Chromatography Forum

Hi, all,

I am a freshman in LC/MS. We change a new tank of liquid nitrogen this Monday, and regular maintanence was carried out to clean the needle, cone and metal capillary by sonicating them in methanol for ~30min.

In the following test, the noise is obviously increased and the resolution dropped.

The second sonication of needle, cone and capillary did not eliminate this problem.

I replaced the old capillary with brand new one could not recovery low noise.

Furthermore, this problem does not come from HPLC, it is still there if disconnected the HPLC to MS.

please see the TIC, enlarged part of TIC and MS.


need your help.

thanks in advance.







here, the sharp peak are noise, not real singal form sample. because it is a blank run.

Have you used PPG ( Polypropylene Glycol) as a tuning compound on the instrument since the cleaning, or with any of the lines between the inlet and source?

http://www.lc-ms.nl/contaminants.htm

Check this document. Your contamination seems to correspond to the polysiloxanes from silicone rubber contamination. Does that give you any ideas? Did any of your parts come in contact with any silicone rubber? Did you change any hoses or anything like that?

Have you used PPG ( Polypropylene Glycol) as a tuning compound on the instrument since the cleaning, or with any of the lines between the inlet and source?

no.

I just change a new tank of liquid nitrogen, and sonicate the needle and capillary in methanol for ~30min and reinstall them.

keep other MS parameters just like cleaning before.

After replacing a brand new capillary, the serious noise decrease, not gone.

http://www.lc-ms.nl/contaminants.htm

Check this document. Your contamination seems to correspond to the polysiloxanes from silicone rubber contamination. Does that give you any ideas? Did any of your parts come in contact with any silicone rubber? Did you change any hoses or anything like that?

thanks.

I did not do anything except cleaning the needle, cone and capillary by sonicating them in methanol for ~30min after changing a new nitrogen resource.

I also had a test run with some peptides, the intensity obviously decreased and some weak peaks would be overlapped by the noise or could not be detected.

Have you tried a different nitrogen tank? What kind of vessel did you sonicate your parts in? How had that vessel been cleaned prior to your using it? Have you re-cleaned the cone and capillary?

Have you tried a different nitrogen tank? What kind of vessel did you sonicate your parts in? How had that vessel been cleaned prior to your using it? Have you re-cleaned the cone and capillary?

not try another different nitrogen, the vessel I used for sonication is a glass beaker, it is clean and always for this kind of sonication, and the second sonication was carried out, but the noise did not disapper. Furthermore, I change a brand new capillary will decrease the noise.

anyway, thanks.

Have you tried a different nitrogen tank? What kind of vessel did you sonicate your parts in? How had that vessel been cleaned prior to your using it? Have you re-cleaned the cone and capillary?

not try another different nitrogen, the vessel I used for sonication is a glass beaker, it is clean and always for this kind of sonication, and the second sonication was carried out, but the noise did not disapper. Furthermore, I change a brand new capillary will decrease the noise.

anyway, thanks.

Today I replace a new needle and a new capillary and run a blank test while disconnecting LC to MS.

please see screen shot below.



it is very strange, right?

What's weird? The pattern of masses is gone, now it looks like this is random background noise. A little bit much in the high-mass range (I normally don't see anything past about 550 or so), but if this is normal, run a standard and see if all is well.

What's weird? The pattern of masses is gone, now it looks like this is random background noise. A little bit much in the high-mass range (I normally don't see anything past about 550 or so), but if this is normal, run a standard and see if all is well.

Exactly it is weird.

Infusing calibration mixture using tune function, it is normal, and all MS parameters are OK.

So, the only new component that lead to the cleaned up background was a new needle? You stated previously that a new capillary (what instrument are you using, by the way?) decreased but did not eliminate the noise.

I would try to place the old capillary and needle back in the instrument, just to see if this is something directly associated with those parts, or if this was just some in-source contamination that needed to bake out to reduce to undetectable levels.

Another thought - I saw an article about siloxane contamination in nanoESI, and they were able to reduce the level of interference by increasing nitrogen flow around the needle and repositioning the needle in the source. Maybe in replacing the needle you inadvertently repositioned it and reduced the interfering signals to undetectable levels? Maybe you can try different needle positions to see if the contamination comes back?

http://www.ncbi.nlm.nih.gov/pubmed/12794873

So, the only new component that lead to the cleaned up background was a new needle? You stated previously that a new capillary (what instrument are you using, by the way?) decreased but did not eliminate the noise.

I would try to place the old capillary and needle back in the instrument, just to see if this is something directly associated with those parts, or if this was just some in-source contamination that needed to bake out to reduce to undetectable levels.

Another thought - I saw an article about siloxane contamination in nanoESI, and they were able to reduce the level of interference by increasing nitrogen flow around the needle and repositioning the needle in the source. Maybe in replacing the needle you inadvertently repositioned it and reduced the interfering signals to undetectable levels? Maybe you can try different needle positions to see if the contamination comes back?

http://www.ncbi.nlm.nih.gov/pubmed/12794873

Thermo Finnigan LTQ

step 1: disconnect LC from MS, the high background is still there, so it is not associated with LC.

step 2: sonicate the needle and cone again, problem remaining;

step 3: the thermo engeneer adviced to replace a new capillary, I did it, the noise decreased a little and still high background;

step 4: the thermo engeneer adviced to replace a new needle, I did it, the action does not work;

step 5: infusing calibration mixture using tune function, all MS parameters are normal;

step 6: increase nitrogen flow rate, it does not eliminate the problem;


I am not sure if I inadvertently repositioned the ESI probe while changing the needle or installing the probe back. Because the noise is dramatically increasing, the intensity and resolution decreased for real samples. The needle is fixed on the ESI probe, the needle tip would vary the position in a small 3D space.

Anyway, thanks a lot.

Probably time for a service call, or time to pull the Q0 and Q1 sections for some cleaning. I still think you should try a different nitrogen tank, just to absolutely rule out the possibility of a contaminated tank.

See section 4.5 of the manual copied below, in case you don't have a copy at the lab.

http://www.thermo.com/eThermo/CMA/PDFs/ ... _26638.pdf

Probably time for a service call, or time to pull the Q0 and Q1 sections for some cleaning. I still think you should try a different nitrogen tank, just to absolutely rule out the possibility of a contaminated tank.

See section 4.5 of the manual copied below, in case you don't have a copy at the lab.

http://www.thermo.com/eThermo/CMA/PDFs/ ... _26638.pdf

Actually I contacted the thermo engineer for some advice. According their advice, I replaced the needle, capillary and tubing for ESI probe. Unfortunately, no improvement.

The pressure and flow rate of nitrogen are normal. I am not sure if the problem results from nitrogen.

Service request has been sent out, waiting for the schedule to have on-site checking.

I can not clean the Q0 and Q1 by myself.

Thanks a lot.

What system are you using? It looks like a trap to me, in which case you don't have quadrupoles to clean.

There also seem to be two sorts of noise that are fundamentally different. Earlier you showed a spectrum that clearly contained a contaminant. But you are also showing chromatograms with lots of very narrow "peaks" or "spikes". If you look in Xcalibur, in the display options you can show the chromatogram as single spikes instead of join-the-dots; if you do this, are these spikes just one scan wide? I.e. a lot less than a real chromatographic peak, and probably random events?

There are a number of things that can be going wrong. Were it a quadrupole instrument, I'd definitely be suspicious of bad drying, because if a tiny droplet of undried material gets drawn through an instrument and hits the detector at a random time, the instrument will interpret the time it got there as a mass, and display a sudden, random peak. The sorts of chromatograms you're showing can easily be generated in a single quad by poor adjustment of spray needle (so the spray is bad, and drying therefore less effective), or by inadequate drying. I'm not sure if traps do the same thing.

When you infuse calibration solution in a continuous way, do you have strange mass spikes then, or is it just a clean spectrum of calibrant?