I'm currently analyzing PFAS in Water samples via LC/Q-TOF with 2 targeted MSMS methods for 2 Ions each with several experiments of different collision energies per compound. So I'm basically doing two identical runs, only differing in the retention time and mass of the precursors. When using the MassHunter Qualitative Analysis software to analyze both, I use the target/suspect screening workflow and a selfmade PCDL with the 4 compounds. When running the workflow, the software generates all product ion MS for 2 of the compounds (one run) as intended to evaluate the fragmentation of the compunds at different collision energies, but not for the other 2 (the other run), even though the acquisition methods and the used workflow, as mentioned target/suspect screening, are identical.
Can anyone tell me what the generation of product ion MS depends on or what else I'm getting wrong here?