LC/MS contamination problem

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

14 posts Page 1 of 1
We have been having an issue with some contamination in our Agilent 1100 LC system coupled to an API 3000 MS. For multiple compounds, the background noise was extremely high (1000 to 10000 cps) when injecting no sample (just MeOH) without a column. After replacing all parts (tubing, PVDF filter, needle, needle seat, six port valve, etc.), flushing the system with 20% nitric acid, cleaning the MS (plate, quadrupoles, and cone), and flushing for 24 hours with DI water, the signal remains. When we bypass the autosampler and degasser, the signal is not as high but still above 1000 cps. We cannot figure out where else the system could be contaminated. Help please?!

:?:

Thanks,
Nick

Can you try to infuse the methanol with just a syringe pump? This will narrow down where the contamination might be coming from (i.e. LC instrumentation or mass spectrometer or mobile phase)...

Re:

Kostas Petritis wrote:
Can you try to infuse the methanol with just a syringe pump? This will narrow down where the contamination might be coming from (i.e. LC instrumentation or mass spectrometer or mobile phase)...


We tried that, and it is not coming from the MS.

Maybe you can try to flush your instrument with isopropanol (or thf if your system allows it and you don't use PEEK).
mordwink wrote:
We have been having an issue with some contamination in our Agilent 1100 LC system coupled to an API 3000 MS. For multiple compounds, the background noise was extremely high (1000 to 10000 cps) when injecting no sample (just MeOH) without a column. After replacing all parts (tubing, PVDF filter, needle, needle seat, six port valve, etc.), flushing the system with 20% nitric acid, cleaning the MS (plate, quadrupoles, and cone), and flushing for 24 hours with DI water, the signal remains. When we bypass the autosampler and degasser, the signal is not as high but still above 1000 cps. We cannot figure out where else the system could be contaminated. Help please?!

:?:

Thanks,
Nick


If you really think it’s your LC:
I have never rinsed an LC with a nitric acid solution or simply DI water as you have described but will assume if you have done this in the past it wasn’t a problem then nor a solution now. I have used TEA in reagent grade water to rinse an LC but also know it takes awhile to rid it from the system before you are back up and running.
This background noise, just how did it make it’s appearance? You have a particular method where you expect a particular baseline and it suddenly changed or did this baseline rise over time? You say for multiple compounds, that means you have loaded another method (maybe using different channels) and that methods solvent blank does the same thing? Have you given the instrument sufficient time to settle down from your recent maintenance? I find them usually finicky for awhile after making such replacements (or cleaning the MS). I would put reagent grade water w/0.1% formic acid on channel A and 100% CH3CN on B. run for an hour or so with a column in place but detached from MS. After the hour plump to MS and run a simple isocratic method shooting a sample matching your mobile phase maybe 10 min long. Monitor your baseline on the first injection and then tell it to shoot it 10 times and come back and see what your baseline looks like on the last one. If your baseline is unchanged over this time period then I would start looking at your MS. If it’s significantly reduced, shoot that blank 10 more times.


If you think it may be your MS:
If you are running turbo spray and have multiple methods that give you this elevated baseline do you have another ion source? Another Turbo spray would be ideal to try but if not can you put on a nebulizer and try running a method using that? If you can get any of them to work it’s not your LC. Have you been infusing something recently? I will typically get a significant increase in baseline after infusing something and switching back to LC+MS mode. Again, usually successive injections of a standard and it tapers off.

Good luck. Hope something I’ve said can help you.J

Re:

mordwink wrote:
Kostas Petritis wrote:
Can you try to infuse the methanol with just a syringe pump? This will narrow down where the contamination might be coming from (i.e. LC instrumentation or mass spectrometer or mobile phase)...


We tried that, and it is not coming from the MS.


If you spent a significant amount of time infusing anything I would be sure to run in LC+MS mode something simple like I described above before coming to any conclusions. I think time may be your best tool.

Maybe others employ their MS's for more MS mode only work but I usually try and get in and out as quick as I can. I find what I'm looking for, auto optimize to get my method and get out, I find it always takes awhile for the instrument to settle down baseline wise following infusion.
I have exactly the same problem you had 6 years ago (using the HPLC 1100 and API3000 by AB Sciex).

I analyse polyfluorinated compounds for several months now, never had a problem with contaminated blanks because I changed all the Teflon parts of the LC. During one measurement last weekend I recognized an extremely high base/noiseline for several compounds. My first thought was that the column was overloaded because of one sample. But the baseline level didn't decrease after days of cleaning, it's still around 3000-5000 cps (there is no difference in using column or not). So I assumed a problem with the spray, I changed to a new electrode and PEEK Tubing Transfer Line but the noise is still there. I also cleaned the Q0, Orifice, Curtain Plate etc. I have no idea except for changing the Nozzle Nut (I have to wait for the order), but I can't explain why the Nozzle Nut should be able to change this problem. I am pretty sure that this is not an LC problem, the high baseline can also be observed when I infuse MeOH with a syringe pump and when the MS is connected before the Six Port Valve right after the Inline Guard. It is strange that this problem was observed during one sample run and never disappears....it's the second time I have the problem now, I changed the whole Turboionspray two months ago and the problem disappeared but it is there again after analysing just 50 samples.

Did you solve the problem in those days?

Please have a look on the pictures (MRM of one compound, injection of 10uL MeOH)

before measurement/how it should loook like
http://de.share-your-photo.com/91f6aed0b8

after measurement
http://de.share-your-photo.com/04d661e67c

today (5 days later) after cleaning etc.
http://de.share-your-photo.com/d75a67fdd3
To identify the source of contamination, it is often very helpful to identify the contamination, e.g. plasticizer, tuning compound, column bleed, "sticky" analyte etc.

What does the mass spectrum show ??
another part that is frequently ignored is the drain from the spray chamber, where the gas and any remaining liquid drops get blown out. It frequently contains plastic parts that may well harbour polyfluorinated compound contamination, and because of the (possibly a bit turbulent and unpredictable) whirling of gas in the spray chamber, it can get blown back in. I've seen this in a Thermo LCQ DecaXP a long time ago, where detaching the drain halved the size of the contaminant peak (in that case, an ill-advised perfluorinated acid ion pair reagent).
Thank you. I have to tell you that my lab measures polyfluorinated compounds with the same instrument for 10 years now. Never had problems with a high noise level. It's also strange, I measure 3000 cps one day and the next day something around 600 cps, next day 2000 and 3000 again (same solvent, same bottle, same tubing, same flow). There is no system behind the noise level. When I measure on these specific masses e.g. for 120 min, I can observe a slowly increasing noise level, but sometimes it's also stagnating. The noise level is very unsteady, but too high.
WhiteBloodCells wrote:
Thank you. I have to tell you that my lab measures polyfluorinated compounds with the same instrument for 10 years now. Never had problems with a high noise level. It's also strange, I measure 3000 cps one day and the next day something around 600 cps, next day 2000 and 3000 again (same solvent, same bottle, same tubing, same flow). There is no system behind the noise level. When I measure on these specific masses e.g. for 120 min, I can observe a slowly increasing noise level, but sometimes it's also stagnating. The noise level is very unsteady, but too high.


What mass is the interfering ion(s)?

Could something have contaminated your gas supply?
The past is there to guide us into the future, not to dwell in.
I have been fighting a contamination/high baseline on API 3000 myself.
I have, like you, cleaned the front end several times. I even pulled the quads out and cleaned behind IQ1 and rinsed the Q1 rods.
I infused some methanol /Formic acid or such after my last attempt. I have not resolved the problem.
1) I think you should tell which masses you are exactly seeing.
2) Have you tried monitoring for very long time periods (I am talking about days or weeks) the background? Maybe it appears as there is no logic behinf the noise, but monitoring for a long time will make patterns obvious. I had a problem with shifting mass on a TOF machine, and we monitored a single reference mass every 30 seconds for two weeks. It sounds like a lot of time, but if the problem persists, you are going tolose even more time....
I have also this Problem with Sciex API 5000,
did you Solve your problem? if yes, could you please tell me how?
Thanks
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