public static TypedMass GetFragmentMassFromFormula(SrmSettings settings, MoleculeMassOffset formula)
{
var fragmentedMoleculeSettings = FragmentedMolecule.Settings.FromSrmSettings(settings);
MassType massType = settings.TransitionSettings.Prediction.FragmentMassType;
if (massType.IsMonoisotopic())
{
return(new TypedMass(fragmentedMoleculeSettings.GetMonoMass(formula.Molecule) + formula.MonoMassOffset + BioMassCalc.MassProton, MassType.MonoisotopicMassH));
}
else
{
return(new TypedMass(fragmentedMoleculeSettings.GetAverageMass(formula.Molecule) + formula.AverageMassOffset + BioMassCalc.MassProton, MassType.AverageMassH));
}
}
public TypedMass GetPrecursorMass(MassType massType)
{
var formula = GetPrecursorFormula();
var fragmentedMoleculeSettings = GetFragmentedMoleculeSettings();
double mass = massType.IsMonoisotopic()
? fragmentedMoleculeSettings.GetMonoMass(formula)
: fragmentedMoleculeSettings.GetAverageMass(formula);
if (massType.IsMassH())
{
mass += BioMassCalc.MassProton;
}
return(new TypedMass(mass, massType));
}
public static Molecule AddFragmentLosses(Molecule molecule, IList <FragmentLoss> fragmentLosses,
MassType massType, ref double unexplainedMass)
{
MoleculeMassOffset moleculeMassOffset = new MoleculeMassOffset(molecule, unexplainedMass, unexplainedMass);
foreach (var fragmentLoss in fragmentLosses)
{
moleculeMassOffset = moleculeMassOffset.Minus(ToMoleculeMassOffset(fragmentLoss));
}
if (massType.IsMonoisotopic())
{
unexplainedMass = moleculeMassOffset.MonoMassOffset;
}
else
{
unexplainedMass = moleculeMassOffset.AverageMassOffset;
}
return(moleculeMassOffset.Molecule);
}
private static Molecule GetSequenceFormula(ModifiedSequence modifiedSequence, MassType massType, out double unexplainedMassShift)
{
unexplainedMassShift = 0;
var molecule = new Dictionary <string, int>();
string unmodifiedSequence = modifiedSequence.GetUnmodifiedSequence();
var modifications = modifiedSequence.GetModifications().ToLookup(mod => mod.IndexAA);
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
char aminoAcid = unmodifiedSequence[i];
AddAminoAcidFormula(massType, aminoAcid, molecule, ref unexplainedMassShift);
foreach (var mod in modifications[i])
{
string formula = mod.Formula;
if (formula == null)
{
var staticMod = mod.StaticMod;
var aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
formula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
}
}
if (formula != null)
{
var modFormula = Molecule.ParseExpression(formula);
Add(molecule, modFormula);
}
else
{
unexplainedMassShift += massType.IsMonoisotopic() ? mod.MonoisotopicMass : mod.AverageMass;
}
}
}
return(Molecule.FromDict(molecule));
}
public double GetMass(MassType massType)
{
return(massType.IsMonoisotopic() ? MonoisotopicMass : AverageMass);
}
public bool IsMonoIsotopic()
{
return(_massType.IsMonoisotopic());
}
