These authors have contributed equally to this work.
Standardization and Guidelines
How to submit MS proteomics data to ProteomeXchange via the PRIDE database
Article first published online: 21 AUG 2014
© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
How to Cite
Ternent, T., Csordas, A., Qi, D., Gómez-Baena, G., Beynon, R. J., Jones, A. R., Hermjakob, H. and Vizcaíno, J. A. (2014), How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics. doi: 10.1002/pmic.201400120
Colour Online: See the article online to view Figs. 1–3 in colour.
- Article first published online: 21 AUG 2014
- Accepted manuscript online: 21 JUL 2014 04:52PM EST
- Manuscript Accepted: 17 JUL 2014
- Manuscript Revised: 11 JUN 2014
- Manuscript Received: 2 APR 2014
- EU FP7. Grant Number: 260558
- Wellcome Trust. Grant Number: WT101477MA
- Data standard;
- Data submission;
- Data visualization;
- Proteomics repositories
The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission and dissemination of MS-based proteomics data in the public domain. In the consortium, the PRIDE database at the European Bioinformatics Institute, acts as the initial submission point of MS/MS data sets. In this manuscript, we explain step by step the submission process of MS/MS data sets to PX 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 data set containing identification and quantification data, which has been deposited in PRIDE/ProteomeXchange with the accession number PXD000764 (http://proteomecentral.proteomexchange.org/dataset/PXD000764).