Nucleic Acids Research· 2021Q1
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
- 6,779citations
- Q1SCImago
- 2021year
Short summary
The PRIDE database, a major repository for mass spectrometry proteomics data, has significantly expanded its resources and infrastructure since 2019. It now processes around 500 datasets monthly and offers direct access to mass spectra via the PRIDE Spectra Archive.
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Key points
- PRIDE Archive processed ~500 datasets per month in 2021.
- PRIDE Spectra Archive provides direct access to mass spectra.
- MAGE-TAB format developed for enhanced proteomics metadata annotation.
- Increased data reuse and dissemination to resources like UniProt and Ensembl.
AI-generated from the title and abstract; the full text is not read.
Abstract
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.
The authors' abstract, as published at the source. Nucleic Acids Research, 2021 · DOI ↗
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Field: Spectroscopy
SpectroscopyChemistry