Using a DIA-NN Predicted Spectral Library in Skyline

[pliuni-dotcom]

Hi Vadim,

Sorry if this question has been addressed somewhere, but I have yet to find an answer.

I would like to take the predicted spectral library generated from a .FASTA file in DIA-NN, and use it as a general reference spectral library in Skyline for whenever I am doing some early targeted peptide selection

I am able to generate the .parquet and .predicted.speclib files from the initial Prediction from FASTA processing step.

But I am having trouble generating a file that is compatible with Skyline after this.

After setting the .parquet file as the Spectral Library, I have tried using —gen-spec-lib in additional options, and it produces the skyline.speclib files, but when importing into Skyline it produces this error:

“ System.IO.IOException: ERROR: file report.parquet does not have a column called Global.Q.Value”

Could you advise perhaps on how I can proceed, or if there is some step I am missing with my process?

[vdemichev]

Hi, sorry for delay with the reply.

This is not really possible I think, Skyline will only read .skyline.speclib libraries, which DIA-NN auto-generates when saving empirical libs. So I would just recommend to work with those.

System.IO.IOException: ERROR: file report.parquet does not have a column called Global.Q.Value

Skyline thinks it's loading a main report here.

Best,
Vadim