• Sign In
  1. Requests

skyline document not generated in FragPipe 24.0 with Skyline 26.1

support

View Request

view list print
skyline document not generated in FragPipe 24.0 with Skyline 26.1 j xu  2026-03-19 14:49
 

There is no .sky file in the skyline_flies folder, and the files generated in the same folder are:
fragpipe.blib
fragpipe.redudant.blib
fragpipe.slc
peptide_list
psm.ssl

I have contacted the Fragpipe team, and Fengchao helped to check the zipped log file. It turned out that they had no idea about the error and suggested we contact the skyline team instead.

Many thanks,
Jin
 
 
Nick Shulman responded:  2026-03-19 15:01
The error that I see there is:
Error: Failed to build the spectral library

Can you send me all of the files from that "skyline_files" folder.
You can package it all in a .zip file and upload it here:
https://skyline.ms/files.url

-- Nick
 
j xu responded:  2026-03-20 02:37
Thanks Nick.
I have uploaded two sets of zipped files - one from using skyline 25.1, and the other from using 26.1.
 
Nick Shulman responded:  2026-03-20 02:57
Thanks for uploading those files.
Can you also send me the following files:
20260318_P230_APOA1.raw
202600318_P230_APOE2.raw
20260318_P230_APOE4.raw
20260318_P230_APOAM.raw

They are probably all in the following folder on your computer:
D:/User_Data/Frances_Sidgwick/2602_Inoviv_P230/reruns_fragpipr/

It sounds like you are saying that this did work in Skyline 25.1 but fails with Skyline 26.1.
After I see your .raw files I might be able to figure out what is going wrong.
-- Nick
 
j xu responded:  2026-03-20 03:54
We first tested with skyline 25.1 for only 4 standards file you mentioned above, the fragpipe search worked, but there was not .sky file in the skeline_files folder.

Then we updated skyline to 26.1 hoping that the .sky file can be generated with the newer version. For this round, we searched for the whole batch of >80 raw files - not only the 4 standards.

For the skyline 26.1 installation on our server, the IT staff did shared that there was something unusual. I have attached the message shared by him.

Many thanks,
Jin
 
Nick Shulman responded:  2026-03-20 14:29
Could you send me the log file from when you ran this with Skyline 25.1?

In the log file that you attached to your original message, the first error is "Error: Failure starting command "BlibBuild ..." which probably means that fragpipe has no idea where Skyline is installed, and so it does not know how to execute BlibBuild.exe which can be found in the same folder as Skyline.exe.

With your "skyline_files-25.1" folder that you sent me, I see that a .blib file was successfully created, so there was probably a different problem that happened later. If you could send me the log file from that run where you actually managed to create a .blib file, I might be able to tell you what went wrong after that.
-- Nick