The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

2013 | Juan Antonio Vizcaíno, Richard G. Côté, Attila Csordas, José A. Dianes, Antonio Fabregat, Joseph M. Foster, Johannes Griss, Emanuele Alpi, Melih Birim, Javier Contel, Gavin O’Kelly, Andreas Schoenegger, David Ovelheiro, Yasset Pérez-Riverol, Florian Reisinger, Daniel Ríos, Rui Wang and Henning Hermjakob
The PRoteomics IDEntifications (PRIDE) database, hosted at the European Bioinformatics Institute, is a major repository for mass spectrometry (MS)-based proteomics data. This summary outlines recent developments in PRIDE and related tools as of 2013. PRIDE provides up-to-date statistics on data content, including protein and peptide identifications, post-translational modifications, and data access methods. The PRIDE submission pipeline includes tools like PRIDE Converter 2 and PRIDE Inspector, which facilitate data submission and visualization. PRIDE is integrated with the ProteomeXchange consortium, enhancing data sharing and standardization. Quality control efforts are ongoing, with future plans to release PRIDE-Q, a quality-controlled subset of PRIDE. PRIDE supports various proteomics approaches, including bottom-up, top-down, and targeted proteomics. The database includes extensive data on proteins, peptides, and post-translational modifications, with a focus on human and model organisms. PRIDE offers multiple access methods, including web interfaces, BioMart, FTP, and DAS. The PRIDE Converter 2 is the recommended submission tool, supporting various data formats and enabling integration with other resources. PRIDE Inspector is a popular tool for data visualization and quality assessment. PRIDE is a key resource for proteomics research, supporting publication and data sharing. The database continues to grow, with a significant increase in the number of stored experiments and data. PRIDE is also involved in the Human Proteome Project and other initiatives, contributing to the advancement of proteomics research.The PRoteomics IDEntifications (PRIDE) database, hosted at the European Bioinformatics Institute, is a major repository for mass spectrometry (MS)-based proteomics data. This summary outlines recent developments in PRIDE and related tools as of 2013. PRIDE provides up-to-date statistics on data content, including protein and peptide identifications, post-translational modifications, and data access methods. The PRIDE submission pipeline includes tools like PRIDE Converter 2 and PRIDE Inspector, which facilitate data submission and visualization. PRIDE is integrated with the ProteomeXchange consortium, enhancing data sharing and standardization. Quality control efforts are ongoing, with future plans to release PRIDE-Q, a quality-controlled subset of PRIDE. PRIDE supports various proteomics approaches, including bottom-up, top-down, and targeted proteomics. The database includes extensive data on proteins, peptides, and post-translational modifications, with a focus on human and model organisms. PRIDE offers multiple access methods, including web interfaces, BioMart, FTP, and DAS. The PRIDE Converter 2 is the recommended submission tool, supporting various data formats and enabling integration with other resources. PRIDE Inspector is a popular tool for data visualization and quality assessment. PRIDE is a key resource for proteomics research, supporting publication and data sharing. The database continues to grow, with a significant increase in the number of stored experiments and data. PRIDE is also involved in the Human Proteome Project and other initiatives, contributing to the advancement of proteomics research.
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[slides and audio] The Proteomics Identifications (PRIDE) database and associated tools%3A status in 2013