Protein Prospector – tools for proteomics from UCSF
http://prospector.ucsf.edu/

PROWL – tools for proteomics from Rockefeller Univeristy
http://prowl.rockefeller.edu/

Yates Lab, -- makers of very useful Proteimic tools, Scripps Research Institute
http://fields.scripps.edu/

Thermo Electron Corp. – makers of the LCQ line of mass spectrometers
http://www.thermo.com/com/cda/category/category_lp/1,2152,64,00.html

Ion Source – a  good site for some mass spec tutorials
http://www.ionsource.com/

American Society for Mass Spectrometry
http://www.asms.org/Default.aspx?tabid=1