Chromatography Forum

Was hoping someone could lend me a hand with the current problem:

I'm working with the Agilent 1100 HPLC system in conjunction with the Micromass Quattro LC system. Following tuning of our test compounds, during the running of samples we often see baseline elevation/interference at the column switching timepoints (ON to MS/MS -> baseline jumps). Quantitation of these compounds still work but the signal to noise performance is extremely poor because the baseline jump (caused by excess tuning solution that I suspect is still in the MS system somewhere) interferes with the peak.

After the column switch is OFF the baseline returns to normal.

I've tried thoroughly cleaning what I can readily get to (cone, needle) but I can still see the existence of both parent and daughter ions on the tune page, even when the HPLC unit is OFF.

I've reduced the concentration of the tuning solutions fairly significantly to avoid this problem but it still significantly affects my samples near the LLOQ of the assay.

Thanks in advance,

I often have an elevated baseline after tuning. Some compounds seem to result in higher baseline after tuning than others, but certainly the concentration of the tuning solution can effect it. I typically run high organic after tuning, and it should reduce your baseline. You can either run it through your column or bypass the column and let a steady flow go to the source of the mass spectrometer. I've even had to let my instrument sit over night with a steady flow of high organic in order to decrease the baseline. Good luck.

I've tried running 0.1%FA in ACN (our mobile phase) and also ACN:IPA:MeOH mixtures through to reduce the baseline and it seems to work well but the main thing I guess is that the process is time consuming (often overnight).

I was hoping to see if there was a faster way to clear the baseline interference.

Maybe it's time to change the rotor seal of the switching valve(s)?
What is the concentration of analyte you normally use during tuning?

It varies from compound to compound but ideally we would use something around 10 ug/mL (below 50) to tune the instruments. In the case I illustrated above I was using a 40 ug/mL tuning solution.

I ruled out the rotor seal as part of the potential contamination as after I shut the HPLC portion of the system down, I can still see my test compound in the MS tune page. The daughter ion signals, albeit weak, are still there and produces a pronounced baseline elevation during the sample run. The calibration standard curve runs from 10ng to 8000ng and the elevated baseline affects the peak the most in the 10 to 50 ng/mL range.

In addition, just in case the interference was coming from the compound that has somehow coated the exterior of the system we detached the probe and cone and cleaned them in Methanol. That helped a slight bit but not enough.

we ultrasonicate ours with a mixture of 50/50 methanol/formic acid most of the times,

somtimes DMF, then 50/50 methanol/formic acid, then water, then methanol, blow dry

Not unusual to see rise in chemical noise for the component after tuning, use as little as possible to tune, magnify response a lot on scope.

The baseline issue is different? If I understand correctly you are seeing reference peaks even though you no longer have reference compound in the system?

If this is the case the most suspect areas are the probe capillary and the silica? lines you use to connect to the MS.

It would be very unlikely that descrete sample peaks are seen from internal contamination of the MS.

Try a new set of silica lines for your low concentration samples. And tune using as low concetration of reference sample as possible, though 40 ug seems reasonable, using the old lines.

I suspect that the interference comes from contamination of the probe capillary as well, since during the tuning phase we already use a separate set of silica lines when connecting to the MS.

We have tried putting various organic solvents or solvent mixes through the capillary to clean it off but that does not seem to help. Its been about 2 weeks since the original problem and the interference is now completely gone. Tuning with a solution of roughly 40ug/mL I do not see how even contamination of the probe capillary could linger for such a long time, especially when the instrument is running 24/7.