Dear Skyline team,
I am trying to import peptide search results from Fragpipe outputs but am encountering a format mismatch error between files.
My results are from Fragpipe v23 and am importing into Skyline (64-bit) 25.1.0.142 (7401c644b4).

I have tried multiple times with two different files to follow the Fragpipe tutorial on importing data into Skyline. During the first step, once I select the interact files and click next, I encounter the following warning (attached 1): "[SpectrumList::find] mismatch between spectrum id format of the file (scan=1) and the looked up id (controllerType=0 controllerNumber=1 scan=726)"
This warning seems to be there for every spectrum (attached 2) and thus nothing is imported into the Skyline document. If I click more info, the first line is "System.IO.IOException: WARNING: Could not find native id or title 'controllerType=0 controllerNumber=1 scan=759' in ../250128_Hela_100ng_DDA_3ms_R1_uncalibrated.mzML."

Based on the comments in the submission 'opening.d files on skyline' https://skyline.ms/announcements/home/support/thread.view?entityId=e28a2047-ead0-103d-b4e5-22f535560118&_docid=thread%3Ae28a2047-ead0-103d-b4e5-22f535560118 containing similar mismatch issue discussed in the comments, I tried moving either the raw, uncalibrated mzml or mzml into the folder but all produce the same error.

Is this a file formatting issue from Fragpipe or a Skyline issue?
Thanks for you work,
Best,
Naomi O'Sullivan