Ouch. This goes on the list of techniques I really hope I never have to do -- but if you really really need to quantify that peptide and you don't have any way to enrich for it, deep dive will probably get you there.
This is the overall strategy -- (please note they fall in the non-deplete camp) -- and you are reading that right. Fractionate into 96 well plate, monitor to figure out the well(s?) where your peptide ends up. Fractionate that single well into another 96 well plate -- and then use that final well for quantification.
I guess if it is completely automated and you know that C6 well fraction F4 has what you're looking for it should be the same for every sample...so it wouldn't be that bad? Again...I hope I don't have to do it, but the method is here just in case.
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