Hi William,
This is a pretty small list, and fairly obvious when there is not a peak. I would just use manual inspection to determine when you are measuring a peptide and when not. Otherwise, see the Advanced Peak Picking Models tutorial, if you actually want to create a scoring model that would give you a q value for this, and probably a poor one for the transitions you are showing in your screenshot. Seems like introducing unnecessary complexity at this point to me, though.

You are most likely seeing your filter values not applied, because you have not indicated they should be applied in the Transition Settings - Library tab. If you use "From filtered ion charges and types" then your precursor m/z filter will not be applied. You need to use "From filtered product ions" instead, though this also makes no sense with a filter that includes only "3 ions". If you really want to use such a restrictive filter, then you should just un-check the checkbox "If a library spectrum is available, pick its most intense ions", which is clearly checked, and finding library spectra, based on your screenshot.

Hope this helps. Good luck with your CE optimization.

--Brendan

Thanks for response. I used the small list as a practice. However, our usual list is in a range of 40-50 peptides in which manually check each one will be time intensive. Just find the new tutorial of "Advanced Peak Picking Model", but wonder it will be more convenient (user friendly)to have a threshold option for easy control esp during CE optimization stage. Maybe worth consider in next release?

Thanks,
William

Sure. It is on our list:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=348

Thanks for your feedback.

--Brendan