search

MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
105 stars 20 forks source link

how to know syntax for modifcations other than phophorylation and oxidation? #77

Closed gsaxena888 closed 1 year ago

gsaxena888 commented 1 year ago

If I want to create a library with less common modifications (eg acetylation, methylation, citrulination etc.), is there some documentation or file which indicates which modifications are supported and their syntax?

jalew188 commented 1 year ago

We used the syntax mod_name@site. The modification names and sites are from UniMod, such as Dimethyl@Any N-term, GG@K, Acetyl@Protein N-term, ... Check https://github.com/MannLabs/alphabase/blob/main/alphabase/constants/const_files/modification.tsv.

If you have modifications those are not in UniMod, you can easily add them into AlphaBase/PeptDeep, check https://github.com/MannLabs/alphapeptdeep/blob/main/peptdeep/constants/default_settings.yaml#L41

jalew188 commented 1 year ago

You can also easily add non-UniMod modifications from the GUI. We will make it easier in v1.0.0