In an aim to reduce the number of chemicals involved I would like to use partitioning with aqueous:organic compounds after deproteinization, can i use methanol/spin to do this or will low MW polar metabolites be removed too?
While some proteins will deproteinize, small peptides will not. In fact many polar molecules will remain in the Methanol since it is polar and a protic solvent.
I just completed a study involving precipitation of plasma proteins and then analyzing small, polar molecules by LCMS. Yes, you can precipitate the proteins with methanol and then analyze the supernatant for your low MW compounds. Actually, in my case I found that precipitation with trichloroacetic acid gave better recovery for some of my analytes. So it might be worth trying a couple of different precipitation methods (cold acetonitrile might work too). Two caveats: the supernatants may still be fairly dirty, so use a guard column on your LC column if you can, and watch for signs (e.g. peak broadening) that your column is starting to get gunked up. I found that backwashing just the guard column with water between runs helped a lot. Another thing to check is if your analytes are bound to protein - if they are, they'll precipitate with the protein.
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