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ReDU: a framework to find and reanalyze public mass spectrometry data

Jarmusch, Alan K
Autor Jarmusch, Alan K ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Wang, Mingxun
Autor Wang, Mingxun ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Aceves, Christine M
Autor Aceves, Christine M Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Advani, Rohit S
Autor Advani, Rohit S ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Aguirre, Shaden
Autor Aguirre, Shaden Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Aksenov, Alexander A
Autor Aksenov, Alexander A ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Aleti, Gajender
Autor Aleti, Gajender Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA
Aron, Allegra T
Autor Aron, Allegra T Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Bauermeister, Anelize
Autor Bauermeister, Anelize Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
Bolleddu, Sanjana
Autor Bolleddu, Sanjana Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Bouslimani, Amina
Autor Bouslimani, Amina Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Caraballo Rodriguez, Andres Mauricio
Autor Caraballo Rodriguez, Andres Mauricio Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Chaar, Rama
Autor Chaar, Rama Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Coras, Roxana
Autor Coras, Roxana Department of Medicine, University of California, San Diego, La Jolla, CA, USA
Elijah, Emmanuel O
Autor Elijah, Emmanuel O Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Ernst, Madeleine
Autor Ernst, Madeleine Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
Gauglitz, Julia M
Autor Gauglitz, Julia M Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Gentry, Emily C
Autor Gentry, Emily C Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Husband, Makhai
Autor Husband, Makhai Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Jarmusch, Scott A
Autor Jarmusch, Scott A Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK
Jones, Kenneth L 2nd
Autor Jones, Kenneth L Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Kamenik, Zdenek
Autor Kamenik, Zdenek ORCID Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
Le Gouellec, Audrey
Autor Le Gouellec, Audrey ORCID TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
Lu, Aileen
Autor Lu, Aileen Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
McCall, Laura-Isobel
Autor McCall, Laura-Isobel Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
McPhail, Kerry L
Autor McPhail, Kerry L ORCID Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
Meehan, Michael J
Autor Meehan, Michael J Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Melnik, Alexey V
Autor Melnik, Alexey V Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Menezes, Riya C
Autor Menezes, Riya C Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
Montoya Giraldo, Yessica Alejandra
Autor Montoya Giraldo, Yessica Alejandra Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
Nguyen, Ngoc Hung
Autor Nguyen, Ngoc Hung Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Nothias, Louis Felix
Autor Nothias, Louis Felix ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Nothias-Esposito, Mélissa
Autor Nothias-Esposito, Mélissa Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Panitchpakdi, Morgan
Autor Panitchpakdi, Morgan Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
Petras, Daniel
Autor Petras, Daniel ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
Quinn, Robert A
Autor Quinn, Robert A ORCID Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA
Sikora, Nicole
Autor Sikora, Nicole Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
van der Hooft, Justin J J
Autor van der Hooft, Justin J J ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
Vargas, Fernando
Autor Vargas, Fernando Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
Vrbanac, Alison
Autor Vrbanac, Alison Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
Weldon, Kelly C
Autor Weldon, Kelly C ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
Knight, Rob
Autor Autorita ORCID Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Bandeira, Nuno
Autor Bandeira, Nuno ORCID Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
Dorrestein, Pieter C
Autor Dorrestein, Pieter C ORCID Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu

Nature methods. 2020 Sep ; 17 (9) : 901-904. [epub] 20200817

Nat Methods
ISSN 1548-7105 | 1548-7091
Zdroj

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz https://www.medvik.cz/link/pmid32807955

Grantová podpora
P41 GM103484 NIGMS NIH HHS - United States
T32 AR064194 NIAMS NIH HHS - United States
R03 CA211211 NCI NIH HHS - United States
R01 GM107550 NIGMS NIH HHS - United States
R01 LM013115 NLM NIH HHS - United States

Online Plný text

PubMed 32807955
PubMed Central PMC7968862
DOI 10.1038/s41592-020-0916-7
PII: 10.1038/s41592-020-0916-7
Knihovny.cz E-zdroje

MeSH
chemické databáze * MeSH
chemické modely MeSH
hmotnostní spektrometrie * MeSH
metabolomika metody MeSH
metadata MeSH
software * MeSH
Publikační typ
časopisecké články MeSH
práce podpořená grantem MeSH
Research Support, N.I.H., Extramural MeSH
Research Support, U.S. Gov't, Non-P.H.S. MeSH

We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.

Bioinformatics Group Wageningen University Wageningen the Netherlands

Center for Microbiome Innovation University of California San Diego La Jolla CA USA

Center for Newborn Screening Department of Congenital Disorders Statens Serum Institut Copenhagen Denmark

Collaborative Mass Spectrometry Innovation Center University of California San Diego La Jolla CA USA

Department of Biochemistry and Molecular Biology Michigan State University Lansing MI USA

Department of Bioengineering University of California San Diego La Jolla CA USA

Department of Chemistry and Biochemistry Department of Microbiology and Plant Biology and Laboratories of Molecular Anthropology and Microbiome Research University of Oklahoma Norman OK USA

Department of Computer Science and Engineering University of California San Diego La Jolla CA USA

Department of Medicine University of California San Diego La Jolla CA USA

Department of Pediatrics School of Medicine University of California San Diego La Jolla CA USA

Department of Pharmaceutical Sciences College of Pharmacy Oregon State University Corvallis OR USA

Department of Psychiatry Stein Clinical Research University of California San Diego La Jolla CA USA

Division of Biological Sciences University of California San Diego La Jolla CA USA

Grupo de Investigación en Ciencias Biológicas y Bioprocesos Department of Biological Sciences Universidad EAFIT Medellín Colombia

Institute of Biomedical Sciences Universidade de São Paulo São Paulo Brazil

Institute of Microbiology Czech Academy of Sciences Videnska Czech Republic

Marine Biodiscovery Centre Department of Chemistry University of Aberdeen Old Aberdeen UK

Research Group Mass Spectrometry Max Planck Institute for Chemical Ecology Jena Germany

Scripps Institution of Oceanography University of California San Diego La Jolla CA USA

Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA

TIMC IMAG Univ Grenoble Alpes CNRS Grenoble INP CHU Grenoble Alpes Grenoble France

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