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How I clean a GC injection port

15 Jul 2020

Recently I have been asked by several customers how to clean an injection port.  My initial answer is always the same, you should clean the injection port according to the manufacturer’s recommendations.  But what instructions do I provide when the injection port was manufactured by Restek?  I usually provide the same response but then I provide instructions on how I cleaned an injection port when I was working in the lab.

I hope this post will help those who may not have a set cleaning procedure or are using an instrument where instructions are not provided by a manufacturer.  I would also like to hear from you if you have a different or unique way to clean an injection port.  After all, blog posts are about sharing information.

injection port

Cool the injection port.

Turn off the carrier gas.

Remove the GC column.

Remove all injection port consumables (including items such as the injection port liner, inlet seals, septa, fittings, etc).

If possible, choose at least one polar solvent and one non-polar solvent which will not contaminate your instrument. Or look for a solvent which has a polarity somewhere in between.  In other words, make sure the solvents you choose are not target compounds and will not contaminate your detector.  For example, do not use methylene chloride if your detector is an ECD.  Several of my go-to solvents were acetone (moderately polar), methylene chloride (slightly polar), methanol (polar), acetonitrile (polar), cyclohexane (non-polar), toluene (non-polar) and hexane (non-polar).

Use wooden-handled cotton swabs dipped in one or more of the solvents listed above and begin swabbing the interior walls of the injection port. I usually began with a non-polar solvent and while working my way up the polarity scale I finished with a very polar, low boiling point solvent like methanol.  Never finish with water because the injection port may rust.

If possible, blow dry with clean, dry N2. Never use a compressed gas which contains propellants since they may contaminate the injection port.

When all surfaces are dry, install new/clean consumables and an injection port liner. Install a new injection port septa.  Re-install the GC column.  Double-check to make sure everything was properly assembled and that nothing was left inside the GC oven before you close the oven door.

Do not heat the injection port yet. Turn on clean and dry carrier gas and set the flow rate that whatever it was before you cleaned the injection port.  Purge for at least 30 minutes.  Leak check using an electronic leak detector.

Heat the injection port to 100°C.  Make sure no fittings are loose and that the nut for the injection port septa is not too tight.  Increase the temperature to 150C and once again check the fittings (to make sure nothing is loose) and that the nut holding the injection port septa is not too tight.  Repeat every 50°C until the set point is reached.  Leak check often.

Analyze several solvent blanks to make sure the baseline is free from any contamination.  If unknown peaks are detected, the injection port may still not be clean, or these peaks may be from something else.  If needed, review this post to help locate the source of these ghost peaks. Are your ghost peaks coming from the GC column, or something else?

If you are still having activity issues or ghost peaks, consider installing a Uniliner.  Because a fused-silica GC column connects directly to this injection port liner, the inside of the injection port is prevented from contacting the sample/standard.  This should help confirm if the injection port is the issue.


If the instructions above did not remove the contamination sufficiently, you may need to try something a little more aggressive.  Several suggestions are below.

Try using a nylon brush with a cleaning solution like Detergent 8. This solution (when diluted according to the manufacturer’s instructions) may help remove additional contamination. Make sure you completely rinse the injection port when finished using deionized water and then quickly rinse with a fast-drying solvent like methanol (to prevent any rust from forming).  Please note – if you decide to use a nylon brush with solvents or alcohols, always check its compatibility with nylon.  Please note - because of the high pH, do not use Detergent 8 on an injection port which has been treated with Siltek.

You may want to try using a metal brush instead of a cotton swab or nylon brush if the contamination remains. Choose a brush that will not scratch the walls of the injection port and/or be damaged by solvents.  I usually used brass brushes because I knew they would not scratch the stainless steel injection port.   Please note - never use a metal brush of any kind if the injection port is treated with Siltek or some other inert coating.

If a metal brush and solvents do not remove the contamination, it may be time to replace the injection port.

Finally, you should clean/flush or replace the injection port weldment/septa nut and split vent line to prevent contaminating a clean (or new) injection port.

Thanks for reading.