Questions about skyline read the ion mobility values of the spectral library generated by DIA-NN.

Questions about skyline read the ion mobility values of the spectral library generated by DIA-NN. andyzcq  2021-11-27

I noticed that Skyline has supported the speclib format generated by DIA-NN.
I used the "peptide"-"library"-"edit"-"add", found skyline can not recognize the *.speclib format. I modified "speclib" to "clib", which can be recognized by Skyline. But Skyline kept loading the file for a long time (about several hours), and the speclib file is only 7M.
Then I used the "file"-"import"-"assay library" to load the lib.tsv file generated by DIA-NN, which is successful. I assigned the ion mobility column as "explicit ion mobility" in the import wizard. However, there are no "ion mobility" values in the spectral library explorer.

Brendan MacLean responded:  2021-11-27

It certainly would be nice if the last thing you tried worked. Though, I am not surprised that it will still require code improvement. Probably you are the first to test it.

If you want to go directly from the .speclib file, you will need to use either File > Import > Peptide Search and "build" a (BiblioSpec - .blib) library from the .speclib file, or use Peptide Settings - Library tab and click the "Build" button to build a library. Skyline does not recognize the .speclib format natively as a spectral library, as it does with .clib, .elib, .sptxt, .msp, .hlf formats. Note that these are specific formats, and it is not surprising that changing the file extension from .speclib to .clib works poorly. You are essentially lying to Skyline about the contents of the file.

Hope this helps. Thanks for posting your feedback to the Skyline support board.


Brendan MacLean responded:  2021-11-27

Might we get your .speclib and lib.tsv files for testing, in order to fix any issues they cause? You can upload them to:

If you need something more private, let us know, and we can arrange that as well.

andyzcq responded:  2021-11-28

I used Peptide Setting-Library tab-Build to build the spectral library based on speclib file, found "ERROR: speclib file has version 3, but BiblioSpec only Supports up to version 2".

I have uploaded speclib file and lib.tsv to the server, and their names are "test.speclib" and "test-lib.tsv".

matt.chambers42 responded:  2021-12-15

Hi Andy,

In the next release and current Skyline-daily this should be fixed. However, you will need the report.tsv file from DIA-NN as well as the speclib (not the lib.tsv). The speclib and report.tsv must be in the same directory.

Hope this helps,