I am using an Agilent 1100 HPLC system connected to API2000 quadrupole MS system, and has a contamination problem which I don't know how to solve.

I have eliminated the LC autosampler or column as the source contaminatants. Then I connected the LC pump directly to the API 2000, and run gradient without actual injection. The run takes 18 minutes, and the baseline increases like a hump (up to 3000 counts) when the gradient increases to 95% organic solvent, and drops down (to around 50 counts) when gradient returns to 5% organic solvenl (I'm running MRM modes).

The MS engineer has cleaned the ion-source (up to Q0), and changed the ion source needle. He said he has changed all that he can for the MS. The LC engineer (and I) thinks that the possibility of the contamination of the solvents or the pump are very low.

Desperate needing some suggestions to solve the problem!!!! Thanks!!!

what's the mass of the contaminating peak ?

Mass specs are incredibly sensitive. First, I would change all of the tubing and fittings between the LC and the MS. It sounds like it is a solvent problem, though. Strong organics can leach off contaminants from glassware that you aren't aware were there. Try rinsing the glassware several times with your organic solvent and see if that helps. I have also had problems with solvent from bottle to bottle and lot to lot. Even HPLC grade or omnisolve aren't 100% pure.

Anon1, I detect 2 drugs: one is at 275mz and the other is at 289mz.

Anon2, thanks and I'll look into this. However, I'm looking at specific mass (MRM mode -- parent and daughter ions). So do you mean that my organic solvent got contaminated with the drugs, and so I can see them at there specific MRM? Please clarify.

Thanks for all your help!!!

Are you running the no-injection gradient with column installed? If so, this sounds to me exactly like contaminated mobile phases. It does not sound like an MS problem.

It could be your drugs are contaminating the mobile phases, due to a lab error. Or you could be unlucky enough to have an unrelated contaminant with the same parent and daughter ion as your drug. The chance of this goes up if you are using a nonspecific loss, like 18 or 44.

I see this problem quite often with triple quads in MRM. Recently, I had a problem with an interferent that matched my drug (although not the IS) in two different methanol sources. I switched to ACN for the organic and the problem went away. I have never bothered to track down the cause of interferents, like I said, a different solvent bottle can give different results.

AW,

I suggest that you infuse your mobile phase (i.e. at 5% B and 80% B) and aquire full spectra (i.e. m/z 100-1000 and accumulate 10 to 20 spectra -MCA- mode). This will give you an idea if you have any kind of contamination in your mobile phase, which one and at which m/z.
If you see nothing it means that the contaminants are somewhere in your HPLC (i.e. check valves etc.). If you have another HPLC you can check if a gradient elution with another HPLC gives you similar results...

I take for granded also that when you say that you connected directly the HPLC with the MS that you didn't use any column.

MG, yes, I'm running no-injection gradient and with NO column installed. My MRM pairs are 289.3/140.2 and 275.18/125.94.

Anon2, I will try to switch my ACN source or swith to methanol.

Kostas, I'll do that with my mobile phase, and check if the contaminants are with my mobile phase. Also, I connected the pump directly to the MS without any column.

Thanks for all your help. I really really appreciate it.

What we did today:

1. After intensive overnight MS cleaning, I injected 95% ACN with buffer with syringe pump, and get a constant baseline signal of 400 counts.

2. Then a connection was made from the LC pump to the MS, using same mobile phase composition as above (with same flow rate and no column), we get a constant signal of 2000 counts.

3. Then using previous gradient conditioins, I added in a new guard column in between the LC pump and MS, I get a peak with retention time of 400 counts.

4. I run full scan as Kostas suggested, and couldn't find anything specific as the scan is full of lines. I will do a product ion scan tomorrow.

5. The mobile phase has been changed from ACN to MeOH, but I have the same high counts (2000 psi) when running 95% MeOH with ammonium acetate and I have the same peak as number 3 (with similar counts).

6. All of the above did not happen previously when we are running the same drugs with the same gradient solution. It just came out all of a sudden.

All the experts, do you think is the MS or the LC pump or the mobile phase problem?

Thanks!!

Hmm, I take back what I said earlier. I didn't read your original post carefully enough and assumed you had a column in line. As the normal baseline can vary quite a bit depending on the MRM transition, is the 400 counts you observed from the syringe pump what you would consider "normal" background for this transition? If so, it sounds like there is a contaminant in your pump, in the inlet line for your acetonitrile mobile phase, or in the outlet line leading to the column, that is being extracted out by the acetonitrile.

So then it becomes a matter of tracking it down. Your exact approach might depend on which 1100 pump model you have. I am aware of two: the quaternary pump with low pressure mixing and single pump head, and the binary pump with high pressure mixing and two pump heads. As a diagnostic, you might try running your ACN from a different channel into your pump, and seeing if the background is still there. Other alternatives might include just changing all your inlet and outlet lines without taking the time to find the source, or flushing the heck out of all the lines with a flush solvent. A general flush solvent for cleaning pumps and lines, recommended to me by some Agilent folks, is 25/25/50 cyclohexane / ACN / isopropanol. You should flush with isopropanol before and after using this mixture.

Thanks MG, I'll give it a try today.

I changed to the other 2 channels, and the background noise disappear for now. But now I have a problem with changing RT times in 2 consecutive injections: from 7.26 to 11.20 minutes, and from 10.09 to 11.8 minutes. Do you think there is a problem with my pump?

Thanks for all your help. MG, I did your recommended wash. Thanks so much!!

Glad you got rid of your background for now. It sounds like it was a contaminant in your inlet lines. As for your new problem, assuming this wasn't a problem using the original lines, maybe you introduced a gas bubble into your pump when changing over? You should be able to plot the pump pressure in Chemstation. Do you see a rippling, fluctuating pattern in the pressure as you run your gradient? If so, it's probably a bubble.