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“The problem is the baseline looks lumpy (not steady) instead of being normal or steady. I have tried all the procedures and therefore eliminated the column, the mobile phase and detector. The system has been thoroughly flushed and purged but still my baseline is not as expected. I have tried the column on a different system under the same conditions (ambient temp, flow rate 1.0ml/mins, inj vol 2ul) and the baseline is normal as expected. I have attached a copy for you to see if you can help. Any ideas what could be happening on this system?”
“The baseline in your chromatogram is very far from what you normally expect. The regular cycling pattern in the chromatogram makes me think that the problem is most likely related to the pumping of the mobile phase. Since you have ruled out the detector, and have transferred the mobile phase and column successfully to another system this means that the pump is the most likely source of the problem. Even though it is thoroughly flushed and purged there is still a small chance that it may be due to trapped air, but if not then a faulty check valve is likely. Try flushing and purging the pump with methanol (remove the column) and then with your mobile phase. If this doesn’t work try replacing the inlet check valve (this is the one which usually causes problems), or clean it by placing in a beaker and covering with methanol or isopropanol, then sonicate for about 5 minutes and replace.”