public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
double massH,
TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLibInfo libInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
massH -= losses.Mass;
}
if (id.IsCustom())
{
Mz = new SignedMz(BioMassCalc.CalculateIonMz(massH, id.Charge), id.IsNegative());
}
else
{
Mz = new SignedMz(SequenceMassCalc.GetMZ(massH, id.Charge) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
}
IsotopeDistInfo = isotopeDistInfo;
LibInfo = libInfo;
Results = results;
}
private static string GetMzLabel(TransitionDocNode nodeTran)
{
int? massShift = nodeTran.Transition.DecoyMassShift;
double shift = SequenceMassCalc.GetPeptideInterval(massShift);
return(string.Format(@"{0:F04}{1}", nodeTran.Mz - shift,
Transition.GetDecoyText(massShift)));
}
private static string GetMzLabel(TransitionGroup tranGroup, double precursorMz)
{
int? massShift = tranGroup.DecoyMassShift;
double shift = SequenceMassCalc.GetPeptideInterval(massShift);
return(string.Format(@"{0:F04}{1}", precursorMz - shift,
Transition.GetDecoyText(massShift)));
}
public double GetMassI(int massIndex, int?decoyMassShift = null)
{
// Return the original monoisotopic mass + H, if requested to maintain an exact match.
if (massIndex == 0 && !decoyMassShift.HasValue)
{
return(_monoisotopicMass);
}
// Otherwize use the charge to convert from the peak center m/z values
double shift = SequenceMassCalc.GetPeptideInterval(decoyMassShift); // Correct for shift applied to the distribution
return(_isMassH ? SequenceMassCalc.GetMH(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge) : BioMassCalc.CalculateIonMassFromMz(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge));
}
public TypedMass GetMassI(int massIndex, int?decoyMassShift = null)
{
// Return the original monoisotopic mass + H, if requested to maintain an exact match.
if (massIndex == 0 && !decoyMassShift.HasValue)
{
return(_monoisotopicMass);
}
// Otherwize use the charge to convert from the peak center m/z values
double shift = SequenceMassCalc.GetPeptideInterval(decoyMassShift); // Correct for shift applied to the distribution
// ReSharper disable ImpureMethodCallOnReadonlyValueField
return(_monoisotopicMass.IsMassH() ?
new TypedMass(SequenceMassCalc.GetMH(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _adduct.AdductCharge), _monoisotopicMass.MassType) :
_adduct.MassFromMz(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _monoisotopicMass.MassType));
// ReSharper restore ImpureMethodCallOnReadonlyValueField
}
public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
TypedMass mass,
TransitionQuantInfo transitionQuantInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
mass -= losses.Mass;
}
Mz = id.IsCustom() ?
new SignedMz(id.Adduct.MzFromNeutralMass(mass), id.IsNegative()) :
new SignedMz(SequenceMassCalc.GetMZ(mass, id.Adduct) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
MzMassType = mass.MassType;
IsotopeDistInfo = transitionQuantInfo.IsotopeDistInfo;
LibInfo = transitionQuantInfo.LibInfo;
Results = results;
Quantitative = transitionQuantInfo.Quantititative;
}
private static void ValidateDecoys(SrmDocument document, SrmDocument decoysDoc, bool modifiesSequences)
{
AssertEx.IsDocumentState(decoysDoc, 1, document.PeptideGroupCount + 1, document.PeptideCount * 2,
document.PeptideTransitionGroupCount * 2, document.PeptideTransitionCount * 2);
// Check for the existence of the Decoys peptide group and that everything under it is marked as a decoy.
var nodePeptideGroupDecoy = decoysDoc.PeptideGroups.Single(nodePeptideGroup => nodePeptideGroup.IsDecoy);
var dictModsToPep = document.Peptides.ToDictionary(nodePep => nodePep.ModifiedSequence);
foreach (var nodePep in nodePeptideGroupDecoy.Peptides)
{
Assert.AreEqual(true, nodePep.IsDecoy);
PeptideDocNode nodePepSource = null;
if (!modifiesSequences)
{
Assert.IsNull(nodePep.SourceKey);
}
else
{
Assert.IsNotNull(nodePep.SourceKey, string.Format("Source key for {0}{1} is null", nodePep.ModifiedSequence,
nodePep.IsDecoy ? " - decoy" : string.Empty));
Assert.IsTrue(FastaSequence.IsExSequence(nodePep.SourceKey.Sequence));
Assert.AreEqual(nodePep.SourceKey.ModifiedSequence,
SequenceMassCalc.NormalizeModifiedSequence(nodePep.SourceKey.ModifiedSequence));
if (nodePep.HasExplicitMods)
{
Assert.IsNotNull(nodePep.SourceKey.ExplicitMods);
}
Assert.IsTrue(dictModsToPep.TryGetValue(nodePep.SourceTextId, out nodePepSource));
var sourceKey = new ModifiedSequenceMods(nodePepSource.Peptide.Sequence, nodePepSource.ExplicitMods);
Assert.AreEqual(sourceKey.ExplicitMods, nodePep.SourceExplicitMods);
}
for (int i = 0; i < nodePep.TransitionGroupCount; i++)
{
var nodeGroup = nodePep.TransitionGroups.ElementAt(i);
Assert.AreEqual(true, nodeGroup.IsDecoy);
TransitionGroupDocNode nodeGroupSource = null;
double shift = SequenceMassCalc.GetPeptideInterval(nodeGroup.TransitionGroup.DecoyMassShift);
if (nodePepSource != null && nodeGroup.TransitionGroup.DecoyMassShift.HasValue)
{
nodeGroupSource = nodePepSource.TransitionGroups.ElementAt(i);
Assert.AreEqual(nodeGroupSource.PrecursorMz + shift, nodeGroup.PrecursorMz, SequenceMassCalc.MassTolerance);
}
for (int j = 0; j < nodeGroup.TransitionCount; j++)
{
var nodeTran = nodeGroup.Transitions.ElementAt(j);
Assert.IsTrue(nodeTran.IsDecoy);
if (nodeTran.Transition.IsPrecursor())
{
Assert.AreEqual(nodeGroup.TransitionGroup.DecoyMassShift, nodeTran.Transition.DecoyMassShift);
if (nodeGroupSource != null)
{
Assert.AreEqual(nodeGroupSource.Transitions.ElementAt(j).Mz + shift, nodeTran.Mz, SequenceMassCalc.MassTolerance);
}
}
}
}
}
// Check that the resulting document persists correctly by passing the SrmDocument to AssertEx.IsSerializable().
AssertEx.Serializable(decoysDoc);
}