Providing a portal for research data
The ProteomeXchange consortium has been set up to provide a common framework for the cooperation of biological resources storing mass spectrometry (MS) proteomics data. With this overall goal in mind, we have defined and implemented consistent and user-friendly data deposition and dissemination policies. We have also launched a public portal for accessing centrally proteomics data and information. This integrative infrastructure highlights a growing trend in the sharing of data generated in MS proteomics experiments.
Easy to find data, with accession numbers...
As a result, users can now easily view data and information at different levels of processing, all linked by a universal, shared identifier. In addition, authors are now given a traceable ProteomeXchange accession number for datasets reported in their publications. The portal provides a welcome boost to the long-standing efforts of scientific journals and funding agencies.
Linking publications to data
Through the completion of a series of deliverables, a stable implementation of the ProteomeXchange platform is now operational. A dataset can be submitted to the receiving repository, and then, when the corresponding manuscript is accepted for publication (or when the submitter gives the permission to do it), it is automatically disseminated through the resource ProteomeCentral (see Fig. 1) to the other members of the Consortium and the community as a whole. ProteomeXchange started to accept regular submissions in June 2012 (month 18). Recently the MassIVE repository became a ProteomeXchange member, being the first resource to join that was not originally included in the Consortium.
Figure 1. Representation of the ProteomeXchange data workflow. Raw data represents mass spectrometer output files. ProteomeCentral is the portal for all public ProteomeXchange datasets (Vizcaino et al. 2014, doi:10.1038/nbt.2839).
Over 1,150 datasets!
As of August 2014, more than 1,150 data sets have been submitted to ProteomeXchange (see Fig. 2). The species most represented (including both public and private datasets) are human and some of the main model organisms such as mouse, Arabidopsis, and rat, among others.
Figure 2. ProteomeXchange statistics, August 2014
Sharing and Analysing the Data
Data sharing in the field of proteomics has been on the rise for several years, with supporting infrastructure built at several locations worldwide. Proteomics data resources such as PRIDE and the PeptideAtlas had accepted submissions and handled proteomics data for many years, but until recently they have been acting independently with limited global coordination. This placed a burden on researchers, who had to figure out which repository to choose and which type of data – raw or processed – to share. Conversely, data consumers used to struggle to find supporting data, or to untangle whether a dataset from one resource had been integrated into another. ProteomeXchange addressed these two concerns directly and effectively: large-scale proteomics data sharing between the different resources enables a single point of submission, while allowing convenient access to all publicly available data in any participating resource. Additionally, the use of community standard formats is promoted actively by the Consortium. Data submitters are then able to benefit from a broad platform of software tools tailored to make submission easy.
Publications on OpenAIRE
The project partners have produced so far since January 2011 72 scientific publications acknowledging ProteomeXchange funding. The scientific publications are listed on the ProteomeXchange webpage (www.proteomexchange.org) and can also be accessed through the OpenAIRE website on the ProteomeXchange project page.
Promoting Project Results
The dissemination activities of the ProteomeXchange project were aiming at reaching out to proteomics data producers (as part of the proteomics community), instructing them on data submission guidelines and practical data deposition strategies. In addition to the public website, 32 publications out of 72 are published in open access journals.
Noteworthy Publications
- Vizcaino JA, Deutsch EW, Wang R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014; 32(3):223-226.
- Walzer M, Qi D, Mayer G, et al. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics. 2013; 12(8):2332-2340.
- Wang R, Fabregat A, Rios D, et al. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol. Vol 30. 2012: 135-137.
Data Access and Submission
The ProteomeXchange website contains the instructions for data submission.
- Data Access: ProteomeCentral is the portal for all public ProteomeXchange datasets. In addition, users can also subscribe to an RSS feed to be notified when new datasets are made available.
- Data Access: ProteomeCentral is the portal for all public ProteomeXchange datasets. In addition, users can also subscribe to an RSS feed to be notified when new datasets are made available.
- Data Submission with detailed tutorials and instructions.