An awesome new tool is up on the Protein Prospector and is detailed in this paper, currently in press (and open access) at MCP.
The MS-Viewer takes aim at a lofty goal -- a program that can open post-processed shotgun proteomics data from different sources and open it in a unified format. For example, if someone posted their Mascot runs on Tranche and they don't match your collaborators replication that was processed with Proteome Discoverer, you can use MS-Viewer to open them both in the same format. This might help you to tell whether it is a database issue, a different in false discovery rate calculation, etc., which led to these differences.
Maybe more commonly, it gives you a chance to stop searching around for a characteristic of the data that you are interested in when meta-analyzing data.
Cool new program that makes Prospector even more useful than it already is! And there is even a nice video tutorial on how to use it. Check it out here (video link in red).
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