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Convert .blib to .tsv`

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Convert .blib to .tsv` ronald cutler  2024-08-30 08:09
 

Hello,

I have built a spectra library in Skyline and now would like to use this in DIA-NN. Since the BiblioSpec output is an SQLite3 file and DIA-NN needs a .tsv as specified here: https://github.com/vdemichev/DiaNN?tab=readme-ov-file#spectral-library-formats.

I have found this program which might be able to do the trick, but wondering if I can have any help with this? https://gist.github.com/icedraco/78d9879f2171ecebcbfb

Thank you very much for your time,
Ronnie
 
 
Nick Shulman responded:  2024-08-30 08:36
The Python script to convert a .blib to .tsv would need to be a little more complicated than that because the m/zs and intensities of the fragment ions are stored as zlib compressed blobs in the "peakMz" and "peakIntensity" columns in the "RefSpectraPeaks" table.
It would probably be possible to add a few lines of code to that Python script to handle this, but I am not very good at writing Python.

It might be that the easiest thing to do would be to create a Skyline document that uses the .blib library, add all of the peptides from the .blib to the Skyline document, and then create a custom report which includes the "Product Mz" and "Library Intensity" values from the Transitions in the Skyline document.

Can you send me an example of a .blib file that you want to use with DIA-NN?
Can you also send me an example of the sort of .tsv file that you would want to create? I would be particularly interested in the names of the column headers as well as what modifications in the peptide sequence are supposed to look like.

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
-- Nick
 
ronald cutler responded:  2024-08-30 13:21
Hi Nick,

Thanks for your response!

How you go about creating a new Skyline document with just the library? I tried to open up a blank document and then checked my library, but am unsure how to create a report from this.

In the meantime I have attached the files you requested.

Best,
Ronnie
 
Nick Shulman responded:  2024-08-30 13:58
You can add a library to a Skyline document using the "Edit List" button on the "Libraries" tab at "Settings > Peptide Settings".
After you have added the library to the document you can go to "View > Spectral Libraries" and then push the "Add All" button in the Library Explorer.

If you want to learn how to create a custom report you can see the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
--Nick
 
ronald cutler responded:  2024-09-03 11:32
Hi Nick,

Thanks for the response. I tried this out and it seems to work, but I am unable to get data for certain things. Namely the Precursor Intensity and Precursor Retention time, and Precursor Ion Mobility. Do you know why this is? I've attached the custom report.

Best,
Ronnie