Qing-Wei Xu

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.

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE. The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. The amount of publicly available mass spectrometry (MS)-based proteomics data is rapidly increasing in quality and quantity. This is due to the guidelines promoted by several scientific journals like Molecular and Cellular Proteomics (MCP) and by funding agencies (1.Kinsinger C.R. Apffel J. Baker M. Bian X. Borchers C.H. Bradshaw R. Brusniak M.Y. Chan D.W. Deutsch E.W. Domon B. Gorman J. Grimm R. Hancock W. Hermjakob H. Horn D. Hunter C. Kolar P. Kraus H.J. Langen H. Linding R. Moritz R.L. Omenn G.S. Orlando R. Pandey A. Ping P. Rahbar A. Rivers R. Seymour S.L. Simpson R.J. Slotta D. Smith R.D. Stein S.E. Tabb D.L. Tagle D. Yates J.R. Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).Proteomics. 2012; 12: 11-20Crossref PubMed Scopus (12) Google Scholar). Additionally, there is a growing perception in the community that sharing data is a good scientific practice and beneficial for the field (2.Perez-Riverol Y. Alpi E. Wang R. Hermjakob H. Vizcaíno J.A. Making proteomics data accessible and reusable: current state of proteomics databases and repositories.Proteomics. 2015; 15: 930-949Crossref PubMed Scopus (128) Google Scholar). The ProteomeXchange (PX) Consortium was formally started in 2011 to overcome the challenges in MS proteomics data sharing and dissemination (3.Vizcaíno J.A. Deutsch E.W. Wang R. Csordas A. Reisinger F. Ríos D. Dianes J.A. Sun Z. Farrah T. Bandeira N. Binz P.A. Xenarios I. Eisenacher M. Mayer G. Gatto L. Campos A. Chalkley R.J. Kraus H.J. Albar J.P. Martinez-Bartolomé S. Apweiler R. Omenn G.S. Martens L. Jones A.R. Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination.Nature Biotechnol. 2014; 32: 223-226Crossref PubMed Scopus (2078) Google Scholar, 4.Perez-Riverol Y. Hermjakob H. Kohlbacher O. Martens L. Creasy D. Cox J. Leprevost F. Shan B.P. Pérez-Nueno V.I. Blazejczyk M. Punta M. Vierlinger K. Valiente P.A. Leon K. Chinea G. Guirola O. Bringas R. Cabrera G. Guillen G. Padron G. Gonzalez L.J. Besada V. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.J. Proteomics. 2013; 87: 134-138Crossref PubMed Scopus (17) Google Scholar) by implementing standard pipelines and promoting collaboration, developing an international consortium of major stakeholders in the domain. At present, it includes the PRoteomics IDEntifications (PRIDE) database (5.Vizcaíno J.A. Cote R.G. Csordas A. Dianes J.A. Fabregat A. Foster J.M. Griss J. Alpi E. Birim M. Contell J. O'Kelly G. Schoenegger A. Ovelleiro D. Perez-Riverol Y. Reisinger F. Rios D. Wang R. Hermjakob H. The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013.Nucleic Acids Res. 2013; 41: D1063-1069Crossref PubMed Scopus (1596) Google Scholar), PeptideAtlas (6.Farrah T. Deutsch E.W. Omenn G.S. Sun Z. Watts J.D. Yamamoto T. Shteynberg D. Harris M.M. Moritz R.L. State of the human proteome in 2013 as viewed through PeptideAtlas: Comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.J. Proteome Res. 2014; 13: 60-75Crossref PubMed Scopus (107) Google Scholar) and the related resource PeptideAtlas SRM Experiment Library (PASSEL) (7.Farrah T. Deutsch E.W. Kreisberg R. Sun Z. Campbell D.S. Mendoza L. Kusebauch U. Brusniak M.Y. Hüttenhain R. Schiess R. Selevsek N. Aebersold R. Moritz R.L. 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Deutsch E.W. Hermjakob H. Reisinger F. Griss J. Vizcaíno J.A. Chambers M. Pizarro A. Creasy D. The mzIdentML data standard for mass proteomics Cell. Proteomics. 2012; Full Full PubMed Scopus Google Scholar) to peptide as as the protein The mzIdentML supported using protein provides of peptide and the in the In the format J. Jones A.R. T. M. Gatto L. J. C. N. Cox J. Neumann S. J. Reisinger F. N. Y. F. Bandeira N. Xenarios I. Kohlbacher O. J.A. Hermjakob H. The data proteomics and experimental results to a Cell. Proteomics. 2014; 13: Full Full PubMed Scopus Google Scholar) was developed to identification and quantification results in the the of the experimental results at different of It is to results the mass spectra in the mzIdentML and to mass spectra data available in formats the data standard The increasing of standard data formats E.W. formats in mass spectrometry Cell. Proteomics. 2012; Full Full PubMed Scopus Google Scholar) the and of results by different and In in the of visualization and supporting the data the of data formats available in the PX on open data standard At present, there different PX submission “complete” and In identification results for data The the formats in results submission the have been it is for the spectrometry and Cellular Identifications Standards to the results with the mass visualization and quality the repositories, the identification results available in open formats mzTab, or the PRIDE XML, the original PRIDE data and the mass spectra in the submission Y. Alpi E. Wang R. Hermjakob H. Vizcaíno J.A. Making proteomics data accessible and reusable: state of proteomics databases and repositories.Proteomics. 2015; 15: PubMed Scopus Google Scholar). In the of identification results accessible in the different formats output by a the available for the visualization of the data is access to the original a few standalone for the visualization of MS proteomics data R. Perez-Riverol Y. Hermjakob H. Vizcaíno J.A. source libraries and for data for 2015; 15: PubMed Scopus Google Scholar). that open source or Y. Wang R. Hermjakob H. M. V. Vizcaíno J.A. source libraries and for mass spectrometry 2014; PubMed Scopus Google Scholar), it is tool for PubMed Scopus Google Scholar), F. R. P. Martinez-Bartolomé S. Reisinger F. Hermjakob H. J.A. Jones A.R. Library and that use of the peptide and protein identification standard Cell. Proteomics. 2013; 12: Full Full PubMed Scopus Google Scholar), A. C. K. Kohlbacher O. and source for data 2011; PubMed Scopus Google Scholar), and Chalkley R.J. for proteomics Cell. Proteomics. 2014; 13: Full Full PubMed Scopus Google Scholar). is that focused on format or on data mass spectrometry Molecular and Cellular Proteomics mass spectrometry Proteomics Identifications Proteomics Standards Initiative peptide ProteomeXchange extensible The original PRIDE Inspector tool R. Fabregat A. Rios D. Ovelleiro D. Foster J.M. R.G. Griss J. Csordas A. Perez-Riverol Y. Reisinger F. Hermjakob H. Martens L. Vizcaíno J.A. PRIDE tool to visualize and validate MS proteomics Biotechnol. 2012; PubMed Scopus Google Scholar) was developed as an open source standalone tool to enable the visualization and validation of proteomics data in PRIDE. The the was to a visualization tool for to to with and of the growing data available in PRIDE. 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The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013.Nucleic Acids Res. 2013; 41: D1063-1069Crossref PubMed Scopus (1596) Google Scholar), and for available in the public in PX We the and of the PRIDE Inspector as the tool of the The PRIDE Inspector tool the libraries and algorithms of the the and quality assessment of proteomics upon the PRIDE is format for of the most popular formats in the PRIDE Inspector supports the handling and visualization of different experimental output files, ranging from mass spectra (mzML, mzXML, and the most popular peak lists and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE to its a for the mzIdentML format is the that to mzIdentML from a of of the most popular proteomics have been and This includes S. P.A. a database tool for 2014; PubMed Scopus Google Scholar), from J. L. Shan B. W. M. D. W. Z. B. database for and peptide Cell. 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PRIDE XML, and the mass spectra data. the mass spectra in with the or as files, the most popular mass spectra formats mzML and its the XML-based and R. M. Deutsch E.W. B. B. E. Apweiler R. K. Hermjakob H. S. E. Omenn G. Simpson R. Smith R. W. Aebersold R. open of mass spectrometry data and its to proteomics Biotechnol. PubMed Scopus Google Scholar), and the J. I. M. N. M. M. to the for PubMed Scopus Google Scholar), and W.H. Tabb D.L. R.G. J. J. J.R. D. Yates J.R. and and formats for the of spectra and Mass PubMed Scopus Google Scholar). The of on PRIDE Inspector from the using the by the J. Reisinger F. Hermjakob H. Vizcaíno J.A. to and visualize and XML-based mass spectrometry data 2012; 12: PubMed Scopus Google Scholar). mzIdentML the mass spectra from a of to the of the available at a for data has been in the Toolsuite by and the PRIDE Inspector Toolsuite is the that supports identification and quantification from different have been and data and U. J. P. Y. H. 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