The Human Serum Metabolome
Nikolaos Psychogios,David Hau,Jun Peng,An Chi Guo,Rupasri Mandal,Souhaila Bouatra,Igor Sinelnikov,Ramanarayan Krishnamurthy,Roman Eisner,Bijaya Gautam,Nelson Young,Jianguo Xia,Craig Knox,Edison Dong,Paul Huang,Zsuzsanna Hollander,Theresa L. Pedersen,Steven R. Smith,Fiona Bamforth,Russell Greiner,Bruce M. McManus,John W. Newman,Theodore L. Goodfriend,David S. Wishart,David S. Wishart +24 more
TLDR
This work has combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome.Abstract:
Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.read more
Citations
More filters
Journal ArticleDOI
HMDB 3.0—The Human Metabolome Database in 2013
David S. Wishart,Timothy Jewison,An Chi Guo,Michael Wilson,Craig Knox,Yifeng Liu,Yannick Djoumbou,Rupasri Mandal,Farid Aziat,Edison Dong,Souhaila Bouatra,Igor Sinelnikov,David Arndt,Jianguo Xia,Philip Liu,Faizath S. Yallou,Trent C. Bjorndahl,Rolando Perez-Pineiro,Roman Eisner,Felicity Allen,Vanessa Neveu,Russell Greiner,Augustin Scalbert +22 more
TL;DR: New database visualization tools and new data content have been added or enhanced to the HMDB, which includes better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps.
Journal ArticleDOI
MetaboAnalyst 3.0—making metabolomics more meaningful
TL;DR: By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, the server has been able to substantially improve its performance, capacity and user interactivity.
Journal ArticleDOI
Pro-resolving lipid mediators are leads for resolution physiology
TL;DR: The mechanisms of specialized pro-resolving mediators and omega-3 essential fatty acid pathways that could help us to understand their physiological functions are covered.
Journal ArticleDOI
The Human Urine Metabolome
Souhaila Bouatra,Farid Aziat,Rupasri Mandal,An Chi Guo,Michael Wilson,Craig Knox,Trent C. Bjorndahl,Ramanarayan Krishnamurthy,Fozia Saleem,Philip B. Liu,Zerihun T. Dame,Jenna Poelzer,Jessica Huynh,Faizath S. Yallou,Nick Psychogios,Edison Dong,Ralf Bogumil,Cornelia Roehring,David S. Wishart,David S. Wishart +19 more
TL;DR: A comprehensive, quantitative, metabolome-wide characterization of human urine and the identification and annotation of several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage are undertaken.
Journal ArticleDOI
Metabolic pathways promoting cancer cell survival and growth.
TL;DR: These adaptive mechanisms that promote metabolic reprogramming in cancer and emerging approaches to probe tumour metabolism in vivo are discussed and their potential to expand the metabolic repertoire of malignant cells even further are discussed.
References
More filters
Journal ArticleDOI
A simple method for the isolation and purification of total lipides from animal tissues.
TL;DR: In this paper, the authors described a simplified version of the method and reported the results of a study of its application to different tissues, including the efficiency of the washing procedure in terms of the removal from tissue lipides of some non-lipide substances of special biochemical interest.
Journal ArticleDOI
REACTIVE OXYGEN SPECIES: Metabolism, Oxidative Stress, and Signal Transduction
Klaus Apel,Heribert Hirt +1 more
TL;DR: The mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions are described and the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
From genomics to chemical genomics: new developments in KEGG
Minoru Kanehisa,Susumu Goto,Masahiro Hattori,Kiyoko F. Aoki-Kinoshita,Masumi Itoh,Shuichi Kawashima,Toshiaki Katayama,Michihiro Araki,Mika Hirakawa +8 more
TL;DR: The scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules, and RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions.
Journal ArticleDOI
HMDB: The human metabolome database
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,Michael J. Lewis,Marie-Aude Coutouly,Ian D. Forsythe,Peter Tang,Savita Shrivastava,Kevin Jeroncic,Paul Stothard,Godwin Amegbey,David Block,David Hau,James Wagner,Jessica Miniaci,Melisa Clements,Mulu Gebremedhin,Natalie Guo,Ying Wen Zhang,Gavin E. Duggan,Glen D. MacInnis,Alim M. Weljie,Reza Dowlatabadi,Fiona Bamforth,Derrick L. J. Clive,Russell Greiner,Liang Li,Thomas J. Marrie,Brian D. Sykes,Hans J. Vogel,Lori M.M. Querengesser +39 more
TL;DR: The Human Metabolome Database is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community.
Related Papers (5)
HMDB 3.0—The Human Metabolome Database in 2013
David S. Wishart,Timothy Jewison,An Chi Guo,Michael Wilson,Craig Knox,Yifeng Liu,Yannick Djoumbou,Rupasri Mandal,Farid Aziat,Edison Dong,Souhaila Bouatra,Igor Sinelnikov,David Arndt,Jianguo Xia,Philip Liu,Faizath S. Yallou,Trent C. Bjorndahl,Rolando Perez-Pineiro,Roman Eisner,Felicity Allen,Vanessa Neveu,Russell Greiner,Augustin Scalbert +22 more
HMDB: The human metabolome database
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,Michael J. Lewis,Marie-Aude Coutouly,Ian D. Forsythe,Peter Tang,Savita Shrivastava,Kevin Jeroncic,Paul Stothard,Godwin Amegbey,David Block,David Hau,James Wagner,Jessica Miniaci,Melisa Clements,Mulu Gebremedhin,Natalie Guo,Ying Wen Zhang,Gavin E. Duggan,Glen D. MacInnis,Alim M. Weljie,Reza Dowlatabadi,Fiona Bamforth,Derrick L. J. Clive,Russell Greiner,Liang Li,Thomas J. Marrie,Brian D. Sykes,Hans J. Vogel,Lori M.M. Querengesser +39 more
'metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological nmr spectroscopic data
Proposed minimum reporting standards for chemical analysis
Lloyd W. Sumner,Alexander Amberg,Dave Barrett,Michael H. Beale,Richard D. Beger,Clare A. Daykin,Teresa W.-M. Fan,Oliver Fiehn,Royston Goodacre,Julian L. Griffin,Thomas Hankemeier,Nigel Hardy,James M. Harnly,Richard M. Higashi,Joachim Kopka,Andrew N. Lane,John C. Lindon,Philip J. Marriott,Andrew W. Nicholls,Michael D. Reily,John J. Thaden,Mark R. Viant +21 more