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

View ORCID ProfileAlan K. Jarmusch, View ORCID ProfileMingxun Wang, View ORCID ProfileChristine M. Aceves, Rohit S. Advani, Shaden Aguire, View ORCID ProfileAlexander A. Aksenov, Gajender Aleti, Allegra T. Aron, View ORCID ProfileAnelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, View ORCID ProfileAndres Mauricio Caraballo Rodriguez, Rama Chaar, View ORCID ProfileRoxana Coras, Emmanuel O. Elijah, View ORCID ProfileMadeleine Ernst, View ORCID ProfileJulia M. Gauglitz, View ORCID ProfileEmily C. Gentry, Makhai Husband, View ORCID ProfileScott A. Jarmusch, Kenneth L. Jones II, View ORCID ProfileZdenek Kamenik, View ORCID ProfileAudrey Le Gouellec, Aileen Lu, View ORCID ProfileLaura-Isobel McCall, View ORCID ProfileKerry L. McPhail, Michael J. Meehan, View ORCID ProfileAlexey V. Melnik, View ORCID ProfileRiya C. Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, View ORCID ProfileLouis Felix Nothias, View ORCID ProfileMélissa Nothias-Esposito, Morgan Panitchpakdi, View ORCID ProfileDaniel Petras, Robert Quinn, Nicole Sikora, View ORCID ProfileJustin J.J. van der Hooft, View ORCID ProfileFernando Vargas, Alison Vrbanac, View ORCID ProfileKelly Weldon, View ORCID ProfileRob Knight, View ORCID ProfileNuno Bandeira, View ORCID ProfilePieter C. Dorrestein
doi: https://doi.org/10.1101/750471
Alan K. Jarmusch
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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  • ORCID record for Alan K. Jarmusch
Mingxun Wang
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Christine M. Aceves
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Rohit S. Advani
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Shaden Aguire
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Alexander A. Aksenov
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Gajender Aleti
3Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States of America
4Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA 92093, United States of America
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Allegra T. Aron
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Anelize Bauermeister
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
5Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo/SP, Brazil
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Sanjana Bolleddu
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Amina Bouslimani
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Andres Mauricio Caraballo Rodriguez
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Rama Chaar
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Roxana Coras
19Department of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
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  • ORCID record for Roxana Coras
Emmanuel O. Elijah
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Madeleine Ernst
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
6Center for Newborn Screening, Department of Congenital Disorders, Center for Newborn Screening, Statens Serum Institut, Copenhagen, Denmark
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  • ORCID record for Madeleine Ernst
Julia M. Gauglitz
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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  • ORCID record for Julia M. Gauglitz
Emily C. Gentry
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Makhai Husband
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Scott A. Jarmusch
7Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, United Kingdom
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Kenneth L. Jones II
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Zdenek Kamenik
8Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20 Praha 4, Czech Republic
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  • ORCID record for Zdenek Kamenik
Audrey Le Gouellec
9Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France
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Aileen Lu
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Laura-Isobel McCall
10Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, United States of America
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Kerry L. McPhail
11Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
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Michael J. Meehan
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Alexey V. Melnik
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Riya C. Menezes
12Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
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Yessica Alejandra Montoya Giraldo
18Grupo de investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
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Ngoc Hung Nguyen
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Louis Felix Nothias
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Mélissa Nothias-Esposito
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Morgan Panitchpakdi
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Daniel Petras
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
13Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, United States of America
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Robert Quinn
14Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, United States of America
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Nicole Sikora
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Justin J.J. van der Hooft
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
15Bioinformatics Group, Wageningen University, Wageningen, Netherlands
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Fernando Vargas
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
20Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
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Alison Vrbanac
16Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
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Kelly Weldon
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
3Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States of America
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Rob Knight
3Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States of America
16Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
17Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, United States of America
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Nuno Bandeira
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
3Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States of America
17Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, United States of America
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Pieter C. Dorrestein
1Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, United States of America
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States of America
3Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States of America
16Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
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  • For correspondence: pdorrestein@ucsd.edu
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Abstract

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 repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

Footnotes

  • https://redu.ucsd.edu/

  • https://gnps.ucsd.edu/

  • https://massive.ucsd.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguire, Alexander A. Aksenov, Gajender Aleti, Allegra T. Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Scott A. Jarmusch, Kenneth L. Jones II, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L. McPhail, Michael J. Meehan, Alexey V. Melnik, Riya C. Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert Quinn, Nicole Sikora, Justin J.J. van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly Weldon, Rob Knight, Nuno Bandeira, Pieter C. Dorrestein
bioRxiv 750471; doi: https://doi.org/10.1101/750471
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Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguire, Alexander A. Aksenov, Gajender Aleti, Allegra T. Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Scott A. Jarmusch, Kenneth L. Jones II, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L. McPhail, Michael J. Meehan, Alexey V. Melnik, Riya C. Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert Quinn, Nicole Sikora, Justin J.J. van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly Weldon, Rob Knight, Nuno Bandeira, Pieter C. Dorrestein
bioRxiv 750471; doi: https://doi.org/10.1101/750471

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