I am doing LC-MS (LC-QToF) of a phosphonate compound (nitrilotris methylene phosphonic acid), for which I add derivatization agent trimethylsilyl diazomethane to each sample and wait 2hours before running them on the instrument. I do not have any mass label internal standard for the compound, so I am using caffeine as the internal standard. I am using C18 column. In the beginning I was getting disturbed peaks with a tail from the start of the runs, then for two weeks I got clean peaks. However, I started getting the same type of disturbed peaks again. What could cause the disturbed peaks in LCMS? I have attached a screenshot of the disturbed peak I am getting. My internal standard peak also looks like this.
Hello, Ah, C18 columns can go a bit wonky with all that extreme pH, blazing hot temperatures, or if the solvent's too rough. If your column's seen better days or it's knackered, it might be worth investing in a new one Athkia F or it may be, make sure you're doing your sample prep right, especially with the derivatization.
Hello, a bit more information would be useful to help diagnose the problem but just looking at the fronting peak shape my guess would be a sample solvent that has an eluotropic strength that is too high combined with an injection volume that is also too high. Try injecting a lower volume or matching the injection solvent with your starting gradient conditions.
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