Closed RalfG closed 1 year ago
Hi @mobiusklein,
I noticed an issue in parsing proforma sequences with modifications on both the final amino acid and the C-terminus:
>>> from pyteomics import proforma >>> proforma.parse("[iTRAQ4plex]-EM[U:Oxidation]EVNES[Phospho]PEK[iTRAQ4plex]-[Methyl]") ([('E', None), ('M', [UnimodModification('Oxidation', None, None)]), ('E', None), ('V', None), ('N', None), ('E', None), ('S', [GenericModification('Phospho', None, None)]), ('P', None), ('E', None), ('K', None)], {'n_term': [GenericModification('iTRAQ4plex', None, None)], 'c_term': [GenericModification('iTRAQ4plexMethyl', None, None)], 'unlocalized_modifications': [], 'labile_modifications': [], 'fixed_modifications': [], 'intervals': [], 'isotopes': [], 'group_ids': [], 'charge_state': None})
Both modifications (iTRAQ4plex and Methyl) get parsed as a single C-terminal modification iTRAQ4plexMethyl.
iTRAQ4plex
Methyl
iTRAQ4plexMethyl
I tried looking into the parser function, but it seems pretty complex. Maybe you can find the issue more quickly? Thanks in advance!
Hi @mobiusklein,
I noticed an issue in parsing proforma sequences with modifications on both the final amino acid and the C-terminus:
Both modifications (
iTRAQ4plex
andMethyl
) get parsed as a single C-terminal modificationiTRAQ4plexMethyl
.I tried looking into the parser function, but it seems pretty complex. Maybe you can find the issue more quickly? Thanks in advance!