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https://www.readbyqxmd.com/read/27797532/tag-count-analysis-of-large-scale-proteomic-data
#1
Owen E Branson, Michael Alan 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 semi-quantitative. 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...
October 31, 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
#2
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...
September 9, 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
#3
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...
October 6, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27601075/correcting-for-frequency-drift-in-clinical-brain-mr-spectroscopy
#4
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...
September 7, 2016: Journal of Neuroimaging: Official Journal of the American Society of Neuroimaging
https://www.readbyqxmd.com/read/27248514/smart-statistical-metabolomics-analysis-an-r-tool
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/26860614/mechanisms-of-snr-and-line-shape-improvement-by-b0-correction-in-overdiscrete-mrsi-reconstruction
#11
Thomas Kirchner, Ariane Fillmer, Anke Henning
PURPOSE: Inhomogeneities of the main magnetic field cause line broadening and location-dependent frequency shifts in brain MRSI. These are often visible despite advanced B0 shimming. The purpose of this work is to propose an advanced B0 correction method that can easily be applied during postprocessing. METHODS: A target-driven overdiscrete reconstruction method previously introduced for MRSI is modified by dividing it into two steps. In a first step, an intermediate spectroscopic image with arbitrarily high resolution is generated, on which B0 correction is performed as an additional processing step based on an additionally acquired B0 map...
February 10, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/26851602/nmr-based-metabonomics-for-understanding-the-influence-of-dormant-female-genital-tuberculosis-on-metabolism-of-the-human-endometrium
#12
E Subramani, M Jothiramajayam, M Dutta, D Chakravorty, M Joshi, S Srivastava, A Mukherjee, C Datta Ray, B N Chakravarty, K Chaudhury
STUDY QUESTION: Does investigation of metabolic perturbations in endometrial tissue of women with dormant genital tuberculosis (GTB) during the window of implantation (WOI) assist in improving the understanding of endometrial receptivity? SUMMARY ANSWER: In dormant GTB cases significant alterations in endometrial tissue metabolites occur, largely related to energy metabolism and amino acid biosynthesis in dormant GTB cases. WHAT IS KNOWN ALREADY: As an intracellular pathogen, Mycobacterium tuberculosis strongly influences the metabolism of host cells causing metabolic dysregulation...
April 2016: Human Reproduction
https://www.readbyqxmd.com/read/26784691/imet-q-a-user-friendly-tool-for-label-free-metabolomics-quantitation-using-dynamic-peak-width-determination
#13
Hui-Yin Chang, Ching-Tai Chen, T Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, Ting-Yi Sung
Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification...
2016: PloS One
https://www.readbyqxmd.com/read/26220962/mettailor-dynamic-block-summary-and-intensity-normalization-for-robust-analysis-of-mass-spectrometry-data-in-metabolomics
#14
Gengbo Chen, Liang Cui, Guo Shou Teo, Choon Nam Ong, Chuen Seng Tan, Hyungwon Choi
MOTIVATION: Accurate cross-sample peak alignment and reliable intensity normalization is a critical step for robust quantitative analysis in untargetted metabolomics since tandem mass spectrometry (MS/MS) is rarely used for compound identification. Therefore shortcomings in the data processing steps can easily introduce false positives due to misalignments and erroneous normalization adjustments in large sample studies. RESULTS: In this work, we developed a software package MetTailor featuring two novel data preprocessing steps to remedy drawbacks in the existing processing tools...
November 15, 2015: Bioinformatics
https://www.readbyqxmd.com/read/26047147/cluster-analysis-of-commercial-samples-of-bauhinia-spp-using-hplc-uv-pda-and-mcr-als-pca-without-peak-alignment-procedure
#15
Jorge Armando Ardila, Cristiano Soleo Funari, André Marques Andrade, Alberto José Cavalheiro, Renato Lajarim Carneiro
INTRODUCTION: Bauhinia forficata Link. is recognised by the Brazilian Health Ministry as a treatment of hypoglycemia and diabetes. Analytical methods are useful to assess the plant identity due the similarities found in plants from Bauhinia spp. HPLC-UV/PDA in combination with chemometric tools is an alternative widely used and suitable for authentication of plant material, however, the shifts of retention times for similar compounds in different samples is a problem. OBJECTIVE: To perform comparisons between the authentic medicinal plant (Bauhinia forficata Link...
September 2015: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/25884293/multiple-reaction-monitoring-ion-pair-finder-a-systematic-approach-to-transform-nontargeted-mode-to-pseudotargeted-mode-for-metabolomics-study-based-on-liquid-chromatography-mass-spectrometry
#16
Ping Luo, Weidong Dai, Peiyuan Yin, Zhongda Zeng, Hongwei Kong, Lina Zhou, Xiaolin Wang, Shili Chen, Xin Lu, Guowang Xu
Pseudotargeted metabolic profiling is a novel strategy combining the advantages of both targeted and untargeted methods. The strategy obtains metabolites and their product ions from quadrupole time-of-flight (Q-TOF) MS by information-dependent acquisition (IDA) and then picks targeted ion pairs and measures them on a triple-quadrupole MS by multiple reaction monitoring (MRM). The picking of ion pairs from thousands of candidates is the most time-consuming step of the pseudotargeted strategy. Herein, a systematic and automated approach and software (MRM-Ion Pair Finder) were developed to acquire characteristic MRM ion pairs by precursor ions alignment, MS(2) spectrum extraction and reduction, characteristic product ion selection, and ion fusion...
2015: Analytical Chemistry
https://www.readbyqxmd.com/read/25843421/retention-time-correction-in-gas-chromatography-by-modeling-concentration-related-effects-applied-to-the-analysis-of-fatty-acid-methyl-esters
#17
R Kapeller
Constant and reproducible retention times are a basic requirement to allow the automatic peak assignment in complex gas chromatograms. Drifting retention times are best handled by frequent updates, based on reference peaks. Some refinements of this concept have been reported as well as alternative concepts, including pattern recognition algorithms to achieve ultimate precision; however, in applications requiring a wide concentration range, the effects of concentration on the retention time of individual peaks may become relevant, requiring special considerations...
May 15, 2015: Journal of Chromatography. A
https://www.readbyqxmd.com/read/25803548/mqtl-nmr-an-integrated-suite-for-genetic-mapping-of-quantitative-variations-of-1-h-nmr-based-metabolic-profiles
#18
Lyamine Hedjazi, Dominique Gauguier, Pierre A Zalloua, Jeremy K Nicholson, Marc-Emmanuel Dumas, Jean-Baptiste Cazier
High-throughput (1)H nuclear magnetic resonance (NMR) is an increasingly popular robust approach for qualitative and quantitative metabolic profiling, which can be used in conjunction with genomic techniques to discover novel genetic associations through metabotype quantitative trait locus (mQTL) mapping. There is therefore a crucial necessity to develop specialized tools for an accurate detection and unbiased interpretability of the genetically determined metabolic signals. Here we introduce and implement a combined chemoinformatic approach for objective and systematic analysis of untargeted (1)H NMR-based metabolic profiles in quantitative genetic contexts...
April 21, 2015: Analytical Chemistry
https://www.readbyqxmd.com/read/25780855/proteomic-profiling-of-the-retinas-in-a-neonatal-rat-model-of-oxygen-induced-retinopathy-with-a-reproducible-ion-current-based-ms1-approach
#19
Chengjian Tu, Kay D Beharry, Xiaomeng Shen, Jun Li, Lianshui Wang, Jacob V Aranda, Jun Qu
Investigation of the retina proteome during hypoxia-induced retinal neovascularization is valuable for understanding pathogenesis of retinopathy of prematurity (ROP). Here we employed a reproducible ion-current-based MS1 quantification approach (ICB) to explore the retinal proteomic changes in early stage of ROP in a rat model of oxygen-induced retinopathy (OIR). Retina proteins, which are rich in membrane proteins, were efficiently extracted by a detergent-cocktail and subjected to precipitation/on-pellet-digestion, followed by nano-LC-MS analysis on a 75-cm column with a 7-h gradient...
May 1, 2015: Journal of Proteome Research
https://www.readbyqxmd.com/read/25702270/a-novel-fourth-order-calibration-method-based-on-alternating-quinquelinear-decomposition-algorithm-for-processing-high-performance-liquid-chromatography-diode-array-detection-kinetic-ph-data-of-naptalam-hydrolysis
#20
Xiang-Dong Qing, Hai-Long Wu, Xi-Hua Zhang, Yong Li, Hui-Wen Gu, Ru-Qin Yu
Five-way high performance liquid chromatography-diode array detection (HPLC-DAD)-kinetic-pH data were obtained by recording the kinetic evolution of HPLC-DAD signals of samples at different pH values and a new fourth-order calibration method, alternating quinquelinear decomposition (AQQLD) based on pseudo-fully stretched matrix forms of the quinquelinear model, was developed. Simulated data were analyzed to investigate the performance of AQQLD in comparison with five-way parallel factor analysis (PARAFAC). The tested results demonstrated that AQQLD has the advantage of faster convergence rate and being insensitive to the excess component number adopted in the model...
February 25, 2015: Analytica Chimica Acta
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