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Martens L. Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics. EUPA OPEN PROTEOMICS 2016; 11:42-44. [PMID: 29900110 PMCID: PMC5988554 DOI: 10.1016/j.euprot.2016.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 12/23/2022]
Abstract
Proteomics data sharing moved from validation to re-use. New tools and services make data very easily accessible. Metadata provision can still benefit from improvements. Quality control metrics will soon be reported along with submitted data. Data re-use will enable the advent of actual in silico proteomics.
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Affiliation(s)
- Lennart Martens
- Department of Medical Protein Research, VIB 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9000 Ghent, Belgium
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Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 2016; 44:D447-56. [PMID: 26527722 PMCID: PMC4702828 DOI: 10.1093/nar/gkv1145] [Citation(s) in RCA: 2569] [Impact Index Per Article: 285.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development 'PRIDE Cluster' and 'PRIDE Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Noemi del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - José A Dianes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johannes Griss
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gerhard Mayer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qing-Wei Xu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Department of Computer Science and Technology, Hubei University of Education, Wuhan, China
| | - Rui Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China
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