Ghost peaks in LC/MS

[snowlotus]

Hello,
I am running into this problem with my LC-MS (QQQ) system, where I see ghost peaks in my MS2 scan. The ghost peaks have high intensity so I could not get a chromatogram of my standards. I tried a few things but the peaks are still persistent in terms of m/z and intensity, and the peaks looked the same when using gradients or not. I removed the column and guard column, disconnected the UV detector, disconnected the column thermostat, changed solvent bottle and flushed the system with isopropanol, but nothing worked. So far, I cannot even tell if the peaks are caused by contamination in the mobile phase (something stuck in the LC) or contamination in the MS unit. The only difference I observed for the ghost peaks is when switching from ESI+ to ESI- the m/z and intensity changed. Could someone please help me? Thanks!

[JMB]

IF you post or list the spectra in +/- ion modes we may be able to identify the contaminants; knowing what they are will suggest the best way to remove them.

Regards,
JMB

[Multidimensional]

So many possible causes. As noted, if you could provide additional details about the observed contamination peaks, that might help. Try to remove the column (use a union and back-pressure restrictor) as fouled columns often result in contamination. Also try to remove modules from the flow path (i.e. Run just the pump to the MS, by-pass everything else). The autosampler/injectors are often sources of contamination from lack of maintenance, worn rotor seals. Solvent bottle frits should be replaced regularly, esp if you use aqueous solution. They are inexpensive, esp relative to the time and expense of troubleshooting.

Another common source of contamination in LC-MS systems that we see is sourced to the inline vacuum degassers. Vacuum degassers are frequently broken, run without servicing and ignored over time. When not formally serviced, they leach contamination into the flow path. Please refer to this article for more info:

An Often Ignored HPLC & LC/MS Contamination Source. Did you check your Vacuum Degasser?

"; https://hplctips.blogspot.com/2015/08/a ... -lcms.html

[snowlotus]

Thank you. I think the ghost peaks come from PEG. I have tried using 25% each of isopropanol, acetonitrile, water, and methanol with 0.2% formic acid to flush the system. The problem remains. I suspect the water source I used is contaminated, so I will try a different water source now. Other than that, I am not sure where the contamination is.

IF you post or list the spectra in +/- ion modes we may be able to identify the contaminants; knowing what they are will suggest the best way to remove them.

Regards,
JMB

[snowlotus]

I flushed the system with a mixture of solvents but the problem remains. I have not run any real samples in the system but standards. Now I suspect maybe the MS unit is contaminated, is there anything else I can do to diagnose?