Ralf Gabriels

Hi @JB91451, Thanks for testing and reporting back! The `generated new fontManager` message could indicate an issue with matplotlib. Is the Windows server a headless environment with only the CLI...

Hi Juergen, There has been some additional refactoring for library generation in MS²PIP [v4.0.0](https://github.com/compomics/ms2pip/releases/tag/v4.0.0). The same functionality can now be called with [`ms2pip predict-library`](https://ms2pip.readthedocs.io/en/v4.0.0/usage/#predict-library), with a slightly modified [JSON config...

Hi Marc, Thanks for sharing your input files! There is indeed a problem in MS²PIP where, while predicting a large amount (>200 000) of spectra, it takes a disproportionate amount...

Hi Jannik, Depending on your use case, it might be better to try out v4.0 of MS²PIP, which is currently in 'dev' releases. This version uses compomics/psm_utils to read the...

Hi @lazear, I was wondering if anyone has started working on implementing database splitting into Sage itself. If not, we might take a look at it. Best, Ralf

Issue was caused by a change from Scipy 1.12 to 1.13 and PyInstaller not being updated yet. A fix should be included in the next PyInstaller release (https://github.com/pyinstaller/pyinstaller/commit/5fe069177c9fda8ae7e362cdaa5b39c5b64fe4f5).

Hi Jesus, Most likely it is a file encoding issue. Could you open the MaxQuant file in an editor such as notepad, notepad++, or vscode and save it with `utf-8`...

Hi @JesusCastano01, The pickling issue should be fixed in the Windows desktop installer for v3.0.3. Best, Ralf

Hi, @vrkosk, Thanks for reporting! We will look into this. Best, Ralf

For internal reference: `_psm_list_to_deeplc_peprec()` has already been removed in the `timsRescore` branch in favor of sending the PSMList directly to DeepLC. However, we should still look into how this behaves...