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Wiley, Proteomics, 20(14), p. 2233-2241, 2014

DOI: 10.1002/pmic.201400120

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How to submit MS proteomics data to ProteomeXchange via the PRIDE database

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

The ProteomeXchange consortium has been established to standardize and facilitate submission and dissemination of mass spectrometry (MS)-based proteomics data in the public domain. In the consortium, the PRIDE database at the European Bioinformatics Institute (EBI), acts as the initial submission point of MS/MS datasets. In this manuscript we explain step by step the submission process of MS/MS datasets to ProteomeXchange via PRIDE. We describe in detail the two available workflows: ’complete’ and ‘partial’ submissions, together with the available tools to streamline the process. Throughout the manuscript, we will use one example dataset containing identification and quantification data, which has been deposited in PRIDE/ProteomeXchange with the accession number PXD000764.This article is protected by copyright. All rights reserved