Not using UPLC for a week or longer between runs

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I use a Waters Binary UPLC for running impurity samples and its a PDA detector, column CSS C18 1.7micton 100mm length with a potassium phosphate buffer in Line B and Acetonitrile in Line A. Method is a gradient. I use it on average once every week and a half or so and my set up before I use it is always to prime the seal wash (90:10 Water:Acetonitrile) then prime out my main mobile phase lines (A1 and B1) in the same seal wash for about 20 minutes, before setting up with fresh buffer/injector washes and starting up system and activating the run etc.

Post-run, i flush the A1/B1 lines in seal wash for an hour and store all lines in 50:50 Methanol until i need it again but the last 2 runs i have been getting my first system suit injection with the retention times way later than normal before it settles down perfectly stable for the remaining injections! Run time is 40 minutes and now i seem to have to try a test injection before activating my run just to "see" if retention times are normal. I always run 3 condition columns before each run, i thought that would be enough to equilibrate the system, should i add more, does anyone know what could cause this?
Wow! You are doing a lot! I agree with everything you say up to using 3 columns. You should be able to equilibrate (30 minutes) your column of the day and go to system suitability.
Hi there, yes but I cant equlibate the column as its a gradient so condition column is my only option.
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