About PRIDE Archive
What is PRIDE Archive?
The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications (and the corresponding expression values, if available), post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert biocurators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets.
All public datasets available in PRIDE Archive in the repository can be accesed via the:
- Website, for users to explore through a web browser.
- Web Service, for programmatic access. It replaces the computational access provided via BioMart (available till December 2014).
- Data servers, for direct access to data files through the FTP and Aspera file transfer protocols, and HTTP.
- PRIDE Inspector stand-alone tool. For detailed data visualisation and basic analysis capabilities.
- To archive all types of proteomics mass spectrometry data for the purpose of supporting reproducible research, allowing the application of quality control metrics and enabling the reuse of these data by other researchers.
- To integrate MS-based data in a protein-centric manner to provide information on protein variants, modifications, and expression.
- To provide mass spectrometry based expression data to the Expression Atlas.
Data submissions to ProteomeXchange via PRIDE
PRIDE welcomes direct user submissions of protein and peptide identification/quantification data with the accompanying mass spectral evidence to be published in peer-reviewed publications. The main focus of PRIDE is to support the deposition of shotgun MS/MS proteomics datasets. However, datasets coming from other proteomics workflows can also be stored.
The submission process, including explanation about supported file formats and related tools, is detailed in the:
- Help section of the PRIDE Archive website.
- Tutorial manuscript: Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA. How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics. 2014 Oct;14(20) 2233-2241. doi:10.1002/pmic.201400120. PubMed PMID: 25047258.
- Train Online tutorial.
Publications / how to cite
- Citing PRIDE generally: 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 related tools. Nucleic Acids Res. 2016 Jan 1;44(D1): D447-D456. PubMed PMID:26527722.
- Citing ProteomeXchange: Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA,Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. PubMed PMID: 24727771.
- Citing a PX identifier for a dataset:
Complete: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository  with the dataset identifier PXD000000 and DOI 10.6019/PXD000000.
Partial: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository  with the dataset identifier PXD000000.
 Vizcaino JA, et al. 2016 update of the PRIDE database and related tools. Nucleic Acids Res. 2016 Jan 1;44(D1):D447-D456.
- Citing PRIDE Inspector. Please, use one of these two publications:
- Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, del Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA. PRIDE Inspector Toolsuite: moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets. Mol Cell Proteomics 2016 Jan; 15(1):305-17. PubMed PMID: 26545397.
- Wang R, Fabregat A, Rios D, Ovelleiro D, Foster JM, Cote RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaino JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol. 2012 Feb 8;30(2):135-7. PubMed PMID: 22318026.
- Citing PRIDE Converter 2: Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HWP, van Breukelen B, Heck AJR, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Riverol Y, Barsnes H, Hermjakob H, Vizcaíno JA (2012). The Proteomics IDEntifications (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics 11:1682-1689. PubMed PMID: 23203882
Please also check out the publications page from the PRIDE team for a more comprehensive list of peer-reviewed papers and posters/oral presentations at international conferences.
The team behind PRIDE
The members of the PRIDE Scientific Advisory Board
The PRIDE project receives advice and guidance from our scientific advisory board. The PRIDE SAB consists of a collection of scientists representing different groups working in the mass spectrometry proteomics field. Our current SAB members are:
- Ruedi Aebersold, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
- Roz Banks, University of Leeds, UK
- Angus Lamond, University of Dundee, UK
- Kathryn Lilley, University of Cambridge, UK
- Juri Rappsilber, University of Edinburgh, UK
- Ioannis Xenarios, SIB Swiss Institute of Bioinformatics, Geneva, University of Lausanne, Switzerland
The PRIDE team would like to thank all data submitters for their contributions. The PRIDE team is funded at present by the Wellcome Trust [grant number WT101477MA], and the BBSRC grants BB/I00095X/1, BB/K01997X/1 and BB/L024225/1] and EMBL core funding.
In recent years, PRIDE has also been funded by the Wellcome Trust [grant number WT085949MA], the EU FP7 grants 'ProteomeXchange’ [grant number 260558], ‘PRIME-XS’ [grant number 262067], and ‘LipidomicNet’ [grant number 202272], and the BBSRC grant ‘PRIDE Converter’ [reference BB/I024204/1].
The PRIDE team would like to thank the following companies for their support through the offering of free software licenses:
|Developed with IntelliJ IDEA.|
|Profiled with YourKit Java Profiler.|
|Consulted with Matrix Science.|