2016, Vol. 44, Database issue | Juan Antonio Vizcaíno, Attila Csordas, Noemi del-Toro, José A. Dianes, Johannes Griss, Ilias Lavidas, Gerhard Mayer, Yasset Perez-Riverol, Florian Reisinger, Tobias Ternent, Qing-Wei Xu, Rui Wang, Henning Hermjakob
The PRIDE database, a leading repository for mass spectrometry-based proteomics data, has undergone significant redevelopment since 2014 with the introduction of the PRIDE Archive. This new system supports widely used data formats (mzML and mzIdentML) and aligns with the ProteomeXchange Consortium's data standards. The PRIDE Archive has seen a surge in submissions, with around 150 new datasets added monthly, leading to a substantial increase in its content. The database now stores approximately 690 million spectra, 298 million peptide identifications, and 66 million protein identifications, totaling about 140 TBs of data. The PRIDE Archive offers various access methods, including a web interface, RESTful web services, a file repository, and the standalone PRIDE Inspector tool. The PRIDE Archive supports both 'Complete' and 'Partial' data sets, with the former allowing direct connection of processed identification results to raw mass spectra. The PRIDE Inspector tool has been updated to support multiple experimental output files and enhanced visualization capabilities. Additionally, the PRIDE Cluster and PRIDE Proteomes resources are under development to provide quality-filtered peptide and protein identification data, respectively. The PRIDE team plans to further enhance the system by supporting additional data formats, integrating reprocessed data sets, and improving documentation.The PRIDE database, a leading repository for mass spectrometry-based proteomics data, has undergone significant redevelopment since 2014 with the introduction of the PRIDE Archive. This new system supports widely used data formats (mzML and mzIdentML) and aligns with the ProteomeXchange Consortium's data standards. The PRIDE Archive has seen a surge in submissions, with around 150 new datasets added monthly, leading to a substantial increase in its content. The database now stores approximately 690 million spectra, 298 million peptide identifications, and 66 million protein identifications, totaling about 140 TBs of data. The PRIDE Archive offers various access methods, including a web interface, RESTful web services, a file repository, and the standalone PRIDE Inspector tool. The PRIDE Archive supports both 'Complete' and 'Partial' data sets, with the former allowing direct connection of processed identification results to raw mass spectra. The PRIDE Inspector tool has been updated to support multiple experimental output files and enhanced visualization capabilities. Additionally, the PRIDE Cluster and PRIDE Proteomes resources are under development to provide quality-filtered peptide and protein identification data, respectively. The PRIDE team plans to further enhance the system by supporting additional data formats, integrating reprocessed data sets, and improving documentation.