Pre-trained MS2/RT/CCS models

Change log:

[2025-05-01]

• Add the default charge model weights for ChargeModelForModAASeq with a unified prediction head.

[2025-03-26]

• Updated the MS2 pretraining weights to include the charged fragment types used during training in the ms2.pth file.
• Added pretrained weights for the generic charge model.

[2024-06-29]

• Add the pretrained LSTM-based HLA-I model (hla_model.zip) for peptide binding prediciton.

[2022-11-28]

• For timsTOF data, fragment intensities for training are no longer extracted from MaxQuant's msms.txt. We extracted fragments of AlphaPept PSMs against the ms_data.hdf, this should be more stable than msms.txt for timsTOF. The previous model is still available on https://datashare.biochem.mpg.de/s/RDSZlAnCRvxfLfk.