Ralf Gabriels

Uncaught exception was fixed with the `DeepLCFeatureGenerator` refactoring in https://github.com/compomics/ms2rescore/commit/8749ddfa8a4fac45ef5a59b02a821b9fd3ca7695. Better logging and exception raising if not enough PSMs are present was implemented in https://github.com/compomics/ms2rescore/commit/4a5ff63ab0eacea5f4ebd8c533f5a74bb80d5abe. Both have been merged with...

Hi @vrkosk, Thanks for the suggestion! We will look into adding this in MS²PIP, so a monkey patch is not required and it simply is provided as an option. If...

Hi @JesusCastano01, You will indeed have to set one (or both) of those settings. Could you share the top of the MaxQuant msms.txt file and a section of an mzML...

Relevant documentation: https://ms2rescore.readthedocs.io/en/stable/userguide/configuration/#mapping-psms-to-spectra

Hi Frank, Thank you for your interest in MS²Rescore! Regarding your issue with MaxQuant, you are indeed right that we must receive a one-to-one relation between PSMs and spectra. In...

Hi Frank, Getting back to this thread, as we have now released MS²Rescore v3.1 with full support for DDA-PASEF data. There is an associated preprint on bioRxiv ([10.1101/2024.05.29.596400](https://doi.org/10.1101/2024.05.29.596400)). To your...

Hi Veit, Could you provide some more details on the errors that you are getting? You can always mail me the log. That might speed up the debugging. Note that...

Control of multi-rank PSM rescoring is now fully implemented in v3.1.0: https://ms2rescore.readthedocs.io/en/v3.1.0/userguide/configuration/#multi-rank-rescoring

@bittremieux, would you then propose a group system that looks like this: ``` . └── library (group) ├── spectrum_001 (group) ├── spectrum_002 (group) ├── ... └── spectrum_n (group) ├── intensity...

Thanks for the input! For future reference, here's the mz5 article: https://doi.org/10.1074/mcp.O111.011379