Keep FASTA information

[SSPuliasis]

I want to convert the predicted HLA peptides into a speclib with peptdeep & run it in DIA-NN. Is there an option to include the protein name/ FASTA header in the output when doing this?

[jalew188]

We have integrated hla module into peptdeep, please check https://github.com/MannLabs/alphapeptdeep/blob/main/docs/tutorials/tutorial_immunopeptidomics.ipynb for the protein mapping