Ralf Gabriels

Hi @thulasis, Thanks for using MS²Rescore! It seems that there is an issue while parsing one of the amino acid modifications from the mzIdentML file from MS-GF+. Could you share...

Regarding the documentation, do let us know which parts of using MS²Rescore or from the documentation were unclear to you. We are always looking to improve user experiences.

Hi @mencian, It seems like the build test fails with a `No space left on device` error. Any idea how to fix this? Thanks!

Agreed that this could be reported somehow. The main issue blocking this is that the (output) object in MS²Rescore is the PSM list, which has only PSM-level entries. Would you...

Hi Nicolas, Apologies in the delay in getting back to you. Your issue seems to be a combination of 2 problems: - We have yet to update the DeepLC integration...

Picking up on this issue again. Apologies for the long delay. @RobbinBouwmeester, any ideas? @NicolasProvencher, could you check if updating DeepLC fixes the issue (`pip install -U deeplc`). Thanks!

Hi @NicolasProvencher, Thanks for reporting! I opened a new issue here: #145 Best, Ralf

This looks great! - Modifications: Perhaps the amino acid letters could be colored to indicate a modification, potentially using different colors for different modifications? - Other ion types: I think...

> Currently I provide additional parameters to the plot method to add the peptide sequence to an existing Axes/spectrum plot. Alternatively I could piggyback on the facet plot introduced in...

May be of interest for this thread: As part of [compomics/ms2rescore](https://github.com/compomics/ms2rescore), Mokapot is also packaged into the executable with a one-click installer. For this we use: - A [PyInstaller spec](https://github.com/compomics/ms2rescore/blob/main/ms2rescore.spec)...