Note that supporting this type of modification is somewhat tricky because in the situation where a peptide occurs more than once in the database, in both terminal and non-terminal locations. When it comes time to print the PSM, if it contains a protein terminal modification, the code should check the list of flanking amino acids and skip printing flanks (and corresponding protein IDs) if there is not a hyphen in the right place.
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There should be a strategy developed for the decoy generation, when the decoy protein cannot be assembled, for example when missed cleavages or partial digestions is used.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Note that supporting this type of modification is somewhat tricky because in the situation where a peptide occurs more than once in the database, in both terminal and non-terminal locations. When it comes time to print the PSM, if it contains a protein terminal modification, the code should check the list of flanking amino acids and skip printing flanks (and corresponding protein IDs) if there is not a hyphen in the right place.
There should be a strategy developed for the decoy generation, when the decoy protein cannot be assembled, for example when missed cleavages or partial digestions is used.
Perhaps during decoy generation, we can allow a terminal modification if and only if the corresponding target allows a terminal modification.
Check what comet does and report back. We may decide not to bother.