sonication to break apart a protein- is this feasible? - (Oct/15/2012 )

I have a probe sonicator and am currently going up to 20 min of 2 second pulses in ice water to keep the temperature down to try this out....but does anyone have any prior experience or protocol specific to breaking proteins up? Are there other, better, ways to mechanically break a protein apart?

are you talking about breaking an aggregate or are you talking about breaking the peptide chain?

sonication can disperse an aggregate. it's difficult to mechanically break peptide bonds.

I actually am trying to break open a compound composed of many subunits.....so I'm guessing it is something inbetween breaking aggregates and peptide bonds.