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Recognising ion suppression

Ion suppression is where a chemical somewhere in your sample or your chromatography run prevents a metabolite of interest from being ionised, and therefore reduces or eliminates its signal. Of course the bully-boy chemical causing the problem might be anything, and might itself not show up in your mass spectra (mass outside the correct range, wrong charge, whatever). So how do you recognise the what you can't see, causing the disappearance of something that might not have been there anyway?

One method is to put a very low concentration of the metabolite of interest in the solvents you are using to run the chromatography. It must be a very low concentration, because most such metabolites are not volatile, and it is bad to put a lot of non-volatile material into a machine that relies on evaporating everything. With the metabolite in the solvent, inject a sample and carry out a normal run.

If you have a syringe pump then you can fit a T-piece between the column and the detector and gently infuse metabolite from the syringe pump into a run, post column.

You should now have a very high base-line, caused by a continuous start-to-finish presence of the metabolite of interest. If a chemical is eluting that causes ion suppression, it will suppress the metabolite in the baseline, and you will see a negative peak.

The example below was not an intentional suppression experiment. It was a (horrible) run where the user had accidentally included something that ionised in one of their buffers, while running a gradient. Therefore they had a gradually increasing base-line. But at about 29 minutes something eluted from the column that did not itself ionise, but suppressed the background ionisation. This caused the negative peak...