After depletion of abundant proteins from my sample, I still see albumin and other abundant proteins after LC-MS analysis. Did the depletion work?
Depletion does not remove all abundant proteins from the sample. Even with 99% depletion of a specific plasma protein, highly abundant proteins will still be the most abundant proteins in the sample detected by MS analysis. However, depletion significantly decreases the most abundant plasma proteins enabling identification of lower abundant proteins.
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