I am having contamination issues with my HPLC, specifically normal phase. We are running a gradient of 99.5% Hexane / 0.5 Ethyl Acetate down to 40% Hexane / 60% Ethyl acetate and the contamination peak appears 70% Hexane / 30% Ethyl Acetate.
We have tried new Hexane, new Ethyl Acetate, removing the guard column, trying a different column, flushing both channels with IPA for 2 hours, bypassing the degassing chamber and replacing the Hexane channel tubing/frit.
The only thing left I can think of removing/disassembling and cleaning the MCGV, would that be worth my time and if not, what are some other ideas that I haven't thought of?
Dear Kyle Neal,
It is possible that your contaminations are substances that you are washing out from the sealing materials of The HPLC.
I always observe the same background masses in our LC-MS systems, that cannot be removed by any rinsing process.
In an HPLC instrument, various seals are installed in the most diverse places. Possibly one or more of these seals is not solventstable, because many users use the HPLC in reversed phase mode, so organic Solvents proceed the washing out.
You should check this with the manufacturer , whether is relevant for you and your application. If necessary, you would have to replace these seals accordingly.
I recommend that you do this before cleaning, in order to avoid the certainly time-consuming cleaning process.
Good luck and stay healthy
Joachim beat me to it and is on the correct track. In addition to routine service concerns, many of the polymeric seals used in HPLC systems are NOT chemically compatible with certain solvents or solvent mixtures. Three seals that are always a concern are: (1) The Pump Pistol Seals and any related wash seals that may be in use; (2) The injector rotary valve seal(s) and (3) Injector Seat.
Additionally, most inline vacuum degasser are not chemically compatible with some of the solvents you listed (so the degasser could be damaged too, and causing the problem). "An Often Ignored HPLC & LC/MS Contamination Source. Did you check your Vacuum Degasser?" https://hplctips.blogspot.com/2015/08/an-often-ignored-hplc-lcms.html
All of these items are subject to damage when used with certain solvents. Please determine which types of polymers are used in the ones that you have and also if more chemically compatible versions are available for whatever brand and model of HPLC system you have.
Please look at the following below links which may help you in your analysis:
http://ccc.chem.pitt.edu/wipf/Web/LCMS%20trouble%20shooting.pdf
https://www.waters.com/webassets/cms/support/docs/715001307d_cntrl_cntm.pdf
Thanks
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