quantify, and visualize the optimal peak alignment and inherent genomic features using ChIP-seq data from NGS experiments...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28208263/visualization-quantification-and-alignment-of-spectral-drift-in-population-scale-untargeted-metabolomics-data
#10
Jeramie D Watrous, Mir Henglin, Brian Claggett, Kim A Lehmann, Martin G Larson, Susan Cheng, Mohit Jain
Untargeted liquid-chromatography-mass spectrometry (LC-MS)-based metabolomics analysis of human biospecimens has become among the most promising strategies for probing the underpinnings of human health and disease. Analysis of spectral data across population scale cohorts, however, is precluded by day-to-day nonlinear signal drifts in LC retention time or batch effects that complicate comparison of thousands of untargeted peaks. To date, there exists no efficient means of visualization and quantitative assessment of signal drift, correction of drift when present, and automated filtering of unstable spectral features, particularly across thousands of data files in population scale experiments...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/27797532/tag-count-analysis-of-large-scale-proteomic-data
#11
Owen E Branson, Michael A Freitas
Label-free quantitative methods are advantageous in bottom-up (shotgun) proteomics because they are robust and can easily be applied to different workflows without additional cost. Both label-based and label-free approaches are routinely applied to discovery-based proteomics experiments and are widely accepted as semiquantitative. Label-free quantitation approaches are segregated into two distinct approaches: peak-abundance-based approaches and spectral counting (SpC). Peak abundance approaches like MaxLFQ, which is integrated into the MaxQuant environment, require precursor peak alignment that is computationally intensive and cannot be routinely applied to low-resolution data...
December 2, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27650662/global-peak-alignment-for-comprehensive-two-dimensional-gas-chromatography-mass-spectrometry-using-point-matching-algorithms
#12
Beichuan Deng, Seongho Kim, Hengguang Li, Elisabeth Heath, Xiang Zhang
Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC[Formula: see text][Formula: see text][Formula: see text]GC-MS) has been used to analyze multiple samples in a metabolomics study. However, due to some uncontrollable experimental conditions, such as the differences in temperature or pressure, matrix effects on samples and stationary phase degradation, there is always a shift of retention times in the two GC columns between samples. In order to correct the retention time shifts in GC[Formula: see text][Formula: see text][Formula: see text]GC-MS, the peak alignment is a crucial data analysis step to recognize the peaks generated by the same metabolite in different samples...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27628670/workflow-for-integrated-processing-of-multicohort-untargeted-1-h-nmr-metabolomics-data-in-large-scale-metabolic-epidemiology
#13
Ibrahim Karaman, Diana L S Ferreira, Claire L Boulangé, Manuja R Kaluarachchi, David Herrington, Anthony C Dona, Raphaële Castagné, Alireza Moayyeri, Benjamin Lehne, Marie Loh, Paul S de Vries, Abbas Dehghan, Oscar H Franco, Albert Hofman, Evangelos Evangelou, Ioanna Tzoulaki, Paul Elliott, John C Lindon, Timothy M D Ebbels
Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robust processing pipelines that can ensure reliable data for statistical analysis. The COMBI-BIO project incorporates serum from ∼8000 individuals, in three cohorts, profiled by six assays in two phases using both (1)H NMR and UPLC-MS...
December 2, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27601075/correcting-for-frequency-drift-in-clinical-brain-mr-spectroscopy
#14
Benjamin C Rowland, Huijun Liao, Fatah Adan, Laura Mariano, John Irvine, Alexander P Lin
PURPOSE: Averaging multiple repetitions to improve signal-to-noise ratio is common practice in magnetic resonance spectroscopy (MRS). However, temporal variations in scanner B0 due to motion or gradient heating may cause spectra to become misaligned, broadening and distorting peaks and impacting on processing and quantification. We present a comparison using in vivo data of different methods for correcting these errors. METHODS: Three different correction methods were applied to 53 brain scans: residual water peak alignment, creatine fitting, and spectral registration...
January 2017: Journal of Neuroimaging: Official Journal of the American Society of Neuroimaging
https://www.readbyqxmd.com/read/27248514/smart-statistical-metabolomics-analysis-an-r-tool
#15
Yu-Jen Liang, Yu-Ting Lin, Chia-Wei Chen, Chien-Wei Lin, Kun-Mao Chao, Wen-Harn Pan, Hsin-Chou Yang
Metabolomics data provide unprecedented opportunities to decipher metabolic mechanisms by analyzing hundreds to thousands of metabolites. Data quality concerns and complex batch effects in metabolomics must be appropriately addressed through statistical analysis. This study developed an integrated analysis tool for metabolomics studies to streamline the complete analysis flow from initial data preprocessing to downstream association analysis. We developed Statistical Metabolomics Analysis-An R Tool (SMART), which can analyze input files with different formats, visually represent various types of data features, implement peak alignment and annotation, conduct quality control for samples and peaks, explore batch effects, and perform association analysis...
June 21, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27237840/an-improved-pseudotargeted-metabolomics-approach-using-multiple-ion-monitoring-with-time-staggered-ion-lists-based-on-ultra-high-performance-liquid-chromatography-quadrupole-time-of-flight-mass-spectrometry
#16
Yang Wang, Fang Liu, Peng Li, Chengwei He, Ruibing Wang, Huanxing Su, Jian-Bo Wan
Pseudotargeted metabolomics is a novel strategy integrating the advantages of both untargeted and targeted methods. The conventional pseudotargeted metabolomics required two MS instruments, i.e., ultra-high performance liquid chromatography/quadrupole-time- of-flight mass spectrometry (UHPLC/Q-TOF MS) and UHPLC/triple quadrupole mass spectrometry (UHPLC/QQQ-MS), which makes method transformation inevitable. Furthermore, the picking of ion pairs from thousands of candidates and the swapping of the data between two instruments are the most labor-intensive steps, which greatly limit its application in metabolomic analysis...
July 13, 2016: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27216666/experimental-variability-and-data-pre-processing-as-factors-affecting-the-discrimination-power-of-some-chemometric-approaches-pca-ca-and-a-new-algorithm-based-on-linear-regression-applied-to-esi-ms-and-rplc-uv-data-application-on-green-tea-extracts
#17
E Iorgulescu, V A Voicu, C Sârbu, F Tache, F Albu, A Medvedovici
The influence of the experimental variability (instrumental repeatability, instrumental intermediate precision and sample preparation variability) and data pre-processing (normalization, peak alignment, background subtraction) on the discrimination power of multivariate data analysis methods (Principal Component Analysis -PCA- and Cluster Analysis -CA-) as well as a new algorithm based on linear regression was studied. Data used in the study were obtained through positive or negative ion monitoring electrospray mass spectrometry (+/-ESI/MS) and reversed phase liquid chromatography/UV spectrometric detection (RPLC/UV) applied to green tea extracts...
August 1, 2016: Talanta
https://www.readbyqxmd.com/read/27181885/gls-finder-a-platform-for-fast-profiling-of-glucosinolates-in-brassica-vegetables
#18
Jianghao Sun, Mengliang Zhang, Pei Chen
Mass spectrometry combined with related tandem techniques has become the most popular method for plant secondary metabolite characterization. We introduce a new strategy based on in-database searching, mass fragmentation behavior study, formula predicting for fast profiling of glucosinolates, a class of important compounds in brassica vegetables. A MATLAB script-based expert system computer program, "GLS-Finder", was developed. It is capable of qualitative and semi-quantitative analyses of glucosinolates in samples using data generated by ultrahigh-performance liquid chromatography-high-resolution accurate mass with multi-stage mass fragmentation (UHPLC-HRAM/MS(n))...
June 1, 2016: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27178551/-1-h-nmr-based-metabolite-profiling-workflow-to-reduce-inter-sample-chemical-shift-variations-in-urine-samples-for-improved-biomarker-discovery
#19
Ryan B Gil, Rainer Lehmann, Philippe Schmitt-Kopplin, Silke S Heinzmann
Metabolite profiling of urine has seen much advancement in recent years, and its analysis by nuclear magnetic resonance (NMR) spectroscopy has become well established. However, the highly variable nature of human urine still requires improved protocols despite some standardization. In particular, diseases such as kidney disease can have a profound effect on the composition of urine and generate a highly diverse sample set for clinical studies. Large variations in pH and the cationic concentration of urine play an important role in creating positional noise within datasets generated from NMR...
July 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/26901849/chemometrics-applied-to-quality-control-and-metabolomics-for-traditional-chinese-medicines
#20
REVIEW
Shao Liu, Yi-Zeng Liang, Hai-tao Liu
Traditional Chinese medicines (TCMs) bring a great challenge in quality control and evaluating the efficacy because of their complexity of chemical composition. Chemometric techniques provide a good opportunity for mining more useful chemical information from TCMs. Then, the application of chemometrics in the field of TCMs is spontaneous and necessary. This review focuses on the recent various important chemometrics tools for chromatographic fingerprinting, including peak alignment information features, baseline correction and applications of chemometrics in metabolomics and modernization of TCMs, including authentication and evaluation of the quality of TCMs, evaluating the efficacy of TCMs and essence of TCM syndrome...
March 15, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
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