Contaminants in solvent

Discussions about sample preparation: extraction, cleanup, derivatization, etc.

11 posts Page 1 of 1
Hi all.

I have been having some problems with contamination in solvents. At our lab our solvents appear to become contaminated with similar substances over time. I am seeing some of ions 83, 281, 73, 267, 355, and 341. From my research these seem like typical column or septum bleed indicator ions, however, I have eliminated the column and septum as the cause of contamination. This leaves only the solvent. I also see two large peaks at the tail end of chromatograms. These compounds are composed of ions 59, 44 and 72. Again I do not know what these compounds are or where they are coming from. From their mass spectra they seem to be some kind of amide or slip agent. Here is an example data file for those interested: https://www.dropbox.com/s/zggheftcg4aiq ... 9.qgd?dl=0

Can anyone suggest where the contamination might be from? We use MS certified vials and septa. Our solvent is DCM. The solvent is dispensed via aspiration using transfer pipettes into the vials. The solvent is stored in a glass Schott bottle with plastic cap away from sunlight.

Any suggestions as to what might be causing the contamination, or how to reduce it? Thanks in advance!
Step 1. Rinse a vial and its cap three times with solvent direct from the bottle that it comes in from the supplier. Pour the solvent into the vial, do not use pipettes etc to do the transfer (yes it's fiddly, that's why they call it troubleshooting). Half fill the vial with solvent, then do a series of three injections.

If there are no contaminants, then the contaminants you usually see are from solvent handling - eliminate/ad/substitute steps one by one to see where the critical step is.

If the first run has peaks, and they get smaller in subsequent runs then you have contamination from solvent handling, plus carryover.

If all three runs have contamination and the peaks stay the same size then the solvent is probably contaminated, but there is also a faint possibility that the contamination is coming from the GC. If it is coming from the GC then it will still show in an injection of a completely different solvent e.g. hexane.

Peter
Peter Apps
Peter Apps wrote:
Step 1. Rinse a vial and its cap three times with solvent direct from the bottle that it comes in from the supplier. Pour the solvent into the vial, do not use pipettes etc to do the transfer (yes it's fiddly, that's why they call it troubleshooting). Half fill the vial with solvent, then do a series of three injections.

If there are no contaminants, then the contaminants you usually see are from solvent handling - eliminate/ad/substitute steps one by one to see where the critical step is.

If the first run has peaks, and they get smaller in subsequent runs then you have contamination from solvent handling, plus carryover.

If all three runs have contamination and the peaks stay the same size then the solvent is probably contaminated, but there is also a faint possibility that the contamination is coming from the GC. If it is coming from the GC then it will still show in an injection of a completely different solvent e.g. hexane.

Peter


Hi Peter.

Thanks very much for the advice. I prepared a vial of solvent as per your instructions. Here are some images of the results:

Run 1:
Image

Run 2:
Image

Run 3:
Image

As you can see the first run was very good. There are peaks beside the solvent front peak but the rest of the chromatogram is clear. I'm not too concerned about these peaks as previously there were other contaminants all over the rest of the chromatogram.

The second run shows some of the contaminants. Looking at the spectra they are similar to the ones I described previously.

The third run shows the contaminants again but at a greater concentration than in the second run.

Looking at the first chromatogram again I can actually see the contaminants that appear in the second run. However; they are so low in abundance that they aren't significant. So, is it correct to conclude that whatever is causing the contamination is naturally occurring in the vial/septum/cap? That is the only conclusion I can come up with. Maybe when the septum is pierced for the first time, fragments of plastic enter the sample and that is what the peaks are. That would also explain why the peaks grow in size. Injector septum bleed and column bleed shouldn't produce peaks that grow in size like this. What do you think?
I have seen a similar phenomenon with HPLC/fluorescence detection: No peak in the first injection, increasing peaks with subsequent injections from the same vial. I narrowed it down to the color of the vial caps: Blue produced highest interference > green > yellow > black produced only minor interferences. This was especially strange, because usually, the sample does not touch the cap but only the septum.
Jörg
cene wrote:

Looking at the first chromatogram again I can actually see the contaminants that appear in the second run. However; they are so low in abundance that they aren't significant. So, is it correct to conclude that whatever is causing the contamination is naturally occurring in the vial/septum/cap? That is the only conclusion I can come up with. Maybe when the septum is pierced for the first time, fragments of plastic enter the sample and that is what the peaks are. That would also explain why the peaks grow in size. Injector septum bleed and column bleed shouldn't produce peaks that grow in size like this. What do you think?


I agree. As a double check, do a series of three injections with no septum on the vial - to limit evaporation you can replace the septum with aluminium foil.

Peter
Peter Apps
Peter Apps wrote:
cene wrote:

Looking at the first chromatogram again I can actually see the contaminants that appear in the second run. However; they are so low in abundance that they aren't significant. So, is it correct to conclude that whatever is causing the contamination is naturally occurring in the vial/septum/cap? That is the only conclusion I can come up with. Maybe when the septum is pierced for the first time, fragments of plastic enter the sample and that is what the peaks are. That would also explain why the peaks grow in size. Injector septum bleed and column bleed shouldn't produce peaks that grow in size like this. What do you think?


I agree. As a double check, do a series of three injections with no septum on the vial - to limit evaporation you can replace the septum with aluminium foil.

Peter


Hi Peter.

I ran the additional test as you suggested. No contaminant peaks appeared in any of the three samples. In conclusion, the contaminant peaks were being caused by the vial septa or caps. As the contamination is only very minor in the first run it is not a big issue. Each sample is generally only analysed once anyway.

Thank you for your help!

I also ran another test out of interest. I have found that the solvent I dispense from the main solvent bottle tends to become contaminated fairly quickly by a mystery compound that appears around 24 minutes as a large tailing peak with main ion 59 and 72. All I could deduce from the mass spectrum was that it may have been some kind of amide or slip agent.

So, when I ran the above three solvent samples in uncapped vials, I also created a fourth vial of solvent and inserted one of my pipettes into it. I use disposable, plastic Pasteur-style bulb pipettes. I left the tip of the pipette in the vial, immersed in the solvent, for several minutes. Then I analysed the sample:

Image

I found an alkane peak in the centre of the chromatogram, and a small peak in the same location as the aforementioned contaminant. In conclusion, I believe the plastic pipettes are being degraded by the solvent each time solvent is taken out of the bottle and that is what the other contaminant is from.
Most lab disposables are fine with aqueous solutions, but not as good with solvents. For applications where contaminants are a critical problem you need to work with glass, or validate the contaminant profile of plastic ware before you use it for samples.

Peter
Peter Apps
Peter Apps wrote:
Most lab disposables are fine with aqueous solutions, but not as good with solvents. For applications where contaminants are a critical problem you need to work with glass, or validate the contaminant profile of plastic ware before you use it for samples.

Peter


Hi Peter.

Thanks for the advice. I will have a look into other possible sampling tools. Do you have any suggestions for how to best profile the pipettes? I was thinking I could leave a pipette in a measuring cylinder of solvent for some time and then inject the contaminated liquid straight from there.
Why use a measuring cylinder ? - you need something that can be sealed, e.g. a test tube with a ground glass stopper. Do not put grease on the stopper.

How are you going to put the pipette tip into the solvent, and get it out again ? - make sure the tools are clean.

Peter
Peter Apps
Peter Apps wrote:
Why use a measuring cylinder ? - you need something that can be sealed, e.g. a test tube with a ground glass stopper. Do not put grease on the stopper.

How are you going to put the pipette tip into the solvent, and get it out again ? - make sure the tools are clean.

Peter


Hi Peter.

I'm only thinking of a measuring cylinder because a pipette would fit into it easily. Unfortunately I don't have any stoppers or appropriately sized test tubes so I may have to get some of those first. A cylinder would keep the headspace relatively stable and limit evaporation quite well I imagine, even without the stopper. I would just take an aliquot of the liquid in the cylinder and dispose of the pipette and contaminated solvent afterwards.

It was just a thought. But perhaps the test tube would be a much better idea so I will look into it.
Solvents, and the surfaces that they touch get contaminated simply by exposure to the air.

Rather than running separate tests, a far more straightforward way of validating the cleanliness of your solvents and containers etc it simply to run blanks. If the blanks are clean enough, then everything is clean enough, if there is dirt in the blank, then eliminate or change one thing at a time until you locate where the dirt is coming from (which is what you have already done). Then try a different brand of that component.

Peter
Peter Apps
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