Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue D1, Pages D543-D552Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab1038
Keywords
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Categories
Funding
- Wellcome [208391/Z/17/Z]
- BBSRC grant `Proteomics DIA' [BB/P024599/1]
- BBSRC grant `PTMeXchange' [BB/S01781X/1]
- BBSRC grant `GRAPPA' [BB/T019670/1]
- UK-Japan Partnership award [BB/N022440/1]
- NIH `Proteomics Standards' grant [R24 GM127667-01]
- EU H2020 project EPIC-XS [823839]
- Luxembourg National Research Fund [C19/BM/13684739]
- EMBL
- German Federal Ministry of Education and Research (BMBF) [FKZ 031 A 534A]
- Center for Protein Diagnostics (PPRODI)
- Ministry of Innovation, Science and Research of North-Rhine Westphalia, Germany
- [OTAR-043]
- BBSRC [BB/P024599/1, BB/S01781X/1, BB/T019670/1] Funding Source: UKRI
- Wellcome Trust [208391/Z/17/Z] Funding Source: Wellcome Trust
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PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.
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