Hello,

I have isolated exosomes from serum of healthy and patient cases using differential ultracentrifugation+ultrafiltration and have validated them for their presence and absence using western blot with specific markers of exosomes. I would want to perform proteomics on these exosomes.

Previously, I had lysed my exosome pellet with an equal amount of RIPA buffer and estimated its concentration using the BCA assay and submitted about 50 ug of protein to our core facility. I ended up getting a lot of serum proteins and could not detect any exosome-specific protein or any marker of exosomes. Could someone let me know an optimal working protocol to perform proteomics and avoid these abundant proteins so that I can detect low abundance proteins? Also, would passing the lysed supernatant through a depletion column before doing the MS analysis serve as a good purpose to get rid of serum proteins?

Any suggestions or answers would be greatly helpful!

Thanks,