Fragpipe output parsing error

Fragpipe output parsing error ho-tak lau  2023-03-08

Hi Skyline Team,

I found a bug parsing Fragpipe 19.1 result using Skyline When I load the interact-filename.pep.xml with filename_uncalibrated.mgf in the same folder. Skyline was unable to find the .mgf. I have to rename the file to filename_uncalibrated_uncalibrated.mgf for Skyline to find it.


Nick Shulman responded:  2023-03-09
There is a long discussion between a Fragpipe developer and a Skyline developer about this issue:
I am not sure I understand what is being said in that thread, but there might be some helpful information in there.

I think they might be saying that this works better in Skyline-daily than it did in Skyline 22.2.
-- Nick