[President1975]

I have a question about a UPLC method development. I need to do Pharmacokinetic in a rat plasma sample. I need to quantify a peptide. So when i tried to run samples after AcN precipitation i take no peak at ESI+-MS. I presume that this is due to proteins that precipitate together with my peptide through the AcN process. My question is what is the best method to clean all parts of UPLC MS MS after taking no peaks. And what is the best method to prepare plasma sample with a peptide. We will try different methods such MetOH, MetOH/AcN, to test the best recovery for our peptide. One point of interest is that i take a big peak over 100% of AcN in my LC  method.

[Arkcon]

You ask too many questions to answer them all systematically, but we can give you a few hints.

Briefly, you can transfer methods from a regular HPLC to a UPLC, with some moderate development work.  So you can start with that, if available.

Its worthwhile to make sure you can get decent separation using a UV detector, if at all possible.  Likewise, its worth optimizing mass spec conditions by perfusing pure analyate.  Once both parts work, then they can be connected.  That's the best way to insure  the analysis works well, and may be necessary if you're having problems.

Cleaning the UPLC doesn't seem at first glance to be a high priority for me, the steel parts should be easy to clean.  If the column can handle it, you may want to flush the system with a gradient of 0.1 % trifluoroacetic in water and acetonitrile.

Often, when working with a plasma sample, a pre-column cleanup with a SPE cartridge, but you'll have to determine cleanup conditions that removes most of the plasma proteins, and leaves most of your analyte.

[EDIT] pre-column, not per-column