Skyline 23.1 has an import wizard to let you easily run a library-free EncyclopeDIA search on your gas-phase fractionated (narrow window) and single injection (wide window) DIA results. You choose a FASTA and Skyline generates a Prosit library from it and uses that to seed the EncyclopeDIA search. After the search, Skyline automatically imports the chromatogram and quantification libraries that were created.
1. Start the wizard
![Select Import > EncyclopeDIA Search](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Screenshot%202023-07-07%20113533.png)
2. Choose FASTA
![Choose FASTA](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Choose%20FASTA.png)
- Enzyme and missed cleavages determine which peptides will be predicted
- Prosit prediction on a whole proteome can take a while so for a quick test choose a targeted FASTA
3. Pick Prosit settings
![Prosit settings](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Prosit%20settings.png)
- m/z min/max can be set to filter peptide predictions on m/z
- Precursor charges between 1 and 6
- Default NCE is the NCE at the default charge
4. Pick GPF (narrow window) DIA results
![Narrow results](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Narrow%20results.png)
- EncyclopeDIA searches these to build chromatogram library
5. Pick single injection (wide window) DIA results
![Wide results](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Wide%20results.png)
- EncyclopeDIA searches these to build quantification library
6. Pick EncyclopeDIA settings
![EncyclopeDIA settings](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=EncyclopeDIA%20settings.png)
- Wizard page currently only exposes peak tolerances
- All EncyclopeDIA settings can be edited in “Additional Settings”
7. Watch progress
![Watch progress](https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=eb21523f-ff02-103b-af2b-22f5355689d6&name=Progress%20log.png)
8. After search finishes, import proceeds with the import peptide search wizard where the EncyclopeDIA libraries have been preselected