Hey everyone,

I’m relatively new to the field of mass spectrometry and proteomics and need some advice. I’m trying to run a recombinant protein on our mass spec. It should be a really straightforward protocol: aliquot out the protein and resuspend in buffer, reduce, alkylate, digest in solution, desalt, dry, resuspend in running solution, and run on the mass spec. But somehow, in the one step that I could possibly have loss - the desalting step - I get around 80% loss. The kit I use is made for the amount of protein I aliquot (20-50ug) so I have no idea why I’m losing so much.

If you guys have any advice for cleaning up recombinant protein digest specifically, I’d be very grateful. Thank you!