Literature DB >> 24489421

Simultaneous Phase and Scatter Correction for NMR Datasets.

Bradley Worley1, Robert Powers1.   

Abstract

Nuclear magnetic resonance (NMR) spectroscopy has proven invaluable in the diverse field of chemometrics due to its ability to deliver information-rich spectral datasets of complex mixtures for analysis by techniques such as principal component analysis (PCA). However, NMR datasets present a unique challenge during preprocessing due to differences in phase offsets between individual spectra, thus complicating the correction of random dilution factors that may also occur. We show that simultaneously correcting phase and dilution errors in NMR datasets representative of metabolomics data yields improved cluster quality in PCA scores space, even with significant initial phase errors in the data.

Entities:  

Keywords:  MSC; NMR; PCA; PLS; Phase-scatter correction; SNV

Year:  2014        PMID: 24489421      PMCID: PMC3907089          DOI: 10.1016/j.chemolab.2013.11.005

Source DB:  PubMed          Journal:  Chemometr Intell Lab Syst        ISSN: 0169-7439            Impact factor:   3.491


  12 in total

1.  Predicting the in vivo mechanism of action for drug leads using NMR metabolomics.

Authors:  Steven Halouska; Robert J Fenton; Raúl G Barletta; Robert Powers
Journal:  ACS Chem Biol       Date:  2011-12-01       Impact factor: 5.100

2.  Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics.

Authors:  Frank Dieterle; Alfred Ross; Götz Schlotterbeck; Hans Senn
Journal:  Anal Chem       Date:  2006-07-01       Impact factor: 6.986

3.  Scaling and normalization effects in NMR spectroscopic metabonomic data sets.

Authors:  Andrew Craig; Olivier Cloarec; Elaine Holmes; Jeremy K Nicholson; John C Lindon
Journal:  Anal Chem       Date:  2006-04-01       Impact factor: 6.986

Review 4.  NMR metabolomics and drug discovery.

Authors:  Robert Powers
Journal:  Magn Reson Chem       Date:  2009-12       Impact factor: 2.447

Review 5.  Analysis of bacterial biofilms using NMR-based metabolomics.

Authors:  Bo Zhang; Robert Powers
Journal:  Future Med Chem       Date:  2012-06       Impact factor: 3.808

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  Multivariate Analysis in Metabolomics.

Authors:  Bradley Worley; Robert Powers
Journal:  Curr Metabolomics       Date:  2013

8.  Utilities for quantifying separation in PCA/PLS-DA scores plots.

Authors:  Bradley Worley; Steven Halouska; Robert Powers
Journal:  Anal Biochem       Date:  2012-10-15       Impact factor: 3.365

9.  Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra.

Authors:  R A Chylla; B F Volkman; J L Markley
Journal:  J Biomol NMR       Date:  1998-08       Impact factor: 2.835

10.  BioMagResBank.

Authors:  Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

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  12 in total

1.  NMR Metabolomics Protocols for Drug Discovery.

Authors:  Fatema Bhinderwala; Robert Powers
Journal:  Methods Mol Biol       Date:  2019

2.  Metabolomics Analyses from Tissues in Parkinson's Disease.

Authors:  Fatema Bhinderwala; Shulei Lei; Jade Woods; Jordan Rose; Darrell D Marshall; Eli Riekeberg; Aline De Lima Leite; Martha Morton; Eric D Dodds; Rodrigo Franco; Robert Powers
Journal:  Methods Mol Biol       Date:  2019

3.  Staphylococcus aureus metabolic adaptations during the transition from a daptomycin susceptibility phenotype to a daptomycin nonsusceptibility phenotype.

Authors:  Rosmarie Gaupp; Shulei Lei; Joseph M Reed; Henrik Peisker; Susan Boyle-Vavra; Arnold S Bayer; Markus Bischoff; Mathias Herrmann; Robert S Daum; Robert Powers; Greg A Somerville
Journal:  Antimicrob Agents Chemother       Date:  2015-05-11       Impact factor: 5.191

4.  GPR55 receptor antagonist decreases glycolytic activity in PANC-1 pancreatic cancer cell line and tumor xenografts.

Authors:  Michel Bernier; Jonathan Catazaro; Nagendra S Singh; Artur Wnorowski; Anna Boguszewska-Czubara; Krzysztof Jozwiak; Robert Powers; Irving W Wainer
Journal:  Int J Cancer       Date:  2017-08-07       Impact factor: 7.396

5.  Assessment of Metabolic Changes in Mycobacterium smegmatis Wild-Type and alr Mutant Strains: Evidence of a New Pathway of d-Alanine Biosynthesis.

Authors:  Darrell D Marshall; Steven Halouska; Denise K Zinniel; Robert J Fenton; Katie Kenealy; Harpreet K Chahal; Govardhan Rathnaiah; Raúl G Barletta; Robert Powers
Journal:  J Proteome Res       Date:  2017-02-14       Impact factor: 4.466

6.  Combining DI-ESI-MS and NMR datasets for metabolic profiling.

Authors:  Darrell D Marshall; Shulei Lei; Bradley Worley; Yuting Huang; Aracely Garcia-Garcia; Rodrigo Franco; Eric D Dodds; Robert Powers
Journal:  Metabolomics       Date:  2015-04       Impact factor: 4.290

7.  Statistical removal of background signals from high-throughput (1)H NMR line-broadening ligand-affinity screens.

Authors:  Bradley Worley; Nicholas J Sisco; Robert Powers
Journal:  J Biomol NMR       Date:  2015-07-09       Impact factor: 2.835

8.  Redox Imbalance Underlies the Fitness Defect Associated with Inactivation of the Pta-AckA Pathway in Staphylococcus aureus.

Authors:  Darrell D Marshall; Marat R Sadykov; Vinai C Thomas; Kenneth W Bayles; Robert Powers
Journal:  J Proteome Res       Date:  2016-03-24       Impact factor: 4.466

9.  Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility.

Authors:  Stewart G Gardner; Darrell D Marshall; Robert S Daum; Robert Powers; Greg A Somerville
Journal:  Antimicrob Agents Chemother       Date:  2017-12-21       Impact factor: 5.191

10.  MVAPACK: a complete data handling package for NMR metabolomics.

Authors:  Bradley Worley; Robert Powers
Journal:  ACS Chem Biol       Date:  2014-03-07       Impact factor: 5.100

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