Literature DB >> 24260723

Databases and Software for NMR-Based Metabolomics.

James J Ellinger1, Roger A Chylla, Eldon L Ulrich, John L Markley.   

Abstract

New software and increasingly sophisticated NMR metabolite spectral databases are advancing the unique abilities of NMR spectroscopy to identify and quantify small molecules in solution for studies of metabolite biomarkers and metabolic flux. Public and commercial databases now contain experimental 1D 1H, 13C and 2D 1H-13C spectra and extracted spectral parameters for over a thousand compounds and theoretical data for thousands more. Public databases containing experimental NMR data from complex metabolic studies are emerging. These databases are providing information vital for the construction and testing of new computational algorithms for NMR-based chemometric and quantitative metabolomics studies. In this review we focus on database and software tools that support a quantitative NMR approach to the analysis of 1D and 2D NMR spectra of complex biological mixtures.

Entities:  

Keywords:  Chemometrics; databases; nuclear magnetic resonance; quantitative metabolomics; software

Year:  2013        PMID: 24260723      PMCID: PMC3832261          DOI: 10.2174/2213235X11301010028

Source DB:  PubMed          Journal:  Curr Metabolomics        ISSN: 2213-235X


  22 in total

1.  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

2.  PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.

Authors:  Kenji Akiyama; Eisuke Chikayama; Hiroaki Yuasa; Yukihisa Shimada; Takayuki Tohge; Kazuo Shinozaki; Masami Yokota Hirai; Tetsuya Sakurai; Jun Kikuchi; Kazuki Saito
Journal:  In Silico Biol       Date:  2008

3.  The human cerebrospinal fluid metabolome.

Authors:  David S Wishart; Michael J Lewis; Joshua A Morrissey; Mitchel D Flegel; Kevin Jeroncic; Yeping Xiong; Dean Cheng; Roman Eisner; Bijaya Gautam; Dan Tzur; Summit Sawhney; Fiona Bamforth; Russ Greiner; Liang Li
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2008-05-08       Impact factor: 3.205

4.  Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data.

Authors:  R A Chylla; J L Markley
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

5.  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

6.  Measurement of absolute concentrations of individual compounds in metabolite mixtures by gradient-selective time-zero 1H-13C HSQC with two concentration references and fast maximum likelihood reconstruction analysis.

Authors:  Kaifeng Hu; James J Ellinger; Roger A Chylla; John L Markley
Journal:  Anal Chem       Date:  2011-11-15       Impact factor: 6.986

7.  New bioinformatics resources for metabolomics.

Authors:  John L Markley; Mark E Anderson; Qiu Cui; Hamid R Eghbalnia; Ian A Lewis; Adrian D Hegeman; Jing Li; Christopher F Schulte; Michael R Sussman; William M Westler; Eldon L Ulrich; Zsolt Zolnai
Journal:  Pac Symp Biocomput       Date:  2007

8.  YMDB: the Yeast Metabolome Database.

Authors:  Timothy Jewison; Craig Knox; Vanessa Neveu; Yannick Djoumbou; An Chi Guo; Jacqueline Lee; Philip Liu; Rupasri Mandal; Ram Krishnamurthy; Igor Sinelnikov; Michael Wilson; David S Wishart
Journal:  Nucleic Acids Res       Date:  2011-11-07       Impact factor: 16.971

9.  From genomics to chemical genomics: new developments in KEGG.

Authors:  Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  HMDB: the Human Metabolome Database.

Authors:  David S Wishart; Dan Tzur; Craig Knox; Roman Eisner; An Chi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; Mike Lewis; Marie-Aude Coutouly; Ian Forsythe; Peter Tang; Savita Shrivastava; Kevin Jeroncic; Paul Stothard; Godwin Amegbey; David Block; David D Hau; James Wagner; Jessica Miniaci; Melisa Clements; Mulu Gebremedhin; Natalie Guo; Ying Zhang; Gavin E Duggan; Glen D Macinnis; Alim M Weljie; Reza Dowlatabadi; Fiona Bamforth; Derrick Clive; Russ Greiner; Liang Li; Tom Marrie; Brian D Sykes; Hans J Vogel; Lori Querengesser
Journal:  Nucleic Acids Res       Date:  2007-01       Impact factor: 16.971

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  19 in total

Review 1.  Emerging new strategies for successful metabolite identification in metabolomics.

Authors:  Kerem Bingol; Lei Bruschweiler-Li; Dawei Li; Bo Zhang; Mouzhe Xie; Rafael Brüschweiler
Journal:  Bioanalysis       Date:  2016-02-26       Impact factor: 2.681

2.  Extending the Scope of 1H NMR-Based Blood Metabolomics for the Analysis of Labile Antioxidants: Reduced and Oxidized Glutathione.

Authors:  G A Nagana Gowda; Vadim Pascua; Daniel Raftery
Journal:  Anal Chem       Date:  2021-10-27       Impact factor: 6.986

3.  Extending the Scope of 1H NMR Spectroscopy for the Analysis of Cellular Coenzyme A and Acetyl Coenzyme A.

Authors:  G A Nagana Gowda; Lauren Abell; Rong Tian
Journal:  Anal Chem       Date:  2019-01-17       Impact factor: 6.986

4.  A hypothetical astrocyte-microglia lactate shuttle derived from a 1H NMR metabolomics analysis of cerebrospinal fluid from a cohort of South African children with tuberculous meningitis.

Authors:  Shayne Mason; A Marceline van Furth; Lodewyk J Mienie; Udo F H Engelke; Ron A Wevers; Regan Solomons; Carolus J Reinecke
Journal:  Metabolomics       Date:  2014-10-11       Impact factor: 4.290

Review 5.  Open-access metabolomics databases for natural product research: present capabilities and future potential.

Authors:  Sean R Johnson; Bernd Markus Lange
Journal:  Front Bioeng Biotechnol       Date:  2015-03-04

Review 6.  Application of metabolomics in thyroid cancer research.

Authors:  Anna Wojakowska; Mykola Chekan; Piotr Widlak; Monika Pietrowska
Journal:  Int J Endocrinol       Date:  2015-04-20       Impact factor: 3.257

7.  OMICtools: an informative directory for multi-omic data analysis.

Authors:  Vincent J Henry; Anita E Bandrowski; Anne-Sophie Pepin; Bruno J Gonzalez; Arnaud Desfeux
Journal:  Database (Oxford)       Date:  2014-07-14       Impact factor: 3.451

Review 8.  Analytical methods in untargeted metabolomics: state of the art in 2015.

Authors:  Arnald Alonso; Sara Marsal; Antonio Julià
Journal:  Front Bioeng Biotechnol       Date:  2015-03-05

Review 9.  Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review.

Authors:  Engy A Mahrous; Mohamed A Farag
Journal:  J Adv Res       Date:  2014-10-18       Impact factor: 10.479

10.  Contribution towards a Metabolite Profile of the Detoxification of Benzoic Acid through Glycine Conjugation: An Intervention Study.

Authors:  Cindy Irwin; Mari van Reenen; Shayne Mason; Lodewyk J Mienie; Johan A Westerhuis; Carolus J Reinecke
Journal:  PLoS One       Date:  2016-12-01       Impact factor: 3.240

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