Assuming that one have APCI and ESI probe available, and that sufficient signal is obtained with any of both probes; is there any preference for the probe to use for further investigation, especially when MS^n experiments are planed? Are there any parameters to take in account for the selection of the probe?

Usually if the signals are similar with preliminary experiments, I use electrospray. There are a couple of reasons for this:

1. With APCI, in addition to the spray shield or curtain plate (common to both), there is a vaporizer tube and discharge needle that can become dirty. ESI is lower maintenance, in my opinion.

2. Acetonitrile can cause buildup of black stuff (soot?) on source parts in APCI. My evidence is anecdotal and I have never seen this published, but have heard it from other instrument operators as well. So I limit my organic modifier to methanol with APCI. With ESI, I am free to choose whatever solvent or mixture in bottle "B" that gives me the best selectivity.

You should also consider flow rate. If you need a high flow (1 ml/min) then APCI is the way to go.