/// <summary>
/// Compute the mass of the peptide sequence; uses the information in modifiedResidues() to determine modification masses
/// </summary>
/// <remarks>Looks for and removes prefix and suffix letters if .RemovePrefixAndSuffixIfPresent = True</remarks>
/// <param name="sequence">One letter amino acid symbols (no modification symbols or numbers)</param>
/// <param name="modifiedResidues">List of modified residues</param>
/// <returns>The computed mass, or -1 if an error</returns>
public double ComputeSequenceMass(string sequence, List <PeptideSequenceModInfo> modifiedResidues)
{
// Note that this call to ComputeSequenceMass will reset mErrorMessage
var mass = ComputeSequenceMass(sequence);
if (mass < 0 || modifiedResidues == null || modifiedResidues.Count == 0)
{
return(mass);
}
var empiricalFormula = new EmpiricalFormula();
foreach (var modifiedResidue in modifiedResidues)
{
// Note: do not use string.IsNullOrWhiteSpace(modifiedResidue.AffectedAtom) since that does not work on a char
if (modifiedResidue.AffectedAtom is default(char) or NO_AFFECTED_ATOM_SYMBOL)
{
// Positional modification (static or dynamic mod)
// Simply add the modification mass to mass
mass += modifiedResidue.ModificationMass;
continue;
}
// Isotopic modification
if (empiricalFormula.ElementCounts.Count == 0)
{
// Initialize empiricalFormula using the amino acid sequence
var empiricalFormulaToAdd = ConvertAminoAcidSequenceToEmpiricalFormula(sequence);
empiricalFormula.AddElements(empiricalFormulaToAdd);
}
if (!mElementMonoMasses.ContainsKey(modifiedResidue.AffectedAtom.ToString()))
{
ErrorMessage = "Unknown Affected Atom '" + modifiedResidue.AffectedAtom + "'";
mass = -1;
break;
}
var elementCount = empiricalFormula.GetElementCount(modifiedResidue.AffectedAtom);
if (elementCount == 0)
{
Console.WriteLine("Warning: no amino acids in {0} contain element {1}", sequence, modifiedResidue.AffectedAtom);
}
else
{
mass += elementCount * modifiedResidue.ModificationMass;
}
}
return(mass);
}
public void TestGetAminoAcidMass(char aminoAcidSymbol, double expectedMass)
{
var computedMass = mPeptideMassCalculator.GetAminoAcidMass(aminoAcidSymbol);
var empiricalFormula = new EmpiricalFormula();
empiricalFormula.AddElements(mPeptideMassCalculator.GetAminoAcidEmpiricalFormula(aminoAcidSymbol));
var computedMassAlt = PeptideMassCalculator.ComputeMonoisotopicMass(empiricalFormula);
Assert.AreEqual(expectedMass, computedMass, 0.0001, "Amino acid does not match the expected value");
Assert.AreEqual(computedMass, computedMassAlt, 1E-05, "GetAminoAcidMass and ComputeMonoisotopicMass do not agree on the mass for the amino acid");
}
/// <summary>
/// Compute the monoisotopic mass of the given empirical formula
/// </summary>
/// <remarks>Throws an exception if an unknown symbol is encountered</remarks>
/// <param name="empiricalFormula"></param>
public static double ComputeMonoisotopicMass(EmpiricalFormula empiricalFormula)
{
double monoisotopicMass = 0;
foreach (var element in empiricalFormula.ElementCounts)
{
if (mElementMonoMasses.TryGetValue(element.Key, out var elementMass))
{
monoisotopicMass += element.Value * elementMass;
}
else
{
throw new Exception("Unrecognized symbol " + element.Key);
}
}
return(monoisotopicMass);
}
