A proteomics sample metadata representation for multiomics integration and big data analysis

Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Björn Grüning, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W. Deutsch, Juan Antonio Vizcaíno, Mingze Bai (), Timo Sachsenberg (), Lev I. Levitsky () and Yasset Perez-Riverol ()
Additional contact information
Chengxin Dai: Chongqing University of Posts and Telecommunications
Anja Füllgrabe: European Bioinformatics Institute, Wellcome Genome Campus
Julianus Pfeuffer: Freie Universität Berlin
Elizaveta M. Solovyeva: Moscow Institute of Physics and Technology
Jingwen Deng: Chongqing University of Posts and Telecommunications
Pablo Moreno: European Bioinformatics Institute, Wellcome Genome Campus
Selvakumar Kamatchinathan: European Bioinformatics Institute, Wellcome Genome Campus
Deepti Jaiswal Kundu: European Bioinformatics Institute, Wellcome Genome Campus
Nancy George: European Bioinformatics Institute, Wellcome Genome Campus
Silvie Fexova: European Bioinformatics Institute, Wellcome Genome Campus
Björn Grüning: Albert-Ludwigs-University Freiburg
Melanie Christine Föll: Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg
Johannes Griss: Medical University of Vienna
Marc Vaudel: University of Bergen
Enrique Audain: Universitätsklinikum Schleswig-Holstein Kiel
Marie Locard-Paulet: University of Copenhagen
Michael Turewicz: Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
Martin Eisenacher: Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
Julian Uszkoreit: Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
Tim Bossche: VIB – UGent Center for Medical Biotechnology, VIB
Veit Schwämmle: University of Southern Denmark, Campusvej 55
Henry Webel: University of Copenhagen
Stefan Schulze: University of Pennsylvania, Department of Biology
David Bouyssié: University of Toulouse, CNRS, UPS
Savita Jayaram: nference Labs
Vinay Kumar Duggineni: nference Labs
Patroklos Samaras: Technical University of Munich
Mathias Wilhelm: Technical University of Munich
Meena Choi: Proteomics and Lipidomics, Genentech
Mingxun Wang: University of California San Diego
Oliver Kohlbacher: University of Tübingen
Alvis Brazma: European Bioinformatics Institute, Wellcome Genome Campus
Irene Papatheodorou: European Bioinformatics Institute, Wellcome Genome Campus
Nuno Bandeira: University of California San Diego
Eric W. Deutsch: Institute for Systems Biology, 401 Terry Ave N
Juan Antonio Vizcaíno: European Bioinformatics Institute, Wellcome Genome Campus
Mingze Bai: Chongqing University of Posts and Telecommunications
Timo Sachsenberg: University of Tübingen
Lev I. Levitsky: N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences
Yasset Perez-Riverol: European Bioinformatics Institute, Wellcome Genome Campus

Nature Communications, 2021, vol. 12, issue 1, 1-8

Abstract: Abstract The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.

Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-021-26111-3 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26111-3

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-26111-3

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().