Has anybody seen the jiggling of FPLC trace like this? I have cleaned the flow cell which was hinted to be the cause of this with 0.5 M NaOH followed by 500 ml wash with MilliQ water. Still, I am seeing the same. Please kindly suggest what can be done to get the smooth trace.
It could be caused by a small air bubble trapped in the UV detector.
See pages 57 and of this manual for advice on cleaning the flow cell. A perfectly clean flow cell should not trap air bubbles.
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Make sure that your buffers are thoroughly degassed.
Make sure you have a flow restrictor in place to maintain back pressure, which helps prevent bubbles from forming.
Dirty cell would cause IMO more regular irregularities. This reminds me of when I opened and closed door of the fridge in which we had the FPLC. Would that be your case?
To remove bubble from your cell, you may need to wash it with methanol (without column!). Afterwards, you need to degass your buffers and connect column with bubbles (while running).
If you do not have flow restrictor, you can make one using long tube with small internal diameter. That will increase backpressure and assure that the dissolved gas does not come out.
Thanks, Adam and Tomas the flow cell looked like the culprit and as Adam suggested washing it with 1M NaOH 30 ml at 1ml/min with flow restrictor in place followed by 60 ml of water at 4-5 ml/min flow rate helped to remove the air bubble.
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