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

Nucleic acids research, 2022-01, Vol.50 (D1), p.D543-D552 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022 ;The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkab1038 ;PMID: 34723319

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Title:
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Author: Perez-Riverol, Yasset ; Bai, Jingwen ; Bandla, Chakradhar ; García-Seisdedos, David ; Hewapathirana, Suresh ; Kamatchinathan, Selvakumar ; Kundu, Deepti J ; Prakash, Ananth ; Frericks-Zipper, Anika ; Eisenacher, Martin ; Walzer, Mathias ; Wang, Shengbo ; Brazma, Alvis ; Vizcaíno, Juan Antonio
Subjects: Amino Acid Sequence ; Bibliometrics ; Database Issue ; Databases, Protein ; Datasets as Topic ; Humans ; Information Storage and Retrieval ; Internet ; Mass Spectrometry ; Metadata - statistics & numerical data ; Molecular Sequence Annotation - statistics & numerical data ; Peptides - chemistry ; Peptides - genetics ; Peptides - metabolism ; Proteins - chemistry ; Proteins - genetics ; Proteins - metabolism ; Proteomics - instrumentation ; Proteomics - methods ; Sequence Alignment ; Software
Is Part Of: Nucleic acids research, 2022-01, Vol.50 (D1), p.D543-D552
Description: 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.
Publisher: England: Oxford University Press
Language: English
Identifier: ISSN: 0305-1048
EISSN: 1362-4962
DOI: 10.1093/nar/gkab1038
PMID: 34723319
Source: Open Access: DOAJ Directory of Open Access Journals
Geneva Foundation Free Medical Journals at publisher websites
MEDLINE
PubMed Central
Open Access: Oxford University Press Open Journals

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

The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022 ;The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkab1038 ;PMID: 34723319

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