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Updated: Jun 13, 2026

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
Published on: June 8, 2020
PRIDE: Data submission and analysis
Juan Antonio Vizcaíno1, Florian Reisinger1, Richard Côté1
1European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
Abstract:
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories designed to store, disseminate, and analyze mass spectrometry-based proteomics datasets. In this unit, an overview of the PRIDE system is given, including its key satellite tools: the Ontology Lookup Service (OLS), the Protein Identifier Cross-Referencing Service (PICR), and Database on Demand (DoD). Also described in detail are procedures for submitting data to PRIDE, and accessing data stored in PRIDE using the BioMart interface. Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross-domain query capabilities available through a combination of BioMarts.
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