RobbinBouwmeester

Sounds interesting! I can provide support for the DeepLC side. @vdemichev can you indicate what you would need for integration?

@KlemensFroehlich @lazear , could this repo be useful? [https://github.com/mafreitas/tdf2mzml](https://github.com/mafreitas/tdf2mzml), in the description they claim to have support for DIA bruker data (and based on a closed discussion/issue on that repo...

Indeed, adding information about the raw file would be useful, but here multiple raw files can be associated to a single peptide. Since there are aligned to each other as...

Hi, there have been some significant updates lately. Can you confirm for the latest versions this is still an issue.

I see, this warning is indeed shown for isotopes. It will still count the atom, but not as an isotope (as far as I know for N and C this...

Indeed is the only difference is a heavier isotope the predictions will be the same. While in most cases this is correct, for example in the case of deuterium it...

Warnings should only be logged once now in v3.1.7

Hi, Yes, msv000088167 has been published: [https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=2f82c5f336a441d7a7aee378d84f7a58](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=2f82c5f336a441d7a7aee378d84f7a58) With regards to the other models, these were mostly trained on internal data. I did make the models public, as they could be...

Actually the documentation is out of data here. It currently uses: https://github.com/compomics/psm_utils Where most of the parsing (as far as I know) of the modifications is done with pyteomics. When...

Will update the documentation soon.