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

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 set...

Full description

Saved in:
Bibliographic Details
Published in:Proteomics (Weinheim) 2014-10, Vol.14 (20), p.2233-2241
Main Authors: Ternent, Tobias, Csordas, Attila, Qi, Da, Gómez-Baena, Guadalupe, Beynon, Robert J., Jones, Andrew R., Hermjakob, Henning, Vizcaíno, Juan Antonio
Format: Article
Language:English
Subjects:
Animals
Bioinformatics
Data standard
Data submission
Data visualization
Databases, Protein
Humans
Proteomics - methods
Proteomics repositories
Tandem Mass Spectrometry - methods
Workflow
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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).
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.201400120