RT selection from multiple DDA file, matching highest dotP peptide

RT selection from multiple DDA file, matching highest dotP peptide af1234  2022-01-12

I have approx ~500 heavy peptides which I want to use to design a PRM-pasef method. I ran them individually in batches of 100 in DDA-pasef and searched all the files with Fragpipe. I then imported all of them into Skyline but, unfortunately, similarly to this https://skyline.ms/announcements/home/support/thread.view?entityId=9a85d70f-db25-1038-8050-e465a3939b46&_docid=thread%3A9a85d70f-db25-1038-8050-e465a3939b46 I want to schedule the PRM using the peptides which are the highest dotP (as each peptide is only in one sample out of 5). It is pretty clear to see which one is correct (see attached), but having to manually change the RT for 500 peptides to match the correct one (and being able to use average RT across the replicates) will take a really long time. I was wondering if there is any update on how to do this.


Brendan MacLean responded:  2022-01-13

Hi Andrea,
Can you provide the document in question? If you want, you can post it to:


I have an idea about how to achieve this in Skyline, but I would like to attempt it myself before explaining something to you that may not work out.

Thanks for posting to the Skyline support board and for the clear description.


Brendan MacLean responded:  2022-01-13

Oops. Remember to use File > Share to create a .sky.zip file and provide that. The .sky file alone is not very useful.

af1234 responded:  2022-01-14

Hi Brendan,

I actually solved it in another way. In the latest skyline daily there is synchronized integration so I just fixed it by hand as I would anyway go through all the peptides to make sure integration boundaries are correct. That feature turned out to be so helpful thanks for adding it!