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The number, size, and format variation for proteomics data files (both raw and processed), annotation, as well as challenges in designing a robust data repository are some of the major factors inhibiting public dissemination of proteomics data. Sharing large amounts of data and software is a legitimate need in the field of proteomics and other scientific disciplines as replication of results and the benefits of data reanalysis relies heavily on having access to the original data. Several journals have already published recommendations for providing access to data associated with proteomics manuscripts; however, researchers have been left with the challenge of how to appropriately satisfy the recommendations. Of particular concern is how potentially large datasets (gigabytes to terabytes of raw data) may be efficiently hosted in a publicly accessible fashion.
Described here is Tranche, a secured peer-to-peer system (http://www.proteomecommons.org/dev/dfs/), along with a reference implementation, supported by Proteome-Commons.org, that is capable of hosting virtually unlimited amounts of data and supporting virtually unlimited users. Furthermore Tranche solves many of the prominent concerns in data dissemination, including hosting raw data associated with a proteomics experiment and maintaining annotation. It is intended as both a reference implementation and a model system for comparison to other proteomics data dissemination efforts. Tranche currently hosts many prominent proteomics datasets and mirrors of other proteomics data resources, including most all of the publicly available proteomics data.