Nucleic Acids Research· 2015Q1
2016 update of the PRIDE database and its related tools
- 3,668citations
- Q1SCImago
- 2015year
Short summary
The PRIDE Archive, a leading mass spectrometry proteomics data repository, has been redeveloped with a new storage backend, submission system, and web interface, supporting key data standards and seeing a significant increase in data submissions.
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Key points
- PRIDE Archive is the new archival system, replacing the original PRIDE database.
- The redevelopment includes a new storage backend, data submission system, and web interface.
- Supports PSI data standard formats (mzML, mzIdentML) and ProteomeXchange Consortium guidelines.
- Data submissions have increased to approximately 150 data sets per month.
- Updates are provided on related tools like PRIDE Inspector and PRIDE Converter 2, and new resources like PRIDE Cluster and PRIDE Proteomes are under development.
AI-generated from the title and abstract; the full text is not read.
Abstract
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 authors' abstract, as published at the source. Nucleic Acids Research, 2015 · DOI ↗
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Field: Spectroscopy
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