Question about Autoselection 'Rules' for Peak Selection

Question about Autoselection 'Rules' for Peak Selection mlane  2019-07-10

We use Skyline for targeted PRM experiments in less common approach: no library because we do HLA peptide screening. Since there is no spectral library, a list of peptides and most common transitions are supplied in the document, and we simply allow Skyline to include all matching spectra upon import and have it autoselect matching peptides. For autoselection, can you explain the prioritization Skyline puts on different factors such as transition intensity, number of transitions, shape, co-elution and mass accuracy in peak picking (if any or some of these are used)? There does seem to be a bias towards the most intense, but it also appears as if there is also requirement for some number of transitions and perhaps mass accuracy. If it uses these attributes or others, can you explain how? Thanks! Monica