alexa ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Proteomics & Bioinformatics

Author(s): Juan A Vizcano, Eric W Deutsch, Rui Wang, Attila Csordas, Florian Reisinger

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There is a growing trend toward public dissemination of proteomics data, which is facilitating the assessment, reuse, comparative analyses and extraction of new findings from published data. This process has been mainly driven by journal publication guidelines and funding agencies. However, there is a need for better integration of public repositories and coordinated sharing of all the pieces of information needed to represent a full mass spectrometry (MS)–based proteomics experiment. An editorial in your journal in 2009, 'Credit where credit is overdue', exposed the situation in the proteomics field, where full data disclosure is still not common practice. Olsen and Mann identified different levels of information in the typical experiment: from raw data and going through peptide identification and quantification, protein identifications and protein ratios and the resulting biological conclusions. All of these levels should be captured and properly annotated in public databases, using the existing MS proteomics repositories for the MS data (raw data, identification and quantification results) and metadata, whereas the resulting biological information should be integrated in protein knowledge bases, such as UniProt. A recent editorial6 in Nature Methods again highlighted the need for a stable repository for raw MS proteomics data. In this Correspondence, we report the first implementation of the ProteomeXchange consortium, an integrated framework for submission and dissemination of MS-based proteomics data.

This article was published in Nat Biotechnol and referenced in Journal of Proteomics & Bioinformatics

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