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Library details missing from spectra library explorer

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Library details missing from spectra library explorer Liyan Chen  2023-08-29 02:38
 

Hi Skyline developers,

I have been using Proteome Discoverer 3.0.0.757 (Sequest node) with Skyline 21.2.0.425 for building spectra libraries. This combination has worked fine for several projects this year till now. The PD result file, generated .blib and Skyline document seem to give a reasonable number of proteins and peptides, but library details are somehow not showing (screencap attached). Nothing in our workflow has changed between the previous projects and this current one except for the number of files in library run dataset: 80 files compared to 20-30 from before. I have also tried re-do of PD search and importing of library under different filename and get the same problem.

Thanks for your help.
 
 
Nick Shulman responded:  2023-08-29 06:43
I do not know what might be going on, but if you send us one of your old Skyline documents and your new Skyline document, we could probably figure out what has become different.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick
 
Liyan Chen responded:  2023-09-07 23:55
Hi Nick,

I've uploaded these files in the sharing folder: "problem_library.sky.zip" and "skyline_okay_library.sky.zip" for new and old documents respectively. Thank you.
 
Nick Shulman responded:  2023-09-08 07:24
Thank you for sending that "problem_library.sky.zip" file.
It turns out that Skyline 21.2 had a bug in it where the Library Details window would be blank like that if any of the raw files that the library was built from had zero "Best Spectra" (that is, peptides where BiblioSpec decided that the best looking spectrum came from the file in question).
If you open that document using Skyline 22.2, you will be able to successfully view the Library Details window and you will be able to see that the file "20230721_CVRI_HF_pool1_F8_reinject.raw" had zero spectra which looked the best.

You probably do not need to worry about this particular thing in Skyline 21.2. I would not expect this characteristic of this library to cause any other problems.

We always recommend that you use the latest version of Skyline unless you are trying to reproduce results that were obtained by an earlier version.
The latest version of Skyline is 22.2, and we will be coming out with Skyline 23.1 soon.
Let us know if anything is preventing you from being able to upgrade to the latest version.
-- Nick
 
Liyan Chen responded:  2023-09-12 19:23
Thank you for solving the mystery with the library! We will upgrade Skyline once we are done with the current projects.