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

Alan K Jarmusch; Mingxun Wang; Christine M Aceves; Rohit S Advani; Shaden Aguirre; 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 2nd; 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 A Quinn; Nicole Sikora; Justin J J van der Hooft; Fernando Vargas; Alison Vrbanac; Kelly C Weldon; Rob Knight; Nuno Bandeira; Pieter C Dorrestein

doi:10.1038/s41592-020-0916-7

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

Nat Methods. 2020 Sep;17(9):901-904. doi: 10.1038/s41592-020-0916-7. Epub 2020 Aug 17.

Authors

Alan K Jarmusch^#^{1

2}, Mingxun Wang^#^{1

2}, Christine M Aceves^#^{1

2}, Rohit S Advani^{1

2}, Shaden Aguirre^{1

2}, Alexander A Aksenov^{1

2}, Gajender Aleti³, Allegra T Aron^{1

2}, Anelize Bauermeister^{1

4}, Sanjana Bolleddu^{1

2}, Amina Bouslimani^{1

2}, Andres Mauricio Caraballo Rodriguez^{1

2}, Rama Chaar^{1

2}, Roxana Coras⁵, Emmanuel O Elijah^{1

2}, Madeleine Ernst^{1

2

6}, Julia M Gauglitz^{1

2}, Emily C Gentry^{1

2}, Makhai Husband^{1

2}, Scott A Jarmusch⁷, Kenneth L Jones 2nd^{1

2}, Zdenek Kamenik⁸, Audrey Le Gouellec⁹, Aileen Lu^{1

2}, Laura-Isobel McCall¹⁰, Kerry L McPhail¹¹, Michael J Meehan^{1

2}, Alexey V Melnik^{1

2}, Riya C Menezes¹², Yessica Alejandra Montoya Giraldo¹³, Ngoc Hung Nguyen^{1

2}, Louis Felix Nothias^{1

2}, Mélissa Nothias-Esposito^{1

2}, Morgan Panitchpakdi^{1

2}, Daniel Petras^{1

2

14}, Robert A Quinn¹⁵, Nicole Sikora^{1

2}, Justin J J van der Hooft^{1

16}, Fernando Vargas^{1

2

17}, Alison Vrbanac¹⁸, Kelly C Weldon^{1

2

19}, Rob Knight^{18

19

20

21}, Nuno Bandeira^{2

19

20}, Pieter C Dorrestein^{22

23

24

25}

Affiliations

¹ Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
³ Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA.
⁴ Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
⁵ Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
⁶ Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
⁷ Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK.
⁸ Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic.
⁹ TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France.
¹⁰ 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.
¹¹ Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
¹² Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany.
¹³ Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia.
¹⁴ Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
¹⁵ Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA.
¹⁶ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
¹⁷ Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
¹⁸ Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
¹⁹ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
²⁰ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
²¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
²² Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
²³ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
²⁴ Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
²⁵ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Databases, Chemical*
Mass Spectrometry*
Metabolomics / methods*
Metadata
Models, Chemical
Software*

Abstract

Publication types

MeSH terms

Grants and funding