Hi,
I noticed the peak boundaries in skyline frequently don't agree with peak boundaries in the combined_ion.tsv files produced by fragpipe.
The psm.ssl file contains different peak boundaries for different psms of the same precursor/sample -mI think this is the source of the problem
I am only using the first part of the skyline panel on fragpipe (to visualize peaks in skyline).
I attached the log file for a dataset that has this issue.
Can you please look into this.
Thanks,
Janos
log_2026-04-13_08-50-46.txt
Hi,
I noticed the peak boundaries in skyline frequently don't agree with peak boundaries in the combined_ion.tsv files produced by fragpipe.
The psm.ssl file contains different peak boundaries for different psms of the same precursor/sample -mI think this is the source of the problem
I am only using the first part of the skyline panel on fragpipe (to visualize peaks in skyline).
I attached the log file for a dataset that has this issue.
Can you please look into this.
Thanks,
Janos
log_2026-04-13_08-50-46.txt