Peptide integrated peak area ranking filtering

Peptide integrated peak area ranking filtering boycea  2021-05-21


We were wondering if there was a way to rank and filter out peptides within proteins based on integrated peak area among all the replicates, as opposed to based on library? I currently have a document with 160 proteins and 2,600+ peptides, with some proteins with 20+ peptides, which is more than what we need (10 being more ideal). We want to streamline the number of peptides to manually go through, and we want to keep all the peptides with the best integrated peak areas among all the replicates before we go through them. I'm assuming when refining the max peptide peak rank is based on the library ranking, and not total replicate integrated peak area. Thanks!


Brendan MacLean responded:  2021-05-21

Have a look at the Refine > Advanced - Results tab. There you can choose a maximum number of peptides per protein ranked based on peak area, and there is also a checkbox to choose only the precursor with the maximum peak area. There is also a maximum number of transitions based on the peak areas imported into Skyline. This could allow you to initially target a larger number of product ions (say 10) based on a spectral library and then reduce the number (say 6) based on experimental data.

The Refine > Advanced form is the place to look. Thanks for posting to the Skyline support board.