I have performed similar experiments in the past and I used magenetic streptavidin beads from invitrogen. After I incubated my biotin labeled samples with the streptavidin beads for 2 hrs at room temperature, (you can also do this at 4 degrees if you are worried about protein degradation) I washed the beads 3 x in PBS using a magnetic rack. After the final wash, I added 100 uL of the following mixture in order to break the biotin-streptavidin complex

2% SDS mixture + 3 mM biotin all made in PBS, and heat to 99 degrees on an incubation rocker.

I then pulled the magnetic beads aside in the magnetic rack and kept the supernatant.

On the day of running the western, I added an equal amount of 2x sample buffer to the original supernatant and loaded 20-30 uL of this mixture in a 10% SDS gel.

The key to breaking the biotin-streptavidin complex is including the excess biotin. Also, depending on your starting material concentration, you could break this complex with more or less of the SDS-biotin mixture. My sample concentration was fairly low so I settled on 100 uL.