New Results
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
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
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
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
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
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
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
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
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
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
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
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
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
Roxana Coras
19Department of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
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
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
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
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
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
Scott A. Jarmusch
7Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, United Kingdom
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
Zdenek Kamenik
8Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20 Praha 4, Czech Republic
Audrey Le Gouellec
9Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France
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
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
Kerry L. McPhail
11Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
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
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
Riya C. Menezes
12Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
Yessica Alejandra Montoya Giraldo
18Grupo de investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
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
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
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
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
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
Robert Quinn
14Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, United States of America
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
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
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
Alison Vrbanac
16Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States of America
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
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
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
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
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
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.
Posted August 29, 2019.
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
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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