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Issue running EncyclopeDIA search lisa walrond  2023-12-13 08:04
 
I'm trying to import an EncyclopeDIA search. It is failing for me in both Skyline and Skyline daily. I have been able to run these searches successfully before. I've included error messages from both failures below.

Thank you, Lisa


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Skyline
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Error
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OK More Info
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pwiz.Skyline.Model.Prosit.PrositNotConfiguredException: Intensity model '' does not exist
   at pwiz.Skyline.Model.Prosit.Models.PrositIntensityModel..ctor(String model) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Prosit\Models\PrositIntensityModel.cs:line 52
   at pwiz.Skyline.Model.Prosit.Models.PrositIntensityModel.GetInstance(String model) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Prosit\Models\PrositIntensityModel.cs:line 65
   at pwiz.Skyline.Model.Prosit.Models.PrositHelpers.PredictBatchesFromPrositCsv(String prositCsvFilePath, IProgressMonitor progressMonitor, IProgressStatus& progressStatus, CancellationToken token) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Prosit\Models\PrositModel.cs:line 408
   at pwiz.Skyline.FileUI.PeptideSearch.EncyclopeDiaSearchControl.Search(EncyclopeDiaSettings settings, CancellationTokenSource token, IProgressStatus status) in C:\proj\skyline_23_1\pwiz_tools\Skyline\FileUI\PeptideSearch\EncyclopeDiaSearchDlg.cs:line 632
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Skyline-daily
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Error
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OK More Info
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Skyline-daily (64-bit) 23.1.1.335 (6a818db84)

pwiz.Skyline.Model.Prosit.PrositNotConfiguredException: Intensity model '' does not exist
   at pwiz.Skyline.Model.Prosit.Models.PrositIntensityModel..ctor(String model) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Prosit\Models\PrositIntensityModel.cs:line 52
   at pwiz.Skyline.Model.Prosit.Models.PrositIntensityModel.GetInstance(String model) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Prosit\Models\PrositIntensityModel.cs:line 65
   at pwiz.Skyline.Model.Prosit.Models.PrositHelpers.PredictBatchesFromPrositCsv(String prositCsvFilePath, IProgressMonitor progressMonitor, IProgressStatus& progressStatus, CancellationToken token) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Prosit\Models\PrositModel.cs:line 408
   at pwiz.Skyline.FileUI.PeptideSearch.EncyclopeDiaSearchControl.Search(EncyclopeDiaSettings settings, CancellationTokenSource token, IProgressStatus status) in C:\proj\pwiz\pwiz_tools\Skyline\FileUI\PeptideSearch\EncyclopeDiaSearchDlg.cs:line 693
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Matt Chambers responded:  2023-12-13 08:19
It looks like somehow your Prosit model settings got reset. Reconfigure them from the Tools -> Options menu and then the Prosit tab.
 
Nick Shulman responded:  2023-12-13 08:19
Before you can use the EncyclopeDIA feature in Skyline you have to go to:
Tools > Options > Prosit
and choose something in the "Intensity Model" dropdown.

For privacy reasons, the Prosit feature starts out disabled in this way, and you have to choose something from that dropdown in order to enable it.

There are other places in Skyline such as building a Library from Prosit where Skyline will tell you that you need to do this step, but there is no such warning when doing "Import EncyclopeDIA search". We should fix that.
-- Nick