Issue in Spectral Library building from Timstof pro data (dda .d files)

Issue in Spectral Library building from Timstof pro data (dda .d files) suresh choudhary  2023-01-05

Dear Skyline team,

I am trying to build spectral library from timsDIA PASEF data. I have raw files (.d folders) that were processed using FragPipe/MSFragger/Philosopher. Which, by the way, works great for these data.

I am not able to build a spectral library using the DDA-MS1 quant workflow and DIA workflow, with Import - Peptide results etc for building the list form the search results. Neither using MSFragger pepXML files nor using interact-.pep.xml files after PeptideProphet work. When using interact-.pep.xml files, I get an error that it cannot find spectral files. When using pepXML, it finds the files to get the spectra (from file_calibrated.mgf files produced by MSFragger) but gives an error at a later stage. Can some one help me to get the solution of it.

Nick Shulman responded:  2023-01-05
I am not sure what is going on, but if you send us your files, we can figure it out.

If it's not too much trouble, could you zip up that whole "temp" folder that you have and send it to us?
You can upload that huge zip file here:

(I am not the expert in this area, so there might be someone else on this support board who could give you an answer without having to see your files)
-- Nick