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error loading fragpipe results into skyline

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error loading fragpipe results into skyline jdemeter  2025-05-27 12:01
 

Hi,

I am trying to load results using a fragpipe dda workflow into skyline and got this error. I asked fragpipe help, but they think it is a skyline error. Can you please take a look?

Thank you,
Janos
 
 
Nick Shulman responded:  2025-05-27 12:41
Can you send us your Skyline document?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

It would also be helpful if you could zip up and send us one of your .d folders such as "20250515_400ngK562_60Min_Post_PM_Slot2-2_1_4709.d".

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

I think the error has something to do with having multiple copies of the same molecule in the document, and I think only one of the molecules has had its Explicit Retention Time set on it. The bug probably also has something to do with the "Retention Time Filtering" setting on the "Full Scan" tab at "Settings > Transition Settings".

This bug has been reported a few times before, but no one has been able to send me their Skyline document so I have not been able to fix it.
After you send me your Skyline document I will probably be able to fix this in a future version of Skyline and I will also be able to tell you what you can do to work around it.
-- Nick
 
jdemeter responded:  2025-05-27 13:04
I uploaded 'skyline_files.zip' and '20250515_400ngK562_60Min_Post_PM_Slot2-2_1_4709.d.zip' files on the upload site.

when I open the skyline file, it's empty, so I zipped the whole directory for 'skyline_files.zip'.

Let me know if you need more of the .d files.

Thanks,
Janos
 
Nick Shulman responded:  2025-05-27 14:10
Thank you for uploading those files.
I might be able to figure out how to reproduce this bug from the files that you sent me, but it might be easier if you could send me the document you were looking at when you saw this error.
I think you ran into this error while doing "File > Import > Peptide Search" or "File > Search > Run Peptide Search".
I believe you see this error message during the chromatogram extraction part of the process.
When you see the error message you can push the "Cancel" button on whatever window you are looking at and then you can do "File > Share" to create a .zip file which will contain a Skyline document with peptides.
-- Nick