I immunoprecipitated a calcium channel and I used an antibody against Ubiquitin, but every time I did that I had ubiquitin signal below the molecular weight of the channel. Does anyone have any idea why is this observed?
Presumably it might correspond to a cleaved fragment of the full-length protein. Alternatively it could be a ubiquitinated protein that is co-immunoprecipitated with the Ca2+ channel (eg. calmodulin, auxiliary subunit etc).