You can set up flow injection analysis to make each injection after changing the fragmentor voltage. Use full scan data, and extract ion chromatograms for each component of your standard mix. If you want to see the difference, make a standard mix containing a range of your favourite analytes, and do flow injection analysis (which makes multiple injections at intervals during a single "chromatography" run), with no column, but some sort of resistance instead (back-pressure regulator or 1m of thin tubing). The fragmentor voltage does make a difference, but if you're doing SIM for target molecules and you're not working near the detection limit, you probably won't notice the difference, or need to worry about it. For the spray voltage, I'd recommend Agilent's defaults.
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