I am hoping to crosslink the protein-protein interactions in cells as well as the protein-DNA interactions (for which I use formaldehyde). Has anyone tried using the crosslinker DSS for this purpose?
DSS would work for protein-protein interactions. however, DSS won't be very efficient and will require you to perform some kind of enrichment to improve your chances of observing the links. since you're going to use formaldehyde anyway, why don't you check first to see what you get there? it's better penetrating crosslinker.