prot. Nter mod. not parsed for Alphapept

[mlocardpaulet]

Describe the bug
The variable modifications on N-ter of proteins is not parsed in AlphaPept. It is not in the parameters listed in the datapoint.

For now, we should at least write it down in the documentation so that this is clear to all.

it looks like this in the parameter file (acetylation):

mods_variable_terminal_prot:
  - a<^

I will merge the current data point and put here the hash it corresponds to. This way parameter file will be available.

[mlocardpaulet]

Here is the link to the data: https://proteobench.cubimed.rub.de/datasets/1bfa914c771321b285a9ca40d4aa538cb9fdc42e/

[mlocardpaulet]

I think that we should combine all modifications mentioned in the paramter file:

fasta:
  AL_swap: false
  KR_swap: false
  fasta_block: 1000
  fasta_size_max: 100
  isoforms_max: 1024
  mods_fixed:
  - cC
  mods_fixed_terminal: []
  mods_fixed_terminal_prot: []
  mods_variable:
  - oxM
  mods_variable_terminal: []
  mods_variable_terminal_prot:
  - a<^
  n_missed_cleavages: 2
  n_modifications_max: 3
  pep_length_max: 27
  pep_length_min: 7
  protease: trypsin
  pseudo_reverse: true
  save_db: true
  spectra_block: 100000

What do you think?

[enryH]

And how do you want to combine these? just as "oxM,a<^"?

[mlocardpaulet]

yes, I think that it would work. The only sure I am not sure is how to differentiate the Protein Nter and Peptide Nter... Maybe it is "<^" and "^"? 🤔

[mlocardpaulet]

So...
https://mannlabs.github.io/alphapept/settings.html
I think that the way they write the modifications are unique anyway. There is no acetylation of peptide N-terminus.
In this case, what you suggest is good. What do you think?
Another option would be "oxM, ac<^ (Protein N-ter)", and have the option "N-ter" for the modifications on peptide N-ter. What do you think?