diff --git a/spectrum_utils/proforma.py b/spectrum_utils/proforma.py index 60ef321..2c15fe4 100644 --- a/spectrum_utils/proforma.py +++ b/spectrum_utils/proforma.py @@ -674,7 +674,9 @@ def parse(proforma: str) -> List[Proteoform]: charge = match_unmod.group(2) if charge is not None: charge = Charge(int(charge[1:])) - return [Proteoform(sequence=match_unmod.group(1), charge=charge)] + return [ + Proteoform(sequence=match_unmod.group(1).upper(), charge=charge) + ] parser = _build_parser() # noinspection PyUnresolvedReferences @@ -806,7 +808,9 @@ def _import_cv( for synonym in term.get("synonym", []): cv[synonym] = mass # Save to the cache if enabled. - _store_in_cache(cache, f"{cv_id}.pkl", (cv, datetime.datetime.utcnow())) + _store_in_cache( + cache, f"{cv_id}.pkl", (cv, datetime.datetime.now(datetime.UTC)) + ) return cv