I'm in the process of optimising a new method for a trace level mixture using an Agilent 7000D. Whilst I am fairly confident with many aspects of the instrument, MS gain (and EM saver) are features that I don't have a lot of knowledge about and would love to know more as been using a gain level of 1 for all the work I have done so far.
Whilst there is some literature online covering how to set the appropriate gain levels, this is a good few years old (referencing Chemstation) and treats gain as an attribute that is applied to an entire run, rather than something that can be applied to individual SIM or MRM time segments. With that in mind I would be hugely grateful for any response on the questions below if somebody would be willing to oblige?
Within the context of a SIM or MRM run, is it acceptable to use different gain levels for different analytes/SIM groups? Whilst I know that increasing gain is going to increase noise, my gain increase experiments so far do show an increase in SNR and I suspect that increasing gain will help to address some of the problems I am having with getting good integration with low levels peaks.
How are gain levels set? From what I understand, we're looking for about 3 x 10^6 counts for SIM (and 10^7 for MRM) from the most intense ion... Is that correct?
Lastly, is setting the EM saver to 1X10^8 default acceptable and reasonable?