Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Autor: Kelly C. Weldon, Alison Vrbanac, Elijah Eo, Pieter C. Dorrestein, Robert A. Quinn, Daniel Petras, Fernando Vargas, Madeleine Ernst, Nothias-Esposito M, Sikora N, Amina Bouslimani, Julia M. Gauglitz, Advani Rs, Nhu H. Nguyen, Riya Christina Menezes, Mingxun Wang, Rob Knight, Aguire S, Laura-Isobel McCall, Giraldo Yam, Rodriguez Amc, Zdeněk Kameník, Alexander A. Aksenov, Jones Kl, Nuno Bandeira, Bolleddu S, Gajender Aleti, Roxana Coras, Gentry Ec, Michael J. Meehan, Nothias Lf, van der Hooft Jj, Husband M, Aceves Cm, Allegra T. Aron, Le Gouellec A, Anelize Bauermeister, Scott A. Jarmusch, Chaar R, Panitchpakdi M, Lu A, Jarmusch Ak, Alexey V. Melnik, Kerry L. McPhail

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f458d78513df08a302211fbf75410b9c
https://doi.org/10.1101/750471

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

Autor: Jarmusch AK; 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 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., Aceves CM; 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 RS; 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 S; 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 AA; 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 G; Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA., Aron AT; 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 A; 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 S; 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 A; 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 AM; 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 R; 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 R; Department of Medicine, University of California, San Diego, La Jolla, CA, USA., Elijah EO; 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 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.; Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark., Gauglitz JM; 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 EC; 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 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., Jarmusch SA; Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK., Jones KL 2nd; 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 Z; Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic., Le Gouellec A; TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France., Lu A; 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 LI; 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 KL; Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA., Meehan MJ; 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 AV; 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 RC; Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany., Montoya Giraldo YA; Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia., Nguyen NH; 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 LF; 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 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., Panitchpakdi 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., Petras D; 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 RA; Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA., Sikora N; 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 JJJ; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands., Vargas F; 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 A; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA., Weldon KC; 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 R; 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 N; 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 PC; 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.

Publikováno v: Nature methods [Nat Methods] 2020 Sep; Vol. 17 (9), pp. 901-904. Date of Electronic Publication: 2020 Aug 17.