thanks for sharing the workflow.
You mentioned "deconvolution of spectra". I suppose you analyzed your samples by DIA, right? We are using instead DDA. We are choosing one vial per compound. For each vial we have five injections by applying five different collision energies.
Is the workflow you mentioned only applicable for DDA, too?
When I look at the intensities of my fragments MS2 spectra I regularily observe the same low value for several fragments, i.e. pure noise. From my opinion, it would be nice, to have the ability to set a cut-off with respect to absolute intensity in MS2 Dial during data processing.