Chromatography Forum

Hi. I was doing some LC/MS analysis using Waters Acquity UPLC system coupled with LCT premier XE ESI-TOF MS. The column used is BEH C18 with VanGuard precolumn and the mobile phase is water/ACN. Recently, I noticed when I have the gradient ramp up to very high organic, 95% ACN, some weird peaks start to show up in both pos and neg ion mode, especially in the neg ion mode, even without injection. These weird peaks, or looks more like high background noise, are not reproducible and the MS is all over the plce. It seems to me that something is causing the ionization unstable at high organic. I was wondering whether anybody have seen something similar and can give some suggestion on how to get rid of those peaks. I've tried clean the entire LC system with mixture of water/ACN/MeOH/IPA/1% formic acid, and I've cleaned the source and capillary of the MS.

At the same time, I've also noticed the reference channel, which is continuously pumping LEu-enk, shows increased intensity when the gradient of the analyte channel went up. I can not explain this and didn't know whether this is related to my previous question.

Thanks a lot and looking forward to some ideas!!

Hi,

we have often had some contaminations using UPLC-LCT premier TOFMS. The thing is, the TOF is very sensitive in "scan" mode and will detect any ion that would be hidden using a triple quad in MS/MS mode.

Most likely you have contaminants somewhere in the UPLC system that are trapped on the C18 column and released at high organic %. If you bypass the column, do you still see them? What are the m/z ions you see in pos and neg mode?

I am sceptical it could come from an MS instability at 95% ACN. ACN is a good solvent in ESI. Concerning your lockmass issue, I am not surprised that it increases: the analyte flow slightly influences the lockspray, and leu-enk presents better ionization at high % org than in water.

ionisation efficiency (of anything) is higher in high organic content than high water. It's quite normal to get increased background at high organic, and it's quite normal for it to be fairly meaningless. Personally I wouldn't worry about it unless it's causing you a problem.

Hi. Thanks for the reply. i agree with Gaetan on the reference channel issue. And I think since we usually don't run gradient at such high organic for so long, we don't see this contamination. I don't see the same contamination if I bypass the column, even though it's not flat baseline either. i suscept it's sth traped in the column too, as I just ran a massprep peptide std and it looks aweful. I am washing the system in pure IPA now, any other suggestions?
I'm afraid I have to figure out what the problem is since I am analyzing Irganox 1010, a potential extractable from a plastic stopper, which can only be eluted from C18 column at very high organic.
Thanks a lot.

Irganox 1010 is a pretty big molecule, you would be very unlucky if an isomeric compound eluted at the same retention time! Just use the extracted ion chromatogram with a window of 0.05 or 0.03 Da, you should get a flat baseline and your peak.