After applying the library on the Skyline, we found that you also calculate the dot product for each peptide. Actually, we want to do high-quality searching and only keep the good result, so can I select the searching results based on the dot product? For example, filtering the peptides with dot product less than 0.8.
Thank you very much!
Best regards, Sunberg
Brendan MacLean responded:
Hi Sunberg, Yes, you can do that with the Edit > Refine > Advanced - Results tab (now Refine > Advanced in Skyline-daily). The Targeted Method Editing tutorial actually goes over this: