indole skatole baseline exceptionally high

[Heikki]

I'm doing a indole analysis on a gc and now for some unknown reason, the standards (and samples as well) I've been using for quite a while (they're fresh, but they've been manufactured the same way as before), give a lot of noise to the chromatogram.

I can see the peaks very clearly, but the baseline is very high compared to my previous analyses (now from 26 to 116 pA, previously from 5 to 25pA).

Where is the problem? Is there something I should clean etc?? Any help is appreciated.

[chromatographer1]

It sounds as if the column phase is damaged and is bleeding. The other possibility is that you have injected something that remained on the column (injector) and is now slowly bleeding off the column.

You could, of course, replace the septum and the injection liner and recondition the column.

If that does not work, then replace the column. They don't last forever.

best wishes,

Rod

[AICMM]

Heikki,

Given that Rod is a column guy and I am a detector guy, I would immediately suspect the detector. If you have a cool oven and cool injector, is your detector still noisy? If yes, I would check the detector flows and clean the detector. I would, at the same time, as a matter of course, replace the liner and septum since this is relatively easy and cheap to do. Then, if noise is still present and related to oven temperature, I would start to suspect the column. You don't say what solvent you are using?

Best regards.

[Heikki]

My samples are suspended in chloroform, and the needle washing solutions are chloroform and MeOH.

I left the sequence running overnight anyways, and the baseline and noise has reduced drastically, but it's still higher than normal. I thank for both of your advice, and shall begin my error tracking with the septum and detector cleaning (they're cheaper, and I don't have a spare column at hand just now, those delivery times are surprisingly long sometimes here in Finland)

[Peter Apps]

Clean/replace the inlet liner, replace the the inlet septum, clean/replace the gold seal (I'm guessing that you have an Agilent from the use of two washing solvents) is the first step. If that does not work clean the detector (guessing an FID from the pA signal).

Did the noise appear suddenly, or has it built up gradually ?. Have you changed any gas bottles lately, do you have scrubbers on your gasses, and how long since you last changed them ?

Peter

[Heikki]

It's fantastic to see the detective work, yes Peter, all assumptions are correct.

I just did few solvent injections and removed about 0.5m from the injection end of the column, they helped a lot. But I'm still having few problems. I've also just changed the synthetic air bottle, but I know that the problem isn't in the gases.

The noise did appear suddenly, but has been vanishing gradually. I intend to do an overnight reconditioning and if that doesn't help, I'll rinse the column with MeOH as mentioned in the column maintenance guide (restek satbilwax - DA). If these won't work, I'll start replacing parts.

I also ordered a new column, so next time I'll be ready to change it. I'm very new at this, I was suddenly given charge of our chromatography without any previous experience. This has been really interesting and fun trying to understand the chemistry behind all this. I appreciate all of your help very much, and this forum has been quite a salvation for many problems.

[WK]

Heikki
I agree that if you replace column & liner/wool this is a good place to start assuming you have clean gases.
Don't forget that FIDs eventually need maintenance and have replaceable parts (seals/ceramic insulators/stainless parts). Check your manual.
I work in a smelly lab and can sympathise with the odour that skatole and indole can produce. I recommend a clothes peg for your nose!!
We had a "beef curry" chemical in the lab once and we ended up throwing our clothes away since the odour never left them after several washes!
WK

[Peter Apps]

BEFORE you rinse the column with anything, do the maintenance on the inlet. If the column is contaminated enough to be worth washing then the inlet must be even dirtier. Inlets are a lot quicker, easier and cheaper to maintain than columns

Column rinsing is a last distch all else has failed solution.

Peter

[AICMM]

Heikki,

I cannot speak for the 6890 FID but if you are using a 5890 FID, chloroform as the solvent of choice will eventually create some issues. When you burn chloroform you make HCl (just like dichloromethane which is what I used to use.) The HCl will dissolve in the water created and and this can attack your collector. Cleaning will help and if you can raise your detector base temperature without adversely affecting your analysis I would advise that as well since this will minimize recondensation in the detector.

Best regards.