Contamination trouble in the LC/MS/MS 6460 AGILENT

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

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We have been experienced some contamination trouble with our LC/MS/MS 6460 Agilent.

The contamination amu is 453 and around 100.000 cps (TIC), it is intermitent.

We have checked and changed all the solvents, washed many times all the lines and after getting some improvement, it appeared again.

Could you let me know if something similar happened to one of you and what else could we do?

Kind regards!!


Here's a list for common background ions in LCMS.

Did you isolate this to the MS by infusing some solvent directly into it? Do you have the background even when not infusing? Does it impact your methods?

Keep in mind there will always be background in full scan LCMS, especially ESI+.
Dear Rndirk:

Thank you very much for the list and your answer! It will be very helpful.

We did isolate the MS and injected the solvents directly to it, and didn´t find any contamination, we were focused at first in the bomb as the source of the contamination and now we are making some test to check if the injection system could be the cause of the trouble.

The contamination does affects to all our methods, but is not constant. Even when the equipment is in the default method (without any solvent runing, and the MS on, seal wash on) we can see the base line going to the clouds and then goes down again. But, we have checked the seal wash already and the trouble persists.


Hi Alita,

Maybe I can help.

There are a few places the contaminant can be, and it is almost always in the LC stack. I would specifically check your autosampler, column compartment (especially if you have a valve in there) and the valve on the MS.

Before we get any deeper, I have a few questions.

1. Can you specify what kind of LC you are using (I am assuming it's Agilent)? What revision and modules are you running (i.e. 1100 / 1200 / 1260, g1311a = quaternary pump)? I would need the entire stack.

2. If you connect your pump outlet directly to the MS, do you still see contamination?

3. If you connect your pump and column compartment together (bypass autosmapler completely), do you still see contamination?

4. If you connect your pump and autosampler together, (by pass column compartment) do you still see contamination?

5. If you run a blank sample (i.e. water or ACN), do you see the contaminant? If you run a blank (no injection) where the needle stays in the needle seat, do you see the contaminant?

*For 2-4, it is important to connect directly to the nebulizer and not the valve on the MS to isolate those that valve as well. Additionally, do not connect a column (use a zero volume union). This will be a direct infusion into the MS. If your system is highly contaminated, I do not recommend doing this. If it is a small contaminant, this is the best way to troubleshoot where the problem is.

5. What analytes do you typically analyze on this instrument? What concentration range do you normally analyze (ug/mL, ng/mL, pg/mL)?Do you use high concentration buffers (above 50 mM)? If so, specifically what kind? Do you wash the system after using salt buffers?

6. When was the last PM done on the system?

7. Does the system pass tune? Do you see the contaminant in the TIC while tuning?

8. Are you seeing the contaminant in MRM runs, full scan or both?

9. Are you sure that your column isn't contaminated? Are you tried with other columns?

Knowing the answer to these questions will help troubleshoot where the issue is.


I've had several issues similar to what you described after purchasing a refurbished MS and attaching it to a used LC. As you can guess, the problem is almost always the LC, and 8/10 times the problem is in the autosampler.

If you are using a g1329 autosampler, the needle seat and needle do not have a built in wash unlike the well plate autosampler (g1367) and 1290 autosampler. If you are working with sticky samples, I've seen them get stuck in the needle seat and elute when the needle dislodges the contaminant through movement. I would try changing the needle seat and washing the needle thoroughly (disconnect it and connect directly to pump outlet and flush at 2-3 mLs / min). You can clean the needle seat by taking it out, connecting it to the pump outlet to back flush it, and sonicating it to remove any residual contaminant on the seat. It is best to replace it if you have isolated that the issue is in the autosampler.

The other place in the autosampler hidden contaminants can be found are in the metering head. If you are injecting high volumes of samples (i.e. 40 uL, 50 uL, 100 uL), it is possible that sample could backflush into the metering head. There is also a plastic lining / o-ring that some Chinese models have in the metering head. If you have been flushing with DCM or anything that can dissolve teflon tape, you will see several peaks (usually PTFE - repeats of 44 m/z). Either way, if you have determined that the problem is in the autosampler, it is worth taking the metering head apart, clean it, and replace with a new seal.

If you find that your contaminant is in the column compartment, I would flush with more caustic solvents (DCM / IPA / THF / DMSO). If you have a valve in your column compartment, I would take it apart and check / change the seal if you have determined that the contaminant is in your column compartment.

If the contaminant is upstream of the ALS / Column compartment, the problem is almost certainly related to your mobile phase. I would change all of the tubes, clean all of the solvent inlet filters (better yet replace them), and clean the pump thoroughly. In this situation, it is likely the degasser is also contaminanted, so it is worth cleaning this out in a similar manner.

From what it sounds like, it is probably an artifact which precipitated somewhere in either one of the seals, capillaries, or elsewhere that cannot be washed out. In situations like this, it is best to troubleshoot every single connection on your system, from beginning to end, and replace the parts that are in question.

Let me know if you have any questions.
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