EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.
蛋白质组鉴定数据库（PRIDE，http://www.ebi.ac.uk/pride）是欧洲生物信息学研究所的一个主要质谱蛋白质组学数据存储库。在过去的两年中，PRIDE 数据的存储量大大增加，包含 60 个不同的物种，超过 250 万个蛋白质鉴定，1150 万个肽和超过 5000 万的光谱在 2009 年 9 月。我们在这里描述了 PRIDE 中的几个新的和改进的功能，包括修订后的提交过程，现在包括片段离子注释的直接提交。相应地，现在可以在串联质谱上可视化光谱碎片化注释，这是符合期刊数据提交要求的关键特征。我们还描述了 PRIDE BioMart 接口的最新发展，现在允许集成查询，可以将 PRIDE 数据与越来越多的生物资源（如 Reactome、Ensembl、InterPro 和 UniProt）进行集成。这种在不同领域进行极其强大的查询的能力将肯定是未来生物信息学分析的基石。最后，我们强调了蛋白质组学领域数据共享的重要性，以及 PRIDE 与 ProteomExchange 联盟中的其他数据库的相应集成。
