We have reason to believe that a particular drug is sticking to a particular amino acid within a particular protein. Due to the fact that this drug is patented property, I can't reveal any other details than this.
In order to directly test this, my preferred method would be using single reaction monitoring (SRM or MRM) on a triple quad instrument.
In this particular case, I don't have access to a triple quad, just an Orbitrap. Therefore, we'll have to get creative.
On a synthetic peptide resembling the active site of our protein of interest, I know exactly the mass shift that occurs when the drug binds.
In silico digestion of the protein of interest + the drug mass shift gives me a z=2 mass of 1131.198
Here is the setup and results
Only the HeLa cells treated with the drug produce the a molecule that falls within my specific mass window.
Now to compare this to an MRM!
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