RT selection from multiple DDA file, matching highest dotP peptide | af1234 | 2022-01-12 12:11 |
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. Thanks! |
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