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Show unknown modifications as delta mass in peptidoform #126

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Show unknown modifications as delta mass in peptidoform #126

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12 changes: 10 additions & 2 deletions psm_utils/io/mzid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

from psm_utils import __version__
from psm_utils.io._base_classes import ReaderBase, WriterBase
from psm_utils.io.exceptions import PSMUtilsIOException
from psm_utils.io.exceptions import PSMUtilsIOException, ModificationException
from psm_utils.peptidoform import Peptidoform
from psm_utils.psm import PSM
from psm_utils.psm_list import PSMList
Expand Down Expand Up @@ -189,7 +189,15 @@ def _parse_peptidoform(seq: str, modification_list: list[dict], charge: Union[in

# Add modification labels
for mod in modification_list:
peptide[int(mod["location"])] += f"[{mod['name']}]"
name = mod.get("name")
if name and name != "unknown modification":
tag = f"[{mod['name']}]"
elif "monoisotopicMassDelta" in mod:
s = mod["monoisotopicMassDelta"]
tag = f"[{s:+.5f}]"
else:
raise ModificationException(f"Not enough information about modification: {mod}")
peptide[int(mod["location"])] += tag

# Add dashes between residues and termini, and join sequence
peptide[0] = peptide[0] + "-" if peptide[0] else ""
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