public static Modification MakeModification(string unmodifiedSequence, ExplicitMod explicitMod)
{
var staticMod = explicitMod.Modification;
int i = explicitMod.IndexAA;
var monoMass = staticMod.MonoisotopicMass ??
SrmSettings.MonoisotopicMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
var avgMass = staticMod.AverageMass ??
SrmSettings.AverageMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
if (monoMass == 0 && avgMass == 0)
{
char aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
string heavyFormula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, heavyFormula,
SequenceMassCalc.MassPrecision);
avgMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, heavyFormula,
SequenceMassCalc.MassPrecision);
}
}
return(new Modification(explicitMod, monoMass, avgMass));
}
public void TestGetHeavyFormula()
{
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("CO2", LabelAtoms.C13));
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("C'O2", LabelAtoms.C13));
Assert.AreEqual("C'", SequenceMassCalc.GetHeavyFormula("C", LabelAtoms.C13));
Assert.AreEqual("N'", SequenceMassCalc.GetHeavyFormula("N", LabelAtoms.N15));
Assert.AreEqual("O'", SequenceMassCalc.GetHeavyFormula("O", LabelAtoms.O18));
Assert.AreEqual("H'", SequenceMassCalc.GetHeavyFormula("H", LabelAtoms.H2));
Assert.AreEqual("Cl'", SequenceMassCalc.GetHeavyFormula("Cl", LabelAtoms.Cl37));
Assert.AreEqual("Br'", SequenceMassCalc.GetHeavyFormula("Br", LabelAtoms.Br81));
Assert.AreEqual("P'", SequenceMassCalc.GetHeavyFormula("P", LabelAtoms.P32));
Assert.AreEqual("S\"", SequenceMassCalc.GetHeavyFormula("S", LabelAtoms.S33));
Assert.AreEqual("S'", SequenceMassCalc.GetHeavyFormula("S", LabelAtoms.S34));
}
public void TestGetHeavyFormula()
{
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("CO2", LabelAtoms.C13));
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("C'O2", LabelAtoms.C13));
Assert.AreEqual("C'", SequenceMassCalc.GetHeavyFormula("C", LabelAtoms.C13));
Assert.AreEqual("N'", SequenceMassCalc.GetHeavyFormula("N", LabelAtoms.N15));
Assert.AreEqual("O'", SequenceMassCalc.GetHeavyFormula("O", LabelAtoms.O18));
Assert.AreEqual("H'", SequenceMassCalc.GetHeavyFormula("H", LabelAtoms.H2));
Assert.AreEqual("Cl'", SequenceMassCalc.GetHeavyFormula("Cl", LabelAtoms.Cl37));
Assert.AreEqual("Br'", SequenceMassCalc.GetHeavyFormula("Br", LabelAtoms.Br81));
Assert.AreEqual("P'", SequenceMassCalc.GetHeavyFormula("P", LabelAtoms.P32));
Assert.AreEqual("S'", SequenceMassCalc.GetHeavyFormula("S", LabelAtoms.S34));
// Make sure IUPAC nicknames don't find their way into our list of heavy symbols
Assume.IsTrue(BioMassCalc.IsSkylineHeavySymbol("H'"));
Assume.IsFalse(BioMassCalc.IsSkylineHeavySymbol("D"));
Assume.IsFalse(BioMassCalc.IsSkylineHeavySymbol("T"));
}
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));
}
private void UpdateMasses()
{
string formula = null;
LabelAtoms labelAtoms = LabelAtoms.None;
if (cbChemicalFormula.Checked)
{
formula = Formula;
}
else
{
labelAtoms = LabelAtoms;
string aaString = comboAA.Text;
if (!string.IsNullOrEmpty(aaString) && aaString.Length == 1 &&
AminoAcid.IsAA(aaString[0]) && labelAtoms != LabelAtoms.None)
{
formula = SequenceMassCalc.GetHeavyFormula(aaString[0], labelAtoms);
}
}
if (string.IsNullOrEmpty(formula))
{
// If the mass edit boxes are already enabled, don't clear what a user
// may have typed in them.
if (!_formulaBox.MassEnabled)
{
_formulaBox.MonoMass = null;
_formulaBox.AverageMass = null;
}
_formulaBox.MassEnabled = (labelAtoms == LabelAtoms.None);
}
else
{
_formulaBox.Formula = formula;
}
}
public const string UnimodPrefix = "unimod:"; // Not L10N
/// <summary>
/// Constructs a ModifiedSequence from SrmSettings and PeptideDocNode.
/// </summary>
public static ModifiedSequence GetModifiedSequence(SrmSettings settings, PeptideDocNode docNode, IsotopeLabelType labelType)
{
if (docNode.Peptide.IsCustomMolecule)
{
return(null);
}
var unmodifiedSequence = docNode.Peptide.Sequence;
bool includeStaticMods = true;
bool includeStaticHeavyMods = false;
List <Modification> explicitMods = new List <Modification>();
if (null != docNode.ExplicitMods)
{
var staticBaseMods = docNode.ExplicitMods.GetStaticBaseMods(labelType);
var labelMods = docNode.ExplicitMods.GetModifications(labelType);
var explicitLabelType = labelType;
if (labelMods == null && !labelType.IsLight)
{
labelMods = docNode.ExplicitMods.GetModifications(IsotopeLabelType.light);
explicitLabelType = IsotopeLabelType.light;
includeStaticHeavyMods = true;
}
if (labelMods != null || staticBaseMods != null)
{
IEnumerable <ExplicitMod> modsToAdd = (labelMods ?? Enumerable.Empty <ExplicitMod>())
.Concat(staticBaseMods ?? Enumerable.Empty <ExplicitMod>());
var monoMasses = docNode.ExplicitMods.GetModMasses(MassType.Monoisotopic, explicitLabelType);
var avgMasses = docNode.ExplicitMods.GetModMasses(MassType.Average, explicitLabelType);
foreach (var mod in modsToAdd)
{
explicitMods.Add(new Modification(mod, monoMasses[mod.IndexAA], avgMasses[mod.IndexAA]));
}
includeStaticMods = docNode.ExplicitMods.IsVariableStaticMods && staticBaseMods == null;
}
}
if (includeStaticMods || includeStaticHeavyMods)
{
var peptideModifications = settings.PeptideSettings.Modifications;
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
IEnumerable <StaticMod> staticMods = peptideModifications.GetModifications(labelType);
if (!labelType.IsLight && includeStaticMods)
{
staticMods = peptideModifications.GetModifications(IsotopeLabelType.light).Concat(staticMods);
}
foreach (var staticMod in staticMods)
{
if (staticMod.IsExplicit || staticMod.IsVariable)
{
continue;
}
if (staticMod.Terminus.HasValue)
{
if (staticMod.Terminus == ModTerminus.N && i != 0)
{
continue;
}
if (staticMod.Terminus == ModTerminus.C && i != unmodifiedSequence.Length - 1)
{
continue;
}
}
if (!string.IsNullOrEmpty(staticMod.AAs) && !staticMod.AAs.Contains(unmodifiedSequence[i]))
{
continue;
}
var monoMass = staticMod.MonoisotopicMass ??
SrmSettings.MonoisotopicMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
var avgMass = staticMod.AverageMass ??
SrmSettings.AverageMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
if (monoMass == 0 && avgMass == 0)
{
char aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
string heavyFormula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, heavyFormula,
SequenceMassCalc.MassPrecision);
avgMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, heavyFormula,
SequenceMassCalc.MassPrecision);
}
}
explicitMods.Add(new Modification(new ExplicitMod(i, staticMod), monoMass, avgMass));
}
}
}
return(new ModifiedSequence(unmodifiedSequence, explicitMods, settings.TransitionSettings.Prediction.PrecursorMassType));
}