ReDU: a framework to find and reanalyze public mass spectrometry data
Open accessPublished version of a preprint
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.
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The ReDU ecosystem provides consistent and comprehensive metadata and crowdsources over 71 K experimental samples.
“The key experimental context is provided by consistent and comprehensive metadata provided by the Reanalysis of Data User (ReDU)156 ecosystem that utilizes controlled vocabularies to crowdsource over 71 K experimental samples.”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [156]
The Abstract says ReDU uses consistent, validated metadata created by users through a template with controlled vocabularies. It reports 38,305 ReDU-compatible files, not over 71,000 experimental samples; the claimed sample count is not supported by this copy. (LLM, conf=0.86)
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References 23 · Cited by 152
- Authors
- Jarmusch, A. K., Wang, M., Aceves, C. M., Advani, R. S., Aguirre, S., Aksenov, A. A., Aleti, G., Aron, A. T., Bauermeister, A., Bolleddu, S., Bouslimani, A., Caraballo Rodriguez, A. M., Chaar, R., Coras, R., Elijah, E. O., Ernst, M., Gauglitz, J. M., Gentry, E. C., Husband, M., Jarmusch, S. A., Jones, K. L., Kamenik, Z., Le Gouellec, A., Lu, A., McCall, L.-I., McPhail, K. L., Meehan, M. J., Melnik, A. V., Menezes, R. C., Montoya Giraldo, Y. A., Nguyen, N. H., Nothias, L. F., Nothias-Esposito, M., Panitchpakdi, M., Petras, D., Quinn, R. A., Sikora, N., van der Hooft, J. J. J., Vargas, F., Vrbanac, A., Weldon, K. C., Knight, R., Bandeira, N., & Dorrestein, P. C.
- Affiliations
- University of California San Diego (US)
- Universidade de São Paulo (BR)
- Statens Serum Institut (DK)
- University of Aberdeen (GB)
- University of Oklahoma (US)
- Oregon State University (US)
- Max Planck Institute for Chemical Ecology (DE)
- Scripps Institution of Oceanography (US)
- Michigan State University (US)
- Corresponding author
- Dorrestein, Pieter C.
- ORCID
- Jarmusch, Alan K.
- Wang, Mingxun
- Aceves, Christine M.
- Advani, Rohit S.
- Aguirre, Shaden
- Aksenov, Alexander A.
- Aleti, Gajender
- Aron, Allegra T.
- Bauermeister, Anelize
- Bouslimani, Amina
- Coras, Roxana
- Ernst, Madeleine
- Gauglitz, Julia M.
- Gentry, Emily C.
- Jarmusch, Scott A.
- Jones, Kenneth L.
- Kamenik, Zdenek
- Le Gouellec, Audrey
- Lu, Aileen
- McCall, Laura-Isobel
- McPhail, Kerry L.
- Meehan, Michael J.
- Melnik, Alexey V.
- Nothias, Louis Felix
- Nothias-Esposito, Mélissa
- Panitchpakdi, Morgan
- Petras, Daniel
- Quinn, Robert A.
- Sikora, Nicole
- van der Hooft, Justin J. J.
- Vargas, Fernando
- Vrbanac, Alison
- Weldon, Kelly C.
- Knight, Rob
- Bandeira, Nuno
- Dorrestein, Pieter C.
- Venue
- Nature Methods
- Published
- 2020-08-17
- Volume
- 17
- Issue
- 9
- Pages
- 901-904
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC7968862
- OpenAlex
- W3049190563
- Cited by
- 152
- References
- 23
- Citations by year
- 2026: 19 · 2025: 24 · 2024: 20 · 2023: 27 · 2022: 19 · 2021: 28 · 2020: 11 · 2019: 4
- FWCI
- 6.89
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- HAL (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- El Repositorio Institucional de la Universidad EAFIT (Universidad EAFIT) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- National Science Foundation (IOS-1656481)
- U.S. Department of Health & Human Services | National Institutes of Health (CA211211, GM107550)
- United States Department of Defense | United States Navy | Office of Naval Research (N00014-15-1-2809)
- University of California, San Diego Center for Microbiome Innovation SEED grant
- American Society for Mass Spectrometry
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- metabolomics, metadata capture, controlled vocabulary, molecular networking, compound identification, data repositories, metadata filtering
- MeSH terms
- Metadata, Models, Chemical, Software, Mass Spectrometry, Metabolomics, Databases, Chemical
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