The new ProteomeCommons.org site has an archive of open source proteomics software and other digital content.
Update: some other open source proteomics sites (from the ABRF meeting).
Ensembl Genome Browser
The Global Proteome Machine Organization
Human Proteome Reference Database
Open Mass Spectrometry Search Algorithm
Thanks for the plug to ProteomeCommons.org! I didn’t know that you were at ABRF, else I would have asked to meet up.
Thanks for keeping such a nice blog on mass spectrometry.