Small Molecule Zero Peak

Small Molecule Zero Peak bwidner  2019-05-16

Hello Skyline Team!
I am measuring small molecules, and I am looking for a way to get "zero" in the Transition Results table for peaks that are non-existent. At present, I am not quantifying and don't have a good sense of LOD. If I had a sense of LOD, I would handle this in post-processing. Without quantification, I am trying to look at presence/absence or fold change. Often when there is no real peak, but there is some noise, the noise is selected. I was getting around this problem by manually drawing a baseline somewhere else, hoping it would put zero in the table. This worked, but sometimes I draw a manual baseline on a peak that looks small and without zooming in I can't tell if it is a small peak or just a single scan.

Is there a way to screen out peaks that are only 1 or 2 scans? I saw the "Points Across Peak" parameter, but when I manually draw the baseline there are often quite a few scans, so that will not work. It would have to account for the number of scans above the baseline, somehow. Does such a parameter exist? I saw elsewhere on the forums the suggestion to use the FWHM, but this is also driven by how wide the base of the peak is, which for manual integration varies randomly.

Thanks in advance!