HILIC - BEH Amide storage soln.
Answers
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I know on some older Waters HPLC columns, storing with even small amounts of TFA messed up the column packing material. Try a mild buffer/ACN solution to store the columns, without any harsh organic acids. What exactly is in your mobile phase? I've run some methods that TFA (even at 0.05%) chewed up the packing material after 80-100 injections (Agilent 1200 LC+Waters column run by Empower2, and tested on an Alliance LC with the same result). TFA is generally not kind to the packing material, in any regard.
(Side note: are you actually disengaging the column from the instrument, or are you leaving it on the instrument under low flow?)
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In general, for periods longer than 4 days, the recommended storage solution is 100% acetonitrile. The flushing and storage procedure is described in the ACQUITY UPLC BEH Columns Care & Use Guide. However, as you've discovered, there is little harm storing your column in your mobile phase for short periods of time in order to reduce column equilibration upon re-installation.
I'm not sure what would cause wild fluctuations in peak area but I am pretty confident that it is not your column storage conditions (which look fine to me).
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