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fix(validate): escape regex quantifiers in Sage sequence parsing #392

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theGreatHerrLebert merged 1 commit into from
Feb 18, 2026
Merged

fix(validate): escape regex quantifiers in Sage sequence parsing #392

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14 changes: 8 additions & 6 deletions packages/imspy-simulation/src/imspy_simulation/timsim/validate/parsing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -443,13 +443,15 @@ def format_sage_sequence(peptide: str) -> str:
The formatted peptide sequence with UNIMOD annotations.
"""
# Common Sage mass-to-UNIMOD mappings
# NOTE: The +/- signs inside brackets must be escaped (\+ / \-)
# otherwise '+' acts as a regex quantifier on '['
mass_replacements = [
(r"\[+57\.0214\d*\]", "[UNIMOD:4]"), # Carbamidomethyl (C)
(r"\[+15\.9949\d*\]", "[UNIMOD:35]"), # Oxidation (M)
(r"\[+42\.0106\d*\]", "[UNIMOD:1]"), # Acetyl (Protein N-term)
(r"\[+79\.9663\d*\]", "[UNIMOD:21]"), # Phospho (STY)
(r"\[-17\.0265\d*\]", "[UNIMOD:385]"), # Ammonia loss (N-term Q)
(r"\[-18\.0106\d*\]", "[UNIMOD:23]"), # Water loss (N-term E)
(r"\[\+57\.0214\d*\]", "[UNIMOD:4]"), # Carbamidomethyl (C) 57.021464
(r"\[\+15\.9949\d*\]", "[UNIMOD:35]"), # Oxidation (M) 15.994915
(r"\[\+42\.0105\d*\]", "[UNIMOD:1]"), # Acetyl (Protein N-term) 42.010565
(r"\[\+79\.9663\d*\]", "[UNIMOD:21]"), # Phospho (STY) 79.966331
(r"\[\-17\.0265\d*\]", "[UNIMOD:385]"), # Ammonia loss (N-term Q) -17.026549
(r"\[\-18\.0105\d*\]", "[UNIMOD:23]"), # Water loss (N-term E) -18.010565
]

result = peptide
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