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

Author(s):Show less -

Jarmusch, Alan K. ^{[1, 2]} ; Wang, Mingxun ^{[1, 2]} ; Aceves, Christine M. ^{[1, 2]} ; Advani, Rohit S. ^{[1, 2]} ; Aguirre, Shaden ^{[1, 2]} ; Aksenov, Alexander A. ^{[1, 2]} ; Aleti, Gajender ^[3] ; Aron, Allegra T. ^{[1, 2]} ; Bauermeister, Anelize ^{[4, 2]} ; Bolleddu, Sanjana ^{[1, 2]} ; Bouslimani, Amina ^{[1, 2]} ; Rodriguez, Andres Mauricio Caraballo ^{[1, 2]} ; Chaar, Rama ^{[1, 2]} ; Coras, Roxana ^[5] ; Elijah, Emmanuel O. ^{[1, 2]} ; Ernst, Madeleine ^{[1, 6, 2]} ; Gauglitz, Julia M. ^{[1, 2]} ; Gentry, Emily C. ^{[1, 2]} ; Husband, Makhai ^{[1, 2]} ; Jarmusch, Scott A. ^[7] ; Jones, II, Kenneth L. ; Kamenik, Zdenek ^[8] ; Le Gouellec, Audrey ^[9] ; Lu, Aileen ^{[10, 11]} ; Mccall, Laura-Isobel ^{[12, 13]} ; McPhail, Kerry L. ^[14] ; Meehan, Michael J. ^{[10, 11]} ; Melnik, V, Alexey ; Menezes, Riya C. ^[15] ; Giraldo, Yessica Alejandra Montoya ^[16] ; Nguyen, Ngoc Hung ^{[17, 18]} ; Nothias, Louis Felix ^[17] ; Nothias-Esposito, Melissa ^{[17, 18]} ; Panitchpakdi, Morgan ^{[17, 18]} ; Petras, Daniel ^{[19, 17, 18]} ; Quinn, Robert A. ^[20] ; Sikora, Nicole ^{[17, 18]} ; van der Hooft, Justin J. J. ^{[21, 17]} ; Vargas, Fernando ^{[22, 17, 18]} ; Vrbanac, Alison ^[23] ; Weldon, Kelly C. ^{[17, 18, 24]} ; Knight, Rob ^{[25, 23, 26, 24]} ; Bandeira, Nuno ^{[26, 18, 24]} ; Dorrestein, Pieter C. ^{[23, 17, 18, 24]}

Affiliation:Show less -

^[1] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 - USA

^[2] Univ Calif San Diego, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA 92093 - USA

^[3] Univ Calif San Diego, Dept Psychiat, Stein Clin Res, La Jolla, CA 92093 - USA

^[4] Univ Sao Paulo, Inst Biomed Sci, Sao Paulo - Brazil

^[5] Univ Calif San Diego, Dept Med, La Jolla, CA 92093 - USA

^[6] Statens Serum Inst, Ctr Newborn Screening, Dept Congenital Disorders, Copenhagen - Denmark

^[7] Univ Aberdeen, Marine Biodiscovery Ctr, Dept Chem, Old Aberdeen - Scotland

^[8] Czech Acad Sci, Inst Microbiol, Videnska - Czech Republic

^[9] Univ Grenoble Alpes, CHU Grenoble Alpes, Grenoble INP, TIMC IMAG, CNRS, Grenoble - France

^[10] Jones, Kenneth L., II, Univ Calif San Diego, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA 92093 - USA

^[11] Jones, Kenneth L., II, Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 - USA

^[12] Univ Oklahoma, Dept Chem & Biochem, Dept Microbiol & Plant Biol, Norman, OK 73019 - USA

^[13] Univ Oklahoma, Labs Mol Anthropol & Microbiome Res, Norman, OK 73019 - USA

^[14] Oregon State Univ, Coll Pharm, Dept Pharmaceut Sci, Corvallis, OR 97331 - USA

^[15] Max Planck Inst Chem Ecol, Res Grp Mass Spectrometry, Jena - Germany

^[16] Univ EAFIT, Dept Biol Sci, Grp Invest Ciencias Biol & Bioproc CIBIOP, Medellin - Colombia

^[17] Melnik, Alexey, V, Jones, Kenneth L., II, Univ Calif San Diego, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA 92093 - USA

^[18] Melnik, Alexey, V, Jones, Kenneth L., II, Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 - USA

^[19] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 - USA

^[20] Michigan State Univ, Dept Biochem & Mol Biol, Lansing, MI - USA

^[21] Wageningen Univ, Bioinformat Grp, Wageningen - Netherlands

^[22] Univ Calif San Diego, Div Biol Sci, La Jolla, CA 92093 - USA

^[23] Univ Calif San Diego, Sch Med, Dept Pediat, La Jolla, CA 92093 - USA

^[24] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 - USA

^[25] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 - USA

^[26] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 - USA

• Document type: Journal article
• Source: NATURE METHODS; v. 17, n. 9 AUG 2020.
• Web of Science Citations: 0

Abstract

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. (AU)

• FAPESP's process: 18/24865-4 - New approaches in metabolomics: 3D Molecular cartography of ascidians based on LC-MS/MS data
• Grantee: Anelize Bauermeister
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor