The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

2022, Vol. 50, Database issue | Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti J. Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaíno
The Proteomics IDEntifications (PRIDE) database, hosted by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), is the world's largest repository for mass spectrometry-based proteomics data. This manuscript summarizes the developments in PRIDE resources and related tools since the last update in 2019. The number of submitted datasets to the PRIDE Archive has averaged around 500 per month in 2021. Key improvements include the development of the PRIDE Spectra Archive for direct access to submitted mass spectra using Universal Spectrum Identifiers, and the MAGE-TAB file format for enhanced sample metadata annotation. The PRIDE Peptidome provides aggregated peptide/protein evidence across PRIDE Archive datasets. PRIDE has also increased efforts to integrate high-quality proteomics data into other resources such as UniProt, Ensembl, and Expression Atlas. The PRIDE ecosystem includes libraries, desktop tools, databases, pipelines, RESTful APIs, and web applications. The PRIDE Archive stores datasets from various proteomics experimental approaches, with a focus on discovery-driven techniques. The PRIDE team has led the creation and implementation of multiple open file formats for proteomics data. The PRIDE Submission tool and PRIDE Inspector facilitate data submission and review. The PRIDE Archive web interface and RESTful API provide access to all data, enabling users to query and visualize proteomics evidence. The PRIDE Spectra Archive offers access to over 540 million PSMs, while the PRIDE Peptidome provides a condensed view of peptide evidence across datasets. PRIDE has become a central hub for proteomics data, supporting data deposition, quality assessment, and reuse, with over 23,000 datasets stored as of August 2021. The manuscript discusses the increasing demand for proteomics data, the integration of proteomics data into other resources, and future plans for improving metadata annotation and ethical considerations for clinical proteomics data.The Proteomics IDEntifications (PRIDE) database, hosted by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), is the world's largest repository for mass spectrometry-based proteomics data. This manuscript summarizes the developments in PRIDE resources and related tools since the last update in 2019. The number of submitted datasets to the PRIDE Archive has averaged around 500 per month in 2021. Key improvements include the development of the PRIDE Spectra Archive for direct access to submitted mass spectra using Universal Spectrum Identifiers, and the MAGE-TAB file format for enhanced sample metadata annotation. The PRIDE Peptidome provides aggregated peptide/protein evidence across PRIDE Archive datasets. PRIDE has also increased efforts to integrate high-quality proteomics data into other resources such as UniProt, Ensembl, and Expression Atlas. The PRIDE ecosystem includes libraries, desktop tools, databases, pipelines, RESTful APIs, and web applications. The PRIDE Archive stores datasets from various proteomics experimental approaches, with a focus on discovery-driven techniques. The PRIDE team has led the creation and implementation of multiple open file formats for proteomics data. The PRIDE Submission tool and PRIDE Inspector facilitate data submission and review. The PRIDE Archive web interface and RESTful API provide access to all data, enabling users to query and visualize proteomics evidence. The PRIDE Spectra Archive offers access to over 540 million PSMs, while the PRIDE Peptidome provides a condensed view of peptide evidence across datasets. PRIDE has become a central hub for proteomics data, supporting data deposition, quality assessment, and reuse, with over 23,000 datasets stored as of August 2021. The manuscript discusses the increasing demand for proteomics data, the integration of proteomics data into other resources, and future plans for improving metadata annotation and ethical considerations for clinical proteomics data.
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Understanding The PRIDE database resources in 2022%3A a hub for mass spectrometry-based proteomics evidences