We run peptides, which elute between minutes 40 and 165. In several runs, the signal fell abruptly and stayed low for 2-30 minutes. Sometimes there were multiple such gaps in a run. In the attached example, the main gap is between minutes 110-142, except where there is a strong ion, such as defensin or a very abundant peptide, which "interrupts" the gap. The instrument is Q-Exactive Plus. It also happened to someone else, from another lab, with different samples, on another Q-Exactive Plus in the same MS facility. In some cases it happened to three runs in a row while in other cases to only one run in the middle of a set.
Have you seen this before? Any idea what is the cause and how to overcome it?
Thanks,
Ilan
This looks like ionisation suppression to me. But, I will admit that I do not have much experience with that, so I cannot give you any advise on how to solve it.
Check out this paper in the meantime. Maybe it is of some use:
http://www.sciencedirect.com/science/article/pii/S0039914013001975
You have an instable electrospray. If you observe your analysis closely, you will either see droplet formation on your tip or sputtering.
Replace the tip with a new one. You may also need to optimize the applied voltage and distance to the orifice.
As Alexander stated above, you may have additional ion suppression effects, if your sample contains residues of salts and detergents that affect the surface tension of your droplets.
Looks like you've got signal supression (e.g. salts, other ionic compounds), tip clogging (too many particles), or else you do not have the right voltage at the ES tip. Looks like you need to work on the sample prep and make it more mass spec friendly, or else improve the chromatography - that always helps. You've got so much stuff coming out in the mid-section I think you probably have loads of sample, so even a simple dilution of the sample might help you?
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