How compatible is a trypsin digestion with DMSO? I've found some passing mentions in discussions of 10-20% DMSO being used by some folks in a trypsin digestion. However, I haven't found any definitive or reliable validations out there. We're doing metaproteomics on messy samples, and we're always on the lookout for the magic solvent that will get the best yield from any given sample. DMSO seems like it would be great for protein solubility (we also have 0.1% SDS and 4M urea present). A typical 50 uL sample will get diluted about 10x by the time we get to the digestion with modified proteomics grade trypsin.
Thanks Andreas! Yes, once we get to the trypsin digestion step the SDS will be below 0.01% and the urea will be below 0.2 M, which seems to be compatible. And, after digestion we dilute / quench with over 10x water / formic acid for strong cation exchange followed by C18 SPE. Hopefully a concentration of less than 1% DMSO will not interfere with the strong cation exchange. We're running a comparison now, with and without DMSO, and the DMSO samples have a lovely yellow color (crossing fingers that this is protein!).
Our speed vac seems to pull off DMSO pretty well, though slowly (we tried pure DMSO to test it and it seems to pull off about 500 uL per hour from a regular microfuge tube). Slower than water, but manageable.
Hi Jeffrey,
I am also attaching, with this message, the publication by Riviere and Tempst, for you attention. It covers many conditions where chaotropic agents and detergents are used in protein proteolysis.
Good luck,
Hediye.
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