Synapt LCMS background_solvent-related contaminant issue - Chromatography Forum

Synapt LCMS background_solvent-related contaminant issue

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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When I perform LCMS analysis on the Synapt G2Si using a binary gradient of water and acetonitrile, a cluster is eluting with prominent peaks in the chromatogram whenever the gradient reaches about 80% to 100% acetonitrile.

Originally, the impression was that the background was the result of LC system contamination until acetonitrile from different brands were examined using direct infusion (directly from solvent bottle with syringe) into the mass spect on the Synapt, Xevo and an ABSciex instrument. The same cluster of ions (m/z 297, 311, 325 and 339) was detected in ES- mode with a separation by 14 Da.

The published lists of common contaminants does not show a match for these ions.

It has been suggested that these may be byproducts of solvent productions that cannot be filtered away at 0.1microns. It has also been indicated that the cluster matches alkylbenzene sulfonate and chloramphenicol which are not used in the preparation of our samples, buffers or solvents .

I have tried different brands and the intensity of the peaks vary from brand to brand while remaining in the chromatogram for data acquired on the Synapt. On other instruments, they are detected by the MS while remaining in the noise level and not evident in the chromatogram.

The main issue is that with some brands/lots of acetonitrile the peaks are well above the noise range thus suppressing the appearance of eluting peaks from the actual sample.

If anyone has seen this issue could you share insight on how it was resolved or what brand of solvent presented the lowest abundance for the cluster?

Thank you
A quick googling suggest that you are dealing with alkylbenzene sulfonates ... +339+m%2Fz ... 16204/full

They are used as laundry detergent. Have you tried using a clean syringe, clean machine, freshly open bottle? Or even analyze the same bottle in another unrelated (third party) lab? sometimes contamination is hard to pinpoint, and comes from unexpected sources such as clothing, personal hygiene products, cleaning products, etc... and not from the solvent as originally suspected!
Please be careful this can be easily mistaken. If you have tested some brands and other MS do not see the contamination your solvents are ok. The contamination is most properly in your mass spectrometer and ionization of the contaminant is with organic liquid or vapor more pronounced.

Just follow rule no 1 for MS user: Clean your MS if you observe a contamination.
was a resolution to this ever found? I'm asking as I am troubleshooting the same contamination issue on my TQD. thanks.

Sorry for being so late in replying...I've had that issue in the past on a Synapt G2 and still sometimes get some of these alkylsulfonate peaks in my chromatograms, which I suspect come from erroneous manipulations by my technicians :x . I struggled a lot to find where it came from and finally found the culprit being gloves! For instance if you put a nitrile glove in your ACN mobile phase bottle, you will get huge peaks at 297, 311, 325, 339. I could get rid of the issue by sonicating all the filters (frits) of the UPLC in pure ACN several times (change ACN between each washing step) and using new bottles. If there is still a bit on the frits they may contaminate the new bottles again. Then we got a maintenance and the engineer touched the pump heads full of ACN with his nitrile gloves and contaminated the UPLC again. So rather than cleaning the mass spec I would clean the UPLC.
Hi Gaetan - and the rest of you!

We are experiencing the exact same problem, to a huge extent - and will now follow the glove-path, and try to use other types of gloves (e.g. Waters own provided gloves) when doing maintenance on LC and MS.
Just to hear - is there any other experience that you can share on this issue (now that more than two years has passed ;-))

Best regards,
That even by trying to carefully avoid them, they periodically appear in chromatograms. No idea where they come from, my aim is to maintain them at a low level which does not impact analyses.
I have the same contamination as well. I determined that it was my nitrile gloves just like you said. My question is how am I suppose to put the frits back on solvent lines with out contaminating them again with my nitrile gloves. What did you do Gaeten?

Good work discovering that nitrile gloves and ACN give this contamination. I dont understand why this combo gives these contamination though.
Two options: i) wait until the frits are completely dry, and/or ii) use these special tissues between your fingers and the frits which do not generate any dust (that we usually use to clean MS sources).
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