Standard Method

[Noser222]

Hi,

I just wanted to pick everyone's brains about what their general starting conditions are to see a wide variety of analytes when you don't have little knowledge of their functional groups or molecular weights.

I was looking for a trace impurity for which we had no information, nothing about MW or functional groups. I was able to see a small peak in UV at 258 nm but the total ion chromatogram showed nothing above the background. Since I was at least told that it was a small molecule, I started with a mobile phase of 10 mM ammonium acetate with a 5-95% methanol gradient through an 2.1 x 3 mm C18 column with a flow of 0.2 mL/min in APCI mode, looking at pos and neg with a scan from 100 - 1000 and fragmentor set to 70V. In my limited experience (2 years), it seems that you have to have to inject a concentrated sample to even see a peak in the total ion chromatogram. My boss (who isn't a chemist) thinks that mass spec is a cure-all and if you shoot anything in there you should see something.

So anyway, if anyone would like to share what their idea of a good general starting point is I'd appreciate it.

[MG]

Oftentimes in my experience, the TIC will look worse than the UV in the situation you described. Since you have UV, you know the retention time of your unknown. Taking into account any time offset between your UV and MS (perhaps you have a known major component you can use for this), you can take a background-subtracted mass spectrum of the region where you expect to see the unknown. If the spectrum has masses above the noise, take extracted ion chromatograms of those masses to confirm that they are real peaks that match the retention time of your unknown.

Another thing you can do is tell your data system to calculate a Base Peak Chromatogram (BPC), if it has that feature. This shows the signal from only the base peak at any given time during the run. Oftentimes it will be less noisy and reveal peaks not visible in the TIC.

[Noser222]

I've dealt a lot more with SIM mode since I usually had standard samples of the analytes I was looking for...hadn't been trained on those features before. I tried it out and was able to get some mass peaks.

[John G]

You might want to try esi if it is available. Generally it is more sensitive then APcI due to lower baseline levels and your flow rate is well suited for it. If you have the option CODA software can be used to pick up low level impurities.

John