Chromatography Forum

I have a Shimazu Nexera LC coupled to Sciex Qtrap 5500 MS for environmental sample analysis, most low molecular weight compounds less than 700 m/z. We noticed that after each preventative maintenance, the background especially for lower masses would be much higher. It usually takes months to the background to subside. Has anyone seen anything like this and have some suggestions? It is frustrating that the instrument is cleaned and maintained, but we get poor sensitivity. Thanks!

What ions are you seeing in the higher background noise?

Yes, it is not uncommon for the background signal to increase after preventative maintenance, especially for lower masses. This can be due to a variety of factors such as residual cleaning agents, contamination from the maintenance procedure, or changes in the instrument settings. Here are some suggestions to help reduce the background signal:

Verify the instrument settings: Ensure that the instrument settings, such as the ion source temperature, ionization mode, and gas flows, are properly set for the specific application. Also, check the collision energy, declustering potential, and other MS parameters to ensure they are optimized for the desired analytes.

Check for contamination: Conduct a thorough check of the instrument and sample preparation process to identify potential sources of contamination. For example, check the sample vials, syringes, and other equipment for cleanliness, and inspect the mobile phase and solvents for impurities.

Run a blank: Before analyzing samples, run a blank to detect any potential contamination in the system. Use the same solvents and conditions as the actual samples to simulate the conditions of the analysis.

Increase the cleaning frequency: If the background signal persists, consider increasing the frequency of preventative maintenance, such as cleaning the ion source, replacing the ion source components, or changing the mobile phase and solvent bottles.

Contact the manufacturer or a service provider: If the above steps do not resolve the issue, contact the instrument manufacturer or a service provider for further assistance. They may be able to identify and resolve the problem.

Overall, it is important to conduct regular maintenance and quality control checks to ensure the instrument is operating at its optimal performance.

Hi,

As already mentioned this is a common issue. Usually after a PM most of the contamination comes from the HPLC side, even though some parts of the MS optics can also generate high background noise. Here is what we do after each PM or new installation:

1. Prepare a mixture of H2O:MeOH:ACN:IPA:formic acid (25:25:25:25:1) that you put instead of your usual mobile phases. Prepare a few HPLC vials with the same mixture, and inject at least 200 times using a short isocratic method. Keep the column installed but make sure the tubing after the column is not connected to the MS.

2. Replace with your normal mobile phases and check sensitivity. If the issue persists, check if the background hasn't changed at all or if it has decreased but not to the level before the PM yet. In the latter case repeat the procedure. In the former case go to point 3.

3. If things have not improved, you can try to verify if the issue comes from the MS itself. For this, if you have another HPLC in the lab which didn't have a PM, you can connect a long tubing from it to the MS and see if the background noise is lower. If you see no difference or if you do not have access to another HPLC, the only thing you can do is to flush the MS with some mobile phase until things slowly get back to normal. As the instrument was cleaned and calibrated by the engineer, venting to clean it again or calibrating will not help unless the engineer did a bad job.

Hope this helps

This may be a stupid question but when you look for contamination do you run full scan positive and full scan negative. I usually just look at my different mrm for a blank and my system suitability mix but perhaps i should also run full scan from time to time to see if new contaminants appear even when mrms are fine?


For pm we run my method with standards before and efter the pm before the engineer leave.

If the MRMs are sensitive and not noisy, I would personally skip the full scan.

If there is background in the MRM like you are describing, then next step is to run both positive and negative full scan and evaluate the background.

Always pump down for at least 24 hours before critical evaluation of signal.

The other step is to examine if the background is from the MS or the LC. This would tell you where to concentrate the background reduction.

If it is just a couple of peaks, there are tables of frequent contaminants. If it is a broad mass (or repeating mass, such as +14 amu) background, then residual detergent is be a suspect.

Thanks for sharing this info . I do save fullscans for reference from time to time just to compare to if problems in my mrm would turn upp, but not very often. Just changing to a new batch of ms grade ACN can give very differen fullscan spectra but usually mrm methods work fine to filter out analyte from background.