Problem building spectral library

Problem building spectral library itv005  2020-10-15


I am a farily new user of Skyline, and I am struggling to build my spectral library. Aside from some of the tutorials, my training is very limited. The source of my spectral library is a search from Proteome Discoverer 2.4 that I exported to a pep.xml file. I also have a used MSconvert to generate mzml files from my raw files.

I suspect that my issue is not due to any of the settings I made when setting up skyline, therefore I have not included those in this request. As seen in the attachment, I get an error saying the wrong directory is used, but I cannot seem to find out how it chooses this directory, or how to change it. I have put the skyline file, the raw files, and the converted spectrum files all in the same folder. The only thing missing, as I see it, is the program itself. However, I struggle to see the logic if this is the missing link, as this would be impractical for further projects.

I used the 20.2 version of Skyline and Windows 10 Home. The data I have is a non-targeted HPLC-MS/MS of CSF. I wish to use this library in a PRM project which is ready to be analyzed.

Thanks in advance! Let me know if I should add more info.

Nick Shulman responded:  2020-10-15

This page has the list of peptide search result formats that you can use to build a spectral library:

It says that for Proteome Discoverer, you are just supposed to use the ".msf" files directly. You should not bother to convert them to .pep.xml.
-- Nick
itv005 responded:  2020-10-16

This worked! Thanks a lot.

Brendan MacLean responded:  2020-10-16
Also, we support the native pdResult file from Proteome Discoverer. Many ways to get there. Glad you found one that worked for you.