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Fix a bug in m/z calculation where the mass of the adduct was not being added to molecules described only as a mass with no chemical formula #3151

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Merged
merged 1 commit into from
Sep 10, 2024
Merged

Fix a bug in m/z calculation where the mass of the adduct was not being added to molecules described only as a mass with no chemical formula #3151

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12 changes: 11 additions & 1 deletion pwiz_tools/Skyline/Test/AdductTest.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -347,12 +347,22 @@ private static void CheckLabel(string label)
private void TestMassOnly(IEnumerable<string>[] adductLists)
{
var formula = @"[456.78]"; // Mass-only molecule description
var molecule = ParsedMolecule.Create(formula);
var massMolecule = molecule.MonoMassOffset;
AssertEx.AreEqual(456.78,massMolecule);
foreach (var adductList in adductLists)
{
foreach (var adductStr in adductList)
{
var adduct = Adduct.FromString(adductStr, Adduct.ADDUCT_TYPE.proteomic, null);
IonInfo.ApplyAdductToFormula(formula, adduct);
var ion = IonInfo.ApplyAdductToFormula(formula, adduct);
var massAdduct = adduct.MonoMassAdduct + adduct.IsotopesIncrementalMonoMass + massMolecule * (adduct.GetMassMultiplier()-1);
var massIon = BioMassCalc.MONOISOTOPIC.CalculateMass(ion);
if (!adduct.IsChargeOnly)
{
AssertEx.AreNotEqual(massIon, massMolecule, "adduct has no effect?");
}
AssertEx.AreEqual(massIon, massMolecule + massAdduct, .0001, $"ion {ion} mass {massIon} vs mol {molecule} mass + adduct {adduct} mass ({massMolecule}+{massAdduct}");
}
}
}
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62 changes: 30 additions & 32 deletions pwiz_tools/Skyline/Util/Adduct.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -70,11 +70,11 @@ public class Adduct : Immutable, IComparable, IEquatable<Adduct>, IAuditLogObjec
{
private Molecule Composition { get; set; } // The chemical makeup of the adduct - the "2H" part in 4M3Cl37+2H
private string Description { get; set; } // The text description (will be empty for protonation, we just use charge)
private TypedMass AverageMassAdduct { get; set; } // Average mass of the adduct itself - the "2H" in 4M3Cl37+2H
private TypedMass MonoMassAdduct { get; set; } // Monoisotopic mass of the adduct itself - the "2H" in 4M3Cl37+2H
public TypedMass AverageMassAdduct { get; private set; } // Average mass of the adduct itself - the "2H" in 4M3Cl37+2H
public TypedMass MonoMassAdduct { get; private set; } // Monoisotopic mass of the adduct itself - the "2H" in 4M3Cl37+2H
private int MassMultiplier { get; set; } // Returns, for example, the 2 in "[2M+Na]", which means the ion is two molecules + the adduct mass.
private TypedMass IsotopesIncrementalAverageMass { get; set; } // The incremental average mass due to (4*3) (Cl37 - Cl) in 4M3Cl37+2H
private TypedMass IsotopesIncrementalMonoMass { get; set; } // The incremental mono mass due to (4*3) (Cl37 - Cl) in 4M3Cl37+2H
public TypedMass IsotopesIncrementalAverageMass { get; private set; } // The incremental average mass due to (4*3) (Cl37 - Cl) in 4M3Cl37+2H
public TypedMass IsotopesIncrementalMonoMass { get; private set; } // The incremental mono mass due to (4*3) (Cl37 - Cl) in 4M3Cl37+2H

private int _hashCode; // We want comparisons to be on the same order as comparing ints, as when we used to just use integer charge instead of proper adducts

Expand Down Expand Up @@ -1368,44 +1368,42 @@ public ParsedMolecule ApplyToMolecule(ParsedMolecule molecule)

var resultDict = new Dictionary<string, int>(molecule.Molecule);

if (!molecule.IsMassOnly)
// Deal with any mass multiplier (the 2 in "[2M+Na]")
if (MassMultiplier != 1)
{
// Deal with any mass multiplier (the 2 in "[2M+Na]")
if (MassMultiplier != 1)
foreach (var element in resultDict.Keys.ToArray())
{
foreach (var element in resultDict.Keys.ToArray())
{
resultDict[element] *= MassMultiplier;
}
resultDict[element] *= MassMultiplier;
}
}

// Add in the "Na" of [M+Na] (or remove the 4H in [M-4H])
foreach (var pair in Composition)
// Add in the "Na" of [M+Na] (or remove the 4H in [M-4H])
foreach (var pair in Composition)
{
if (resultDict.TryGetValue(pair.Key, out var count))
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If you wanted, you could replace these 17 lines with:

                resultDict.TryGetValue(pair.Key, out var count);
                count += pair.Value;
                if (count == 0)
                {
                    resultDict.Remove(pair.Key);
                }
                else
                {
                    resultDict[pair.Key] = count;
                }

{
if (resultDict.TryGetValue(pair.Key, out var count))
{
count += pair.Value;
if (count == 0)
{
resultDict.Remove(pair.Key);
}
else
{
resultDict[pair.Key] = count;
}
}
else if (pair.Value != 0)
count += pair.Value;
if (count == 0)
{
resultDict.Add(pair.Key, pair.Value);
count = pair.Value;
resultDict.Remove(pair.Key);
}
if (count < 0 && !Equals(pair.Key, BioMassCalc.H)) // Treat H loss as a general proton loss
else
{
throw new InvalidDataException(
string.Format(Resources.Adduct_ApplyToMolecule_Adduct___0___calls_for_removing_more__1__atoms_than_are_found_in_the_molecule__2_,
this, pair.Key, molecule.ToString()));
resultDict[pair.Key] = count;
}
}
else if (pair.Value != 0)
{
resultDict.Add(pair.Key, pair.Value);
count = pair.Value;
}
if (!molecule.IsMassOnly &&
count < 0 && !Equals(pair.Key, BioMassCalc.H)) // Treat H loss as a general proton loss
{
throw new InvalidDataException(
string.Format(Resources.Adduct_ApplyToMolecule_Adduct___0___calls_for_removing_more__1__atoms_than_are_found_in_the_molecule__2_,
this, pair.Key, molecule.ToString()));
}
}

return ApplyIsotopeValues(molecule, MassMultiplier, resultDict);
Expand Down