Fix chloride adduct mass

Author: joewandy

tests/test_deisotoping.py

@@ -59,6 +59,15 @@ def test_isotope_distribution_chlorine_m2_peak():
     assert any(np.isclose(delta, 1.997, atol=0.01) for delta in deltas)
 
 
+def test_adduct_terms_chloride_uses_chloride_anion_mass():
+    # [M+Cl]- uses Cl- (atomic mass + electron mass), not neutral Cl.
+    from vimms.Common import ELECTRON_MASS, NATURAL_ISOTOPES
+
+    _, cl_shift = ADDUCT_TERMS["M+Cl"]
+    cl_atomic = NATURAL_ISOTOPES["Cl"][0][0]
+    assert np.isclose(cl_shift - cl_atomic, ELECTRON_MASS, atol=1e-12)
+
+
 def test_isotope_distribution_preserves_mono_when_filtered():
     formula = Formula("C500H1000")
     isotopes = Isotopes(formula)

vimms/Common.py

@@ -72,6 +72,7 @@
 DEFAULT_SOURCE_CID_ENERGY = 0
 
 PROTON_MASS = 1.00727645199076
+ELECTRON_MASS = 0.000548579909065  # u
 
 CHROM_TYPE_EMPIRICAL = "empirical"
 CHROM_TYPE_CONSTANT = "constant"
@@ -110,7 +111,8 @@
     "2M+H": (2, 1.007276),
     "2M+NH4": (2, 18),
     "M-H": (1, -PROTON_MASS),
-    "M+Cl": (1, 34.96885268),
+    # [M+Cl]- adds Cl- (atomic mass + electron mass), not neutral Cl.
+    "M+Cl": (1, 34.96885268 + ELECTRON_MASS),
     "M+FA-H": (1, 44.998201),
     "M+Ac-H": (1, 59.013851),
 }

vimms/Deisotoping.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-from vimms.Common import C13_MZ_DIFF, NATURAL_ISOTOPES
+from vimms.Common import C13_MZ_DIFF, NATURAL_ISOTOPES, ELECTRON_MASS
 
 
 @dataclass(frozen=True)
@@ -328,7 +328,7 @@ def deadduct_with_pyopenms(
     # while MS m/z shifts correspond to charged species (atomic +/- e- mass).
     # Correcting by the electron mass ensures we recover a chemically-sensible
     # neutral mass from observed m/z values.
-    electron_mass = 0.000548579909065  # u
+    electron_mass = ELECTRON_MASS
 
     def infer_negative_mode() -> bool:
         charges = []