Spectral library generation

Spectral library generation smanda  2019-01-16

HI Brendan,

I am using mzid from peptideshaker (3 three search engines results, combined using PeptideShaker) to build a spectral library in Skyline. I export the report on openswath format. This all works fine for me.
What I am concerned is the number of transitions in the resulting library. When I create a library using Peakview, I see the number of transitions and peptides are atleast 5 times more than when I create using Skyline. Is there some setting which I need to be checking before exporting the report in Skyline?
Do you have a tutorial /steps to ONLY create a library in Skyline? The videos I could find are for analyzing the entire data in Skyline and not just library creation and export.


Nick Shulman responded:  2019-01-17
To create a spectral library in Skyline, you go to:
Settings > Peptide Settings > Library
and press the "Build" button to bring up the "Build Library" dialog.

Type something in the "Name" field, and then press the Browse button to find a location on disk to save your .blib file.

Then press the next button, and on the next page, you would use the "Add Files" button to tell Skyline where to find your peptide search results files.
I believe your Peptide Shaker you would be pointing Skyline at files with the ".mzid" extension.

On the first page of the Build Library dialog, there's the Cut-off score (defaults to 0.95) and the "Include ambiguous matches" checkbox. Both of these might have an impact on the number of peptides that make it into your library.

If you would like, you could send us your files. Maybe send us the .blib files that you created, and also your peptide search results. It would probably be helpful if you could send us a screenshot of what you are seeing in PeakView, and we might be able to figure out why certain peptides or transitions did not make it into the library.

Files that are less than 50MB can be attached to this support request. If you need to send us larger files, you can upload them here:

-- Nick