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. 2016 Jan 4;44(D1):D447-56.
doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2.

2016 update of the PRIDE database and its related tools

Juan Antonio Vizcaíno  1 , Attila Csordas  2 , Noemi del-Toro  2 , José A Dianes  2 , Johannes Griss  3 , Ilias Lavidas  2 , Gerhard Mayer  4 , Yasset Perez-Riverol  2 , Florian Reisinger  2 , Tobias Ternent  2 , Qing-Wei Xu  5 , Rui Wang  2 , Henning Hermjakob  6
Affiliations

2016 update of the PRIDE database and its related tools

Juan Antonio Vizcaíno et al. Nucleic Acids Res. .

Erratum in

  • 2016 update of the PRIDE database and its related tools.
    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. Vizcaíno JA, et al. Nucleic Acids Res. 2016 Dec 15;44(22):11033. doi: 10.1093/nar/gkw880. Epub 2016 Sep 28. Nucleic Acids Res. 2016. PMID: 27683222 Free PMC article. No abstract available.

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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Figures

Figure 1.
Figure 1.
Overview of the PRIDE Archive ecosystem, including the resources (in blue, dashed lines mean resource under development), tools (in orange), software libraries and APIs (Application Programming Interfaces, in light blue) and data formats (in green). PRIDE Archive is highlighted in red.
Figure 2.
Figure 2.
Schema representing the PRIDE submission process and internal submission pipeline, highlighting the different file formats and data types involved. The different ways to access the data are also highlighted.
Figure 3.
Figure 3.
Screenshots of the PRIDE Archive web interface showing the project centric page for data set PXD001428, a section of the protein identifications table for that data set and an example of a protein identification page.
See this image and copyright information in PMC

References

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