Please find below links that may be useful for designing and conducting structural proteomics experiments.

 
Proteomics Tools:
prospector.ucsf.edu Probably the best free collection of the proteomics utilities on the web.
expasy.org Good free collection of protein analysis utilities.
Lab Supplies:
hamptonresearch.com Probably the best dialysis buttons.
usbweb.com Miniature spin columns.
Reagents:
piercenet.com Probably the broadest collection of crosslinkers.
sigmaaldrich.com Crosslinkers from Sigma.
trc-canada.com A lot of unique crosslinkers from TRC.