Chromatography Forum

Hi guys, I'm new to LC-MS and I've encountered something I can't explain. I'm using an agilent 1100 series HPLC with a G1946D single quad detector in ESI mode. When I run a sample through, I get positive peaks on the DAD signal, and on one peak, I get a clear positive peak from the mass spec. But on every other DAD peak where I should see a response from the mass spec, I see either no response or negative peaks.

Any ideas? My analytes are in the mass range of 140-200 D, which is what I've set the MS to scan for.

I assume your negative peaks are in the total ion chromatogram? What this usually means is that you have a background ion (it might be something like a phthalate from the solvent, background ions are almost impossible to exclude completely), and the ionisation of the background ion is inhibited by an analyte that is eluting. This means the signal goes down rather than up. It can happen even when the analyte doesn't itself make a signal at all.

I assume your negative peaks are in the total ion chromatogram? What this usually means is that you have a background ion (it might be something like a phthalate from the solvent, background ions are almost impossible to exclude completely), and the ionisation of the background ion is inhibited by an analyte that is eluting. This means the signal goes down rather than up. It can happen even when the analyte doesn't itself make a signal at all.

I'm not sure if that was the problem, but one thing I did that really improved the signal was used 0.1% acetic acid for my ACN/H20 reverse phase LC-MS. Adding the acid really improved the signal.

Don't look just at the TIC though - are there masses that appear during the apparent negative peak that aren't there otherwise in the background? See if any extracted ion chromatograms show a positive peak.

You may also have a scenario where something elutes that is just not ESI-ionizable (or visible using the current settings), but it is capable of suppression.