Novor - uses built-in trypsin-cid-trap instead of unspecific digestion

[ahe2025]

I'm trying to use Novor without any enzyme for immunopeptidomics data. If I select unspecific digestion it automatically uses built-in trypsin-cid-trap settings. Do you know is there any way to use Novor without any enzyme for immunopeptidomics data?

[hbarsnes]

Given that Novor uses de novo sequencing the enzyme should not make a massive difference and in fact we did not even know that Novor supported different enzymes (presumably as training data). However, when looking closer inside the Novor jar file I find the following enzymes (ignore the META-INF file):

The use of these enzymes is not directly supported in SearchGUI, but if you want to test whether this setting makes a real difference you can try to modify the Novor parameter file (novor_params.txt in the folder SearchGUI-X.Y.Z\resources\Novor) and then run the Novor command line. See the Novor README file in the same folder for details on the commend line.

You will basically have to manually modify these three parameters to mimic the names in the above screenshot:

enzyme = Trypsin
fragmentation = HCD
massAnalyzer = FT

We sadly do not have the resources to implement this properly in SearchGUI at the moment, but I'll leave the issue open and hopefully get back to it at a later point.

[ahe2025]

Ok, thanks for your reply. We’ll try the Novor command line with the modified parameter file as you suggested. From: Harald Barsnes ***@***.***> Sent: 06 May 2025 18:31 To: compomics/searchgui ***@***.***> Cc: ***@***.***>; Author ***@***.***> Subject: Re: [compomics/searchgui] Novor - uses built-in trypsin-cid-trap instead of unspecific digestion (Issue #382) [https://avatars.githubusercontent.com/u/13151214?s=20&v=4]hbarsnes left a comment (CompOmics/searchgui#382)<#382 (comment)> Given that Novor uses de novo sequencing the enzyme should not make a massive difference and in fact we did not even know that Novor supported different enzymes (presumably as training data). However, when looking closer inside the Novor jar file I find the following enzymes (ignore the META-INF file): Screenshot.2025-05-06.172104.jpg (view on web)<https://github.com/user-attachments/assets/fee5a61b-f85e-43b3-8dca-46cf7fc6f14e> The use of these enzymes is not directly supported in SearchGUI, but if you want to test whether this setting makes a real difference you can try to modify the Novor parameter file (novor_params.txt in the folder SearchGUI-X.Y.Z\resources\Novor) and then run the Novor command line. See the Novor README file in the same folder for details on the commend line. You will basically have to manually modify these three parameters to mimic the names in the above screenshot: enzyme = Trypsin fragmentation = HCD massAnalyzer = FT We sadly do not have the resources to implement this properly in SearchGUI at the moment, but I'll leave the issue open and hopefully get back to it at a later point.