Hi, I am trying to find effecient way to resolubize the protein. We currenetly use 8M Urea with 50mM DTT and incubate at 37 for 30 min. I do hand pipet and vortex 15 sec before and once in the middle but based on BCA assay and observation, large amount of protein are still in solid form. It occured to me that maybe sonication can help with this, but I have only see people sonicate for cell lysis purpose, so I am wondering if short quick sonication to resolublize the protein pellet will hurt lc-ms result.

Another alternative is adding surfcant such as sds, I am scared to do so because references have showed that it could impair signal. I am also worry that it will remain in the lc-ms system and hurt other ones run especially metablomic folks. On the other hand, I use desalting column before lc-ms run, does that mean I can use surfcant in the middle step and not worried since it will be removed at desalting.