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import of parquet spectral library from DIANN 2.0 and above into skyline

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import of parquet spectral library from DIANN 2.0 and above into skyline dkueltz  2025-04-15 22:52
 

Since version 2.0 DIA-NN no longer generates speclib files for its spectral libraries but instead only parquet files. I used to be able to import the speclib libraries into Skyline but since they are no longer generated by DIA-NN I wonder how I can import the parquet libraries into Skyline. The direct link from DIA-NN to Skyline (Skyline button in DIA-NN) never worked for me but importing the DIA-NN generated spectral libraries worked well until DIA-NN version 2.0 when the speclib libraries are no longer generated. The DIA-NN developers told me that Skyline will soon have parquet import capability - is this already a function that is available in Skyline Daily? If, so where can I find it?
Thanks much,
Dietmar
 
 
Mike MacCoss responded:  2025-04-15 23:30

Hi Dietmar,
Yes, Skyline Daily version 25.1 supports import of DIA-NN parquet files. If you start Skyline daily it should ask you to upgrade.

There have also been significant performance improvements to this import. The easiest way to do this is to File > Import > Peptide Search. Point the Spectral Library UI to the parquet.skyline.speclib file. By default DIA-NN calls this report-lib.parquet.skyline.speclib. This file gets written if you have MBR turned on or --reanalysis from the command line.

DIANN-Import UI

Hope this helps,
Mike
 
dkueltz responded:  2025-04-17 10:15

Thanks much, Mike, for the helpful reply! I think in the initial version 2.0 of DIA-NN the speclib files, which were generated in version 1.92 were apparently no longer generated, only the parquet files. I just downloaded DIA-NN version 2.1 and in that version the speclib files are generated again. At any rate, it works well now. Thanks for all your work on Skyline and Panorama - these are key tools for our proteomics workflows, along with DIA-NN.