Liners are a protective mechanism in an injection port but not all of your injected analyte remains in either the liner or column. When you think about things being in a gas phase, and how fast those molecules are moving, there are certainly some that move outside the liner before entering the column, even as far as the split line. We have found when doing splitless injections that even a dirty split vent line can cause tailing and breakdown of analytes.
If you are using an Agilent GC, make sure that you remove the split vent line and clean or replace it often. Also be sure to clean the port where it attaches to the injector to remove any contaminates there.
Column insertion depth and the smoothness of the column cut can also affect peak shape.
And of course the split vent trap.
For amines I use resteks sky deactivate liners and siltek inlet seals and either a base deactivated wax, db 5 amine or my current favorite, rtx-volatile amine and the similar agilent volamine column. (With an NPD with a blos bead. I like helium as carrier and makeup to deliver a constant flow to the detector, of a constant gas makeup). For particularly bad ones a direct injection liner can help. If you getting degradation in the syringe itself, she makes a series of low dead volume autosampler syringes that can be fitted with needles with hydrophobic or hydrophillic coatings.
Some people passivate the instrument with a shot of pyradine or
such. On some analyses Ive tried adding 50uL of pyradine to the samples themselves. If I have good separation then it seems to work OK and it pasivates every injection. Another way I've done it is to simply have two methods, and do a shot of pyradine, with a run that takes maybe a min, with a high oven temperature and flow, then a sample, with my run conditions, then repeat.
The blue liners and the volamine type columns have eliminated most of that. Agilent has a whole line of ultra inert stuff, from coated deactivated metal ferrules, to ultra inert liners and inlet seals. My take away from the webanar though was that theirs is better, but their competition is almost as good, and in fact usually good enough at a substantially lower cost. In fact, the number on place I'd go if I really needed to push the limits of sensitivity would be to a direct injection liner. It takes the metal in the inlet out of the equation for the most part. (Restek makes an entire deactivated inlet, as well as a deactivated for the detector. I'm skeptical about the jet though. You get less than a half cm of contact between eluent and jet, before its in the plane, and honestly, suppose it breaks down on the Hort metal surface, sine I've not seen my jets clogged with carbon, it must get flushed out, which means its still burned, which means I still get signal. It might cause some tailing, but if it does, it has not been enough to notice above all the other amine issues.
One problem I've had is that some methods collect on a phosphoric acid coated sampler and then later neutralize it with hydroxide. The excess hydroxide can quickly foul your liner. (Like 5 or 10 injections)
If I were in your position, not having the things I have around to deal with these analytes, I'd try passivating with pyradine. I'd also call restek and get a rtx volamine and get a direct injection liner.
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