I am not sure if there is a direct way to determine covalent binding to the beads; however, you could try and desorb the proteins to determine if the proteins are physically or covalently attached.  You could do this with repeated washing and fluorescence detection.  As you repeatedly "wash" the beads you will see the fluorescence signal asymptote to a fixed level.  Whatever will not desorb you can assume is chemically bound.  You could assay the desorbing solution or the beads themselves.  Setting up proper controls for the experiment will be important.

Thanks guys, I had suspected that it would be like this, thanks for the responses.

Boil the beads in SDS-PAGE sample buffer. Chemically crosslinked protein will stay on the beads and will not be seen when you run the supernatant on the gel. The beads can then be washed, and treated with a bit of protease. That should release some peptides, which can be detected by a protein assay or Tricine gel (control: protease without beads)

 Adam's proposed protocol sounds specific and robust.  I would go follow his suggestion.

Hi Adam,

Thanks very much, this seems like a good approach. 

Also, Nolan, thanks again