It would be really helpful to know EXACTLY which make, model and type of HPLC system you are using, esp the model # of the pump. Constructive suggestions depend on it. *Be sure to find and work with an experienced chromatographer when following the below generic suggestions.
FIRST: Dispose of the column used. *Columns are inexpensive consumable items just like filters and solvent. Trying to flush unknown contaminates from a column is a waste of time and money. Any experienced chromatographer will know this. Any inexperienced chromatpgrapher will not and continue to wastet time and money. All of the data collected on the system using the old column afterwards may be considered invalid so dispose of it and replace with a known clean fresh column AFTER flushing down the flow path and servicing the instrument as described below.
Using contaminated mobile phase in your system also implies that the solvent pickup filter(s) (connected to the bottle line) should be: If glass, then disposed of; If stainless steel, then properly cleaned before re-use.
Next, place a restriction line in the HPLC (no column) to create enough back pressure to run the pump(s) and flush, in this order, Pure Water, Pure Methanol, Pure IPA as "flush" solutions through the flow path to waste. Repeat with acidified water, then acidified methanol next, back to pure water, then pure MeOH. This may remove some of the unknown contaminates. Replace the pump's inlet filter again (they are cheap).
Your HPLC inline degasser membranes are probably contaminated from exposure to the dirty solution used. Depending on model, degassers require professional cleaning and service every 3 to 5 years so if due, this may be a good time to have it serviced. The membranes may be fine, they may be damaged or contaminated too and the only way to know if to have the system professionally serviced. The membranes are easily damaged from contact with a long list of chemicals (which may have been in the solution you used). In any case, for now, do not run fresh mobile phase through the degasser to the column. At the very least, make sure you flush out the degasser separately or better yet, have the degasser professionally serviced first. *A contaminated degasser will continue to contaminate the entire flow path of your HPLC system ["
An Often Ignored HPLC & LC/MS Contamination Source. Did you check your Vacuum Degasser?";
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