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Issue with the spectral library building Anjana  2024-11-06 02:51
 

Dear Skyline team,

We were trying to build a spectral library using DIA raw files in Skyline v24.1 through import->peptide search. In the build option, while we were trying to add the raw files, it seems the file format was not supported. In the previous versions of the Skyline, we have found an option to "start from -> DIA raw files". Kindly guide us to generate a spectral library using the DIA raw files in the recent version.
 
 
Nick Shulman responded:  2024-11-06 08:57
In Skyline 24.1, if you want to search raw files, the menu item that you need to use is:
File > Search > Run Peptide Search

The "File > Import > Peptide Search" menu item now is only used for importing search results that were produced elsewhere. If you are creating new search results then you have to use the new "File > Search" menu item.
We made this change because we wanted to make it more obvious that Skyline can be used for running peptide searches, not just importing search results.
Sorry about this confusion.
-- Nick
 
Anjana responded:  2024-11-07 23:03
Dear Skyline team,

Thank you for the help. We were able to create the library, but now the result file (raw data) import is failing due to an error. Can you look into this and guide us.

Thank you
Anjana Aravind
 
Nick Shulman responded:  2024-11-08 09:10
The error "A non-degenerate overlapping window scheme is required." can happen if you are trying to use Skyline's isolation scheme deconvoluter.
That is, in the "Edit Isolation Scheme" dialog, something has been chosen in the "Deconvolution" dropdown.

We recommend not using Skyline's deconvolution.
That is, you should go to the "Full Scan" tab at "Settings > Transition Settings" and choose "Edit Current" in the "Isolation Scheme" dropdown and choose "None" in the "Deconvolution" dropdown.

If your data does have overlapping isolation windows and you would like deconvolution performed then we would recommend using the "Demultiplex" options MSConvert to create .mzML files which have the overlapping isolation windows deconvoluted into separate virtual spectra.

We would have liked to have completely removed the "Deconvolution" option from Skyline, but, unfortunately, that option is necessary for some DIA "Export Method" scenarios.
-- Nick