Abstract
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).
Highlights
The availability of MS-based proteomics data in the public domain is still low when compared with other ‘omics’ disciplines such as genomics and transcriptomics
Several MS proteomics repositories have been established to address the demand for storage and availability of proteomics data in the public domain
The data types and corresponding file tags are as follows: (i) Mass spectrometer output files, labelled as ‘raw files (RAW)’. (ii) Processed peak lists, labelled as ‘PEAK’. (iii) Search engine output files: Processed identification results are labelled either as ‘RESULT’ or ‘SEARCH’
Summary
The availability of MS-based proteomics data in the public domain is still low when compared with other ‘omics’ disciplines such as genomics and transcriptomics. The main objective is to provide the scientific community with an easier and unified way to submit and access MS proteomics data. Once the manuscript is published or the submitters give their permission, data in PRIDE are disseminated through the ProteomeCentral, the portal of all PX submissions (http://proteomecentral.proteomexchange.org/cgi/ GetDataset) [4]. By June 2014, MS/MS data sets in PRIDE have accounted for ß95% of all the PX data sets In this manuscript we will describe in detail how to perform submissions of MS/MS data to PX via the PRIDE database
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