How to configure support for selenocysteine in its carbamidomethylated form? about deeplc

[RobbinBouwmeester]

Dear Karl,

Currently this is unsupported, the issue would (I think) also be to get sufficient examples with Se.

If you want to add Se to the elements it would probably be easiest to adjust the code in the retrainer (https://github.com/RobbinBouwmeester/DeepLCRetrainer/tree/main/deeplcretrainer). I can give you some pointers there if you would like to make changes there. It might not be the best time investment though due to a small number of examples with Se.

What I will do is catch error that is not going to end the execution of DeepLC when an amino acid contains Se. This is already done for modifications, but not for amino acids (with or without modifications).

Kind regards,

Robbin

[KarlClauser]

I think catching the error is the only practical solution. I have only the one U containing peptide so far from immunopeptidomics work. There are a few more in tryptic proteome datasets. I'll check on how close the RT predictions are with Cys virtual substitution. I expect they will typically be outliers.