private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Adduct,
decoyMassShift,
transition.CustomIon ?? CustomMolecule); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
TypedMass massH;
var massType = calc.MassType;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(massType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, new TransitionDocNode.TransitionQuantInfo(isotopeDistInfo, libInfo, nodeTran.IsQuantitative(settings)), nodeTran.ExplicitValues);
return(nodeTranMatching);
}
private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Charge,
decoyMassShift,
transition.CustomIon ?? CustomIon); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
double massH;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(settings.TransitionSettings.Prediction.FragmentMassType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, isotopeDistInfo, libInfo);
return(nodeTranMatching);
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
if (nodeGroup.TransitionGroup.IsCustomIon) // TODO(bspratt) this seems to leave out a lot of detail
{
var customTable = new TableDesc();
using (RenderTools rt = new RenderTools())
{
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodeGroup.CustomMolecule.Name, rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
nodeGroup.TransitionGroup.PrecursorAdduct.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", nodeGroup.PrecursorMz), rt);
if (nodeGroup.CustomMolecule.Formula != null)
{
customTable.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula,
nodeGroup.CustomMolecule.Formula + nodeGroup.TransitionGroup.PrecursorAdduct.AdductFormula.ToString(LocalizationHelper.CurrentCulture), rt);
}
SizeF size = customTable.CalcDimensions(g);
customTable.Draw(g);
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
ExplicitMods mods = (nodePep != null ? nodePep.ExplicitMods : null);
IEnumerable <DocNode> choices = nodeGroup.GetPrecursorChoices(settings, mods, true).ToArray();
HashSet <DocNode> chosen = new HashSet <DocNode>(nodeGroup.Children);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(choices);
setChoices.UnionWith(chosen);
choices = setChoices.ToArray();
Transition tranSelected = (nodeTranSelected != null ? nodeTranSelected.Transition : null);
IFragmentMassCalc calc = settings.GetFragmentCalc(nodeGroup.TransitionGroup.LabelType, mods);
var aa = nodeGroup.TransitionGroup.Peptide.Target.Sequence; // We handled custom ions above, and returned
var masses = calc.GetFragmentIonMasses(nodeGroup.TransitionGroup.Peptide.Target);
var filter = settings.TransitionSettings.Filter;
// Get charges and type pairs, making sure all chosen charges are included
var setCharges = new HashSet <Adduct>(filter.PeptideProductCharges.Where(charge =>
Math.Abs(charge.AdductCharge) <= Math.Abs(nodeGroup.TransitionGroup.PrecursorCharge) &&
Math.Sign(charge.AdductCharge) == Math.Sign(nodeGroup.TransitionGroup.PrecursorCharge)));
HashSet <IonType> setTypes = new HashSet <IonType>(filter.PeptideIonTypes);
foreach (TransitionDocNode nodTran in chosen)
{
var type = nodTran.Transition.IonType;
if (!Transition.IsPeptideFragment(type))
{
continue;
}
setCharges.Add(nodTran.Transition.Adduct);
setTypes.Add(type);
}
setTypes.RemoveWhere(t => !Transition.IsPeptideFragment(t));
var charges = setCharges.Where(c => c.IsProteomic).ToArray();
Array.Sort(charges);
IonType[] types = Transition.GetTypePairs(setTypes);
var tableDetails = new TableDesc();
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
var seqModified = GetModifiedSequence(nodePep, nodeGroup, settings);
if (!Equals(seqModified, nodeGroup.TransitionGroup.Peptide.Target))
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Modified, seqModified.Sequence, rt);
}
var precursorCharge = nodeGroup.TransitionGroup.PrecursorAdduct;
var precursorMz = nodeGroup.PrecursorMz;
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
precursorCharge.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", precursorMz), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mh,
string.Format(@"{0:F04}", nodeGroup.GetPrecursorIonMass()),
rt);
int?decoyMassShift = nodeGroup.TransitionGroup.DecoyMassShift;
if (decoyMassShift.HasValue)
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Decoy_Mass_Shift,
decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeGroup.HasLibInfo)
{
foreach (KeyValuePair <PeptideRankId, string> pair in nodeGroup.LibInfo.RankValues)
{
tableDetails.AddDetailRow(pair.Key.Label, pair.Value, rt);
}
}
if (charges.Length > 0 && types.Length > 0)
{
var headers = new RowDesc
{
CreateHead(@"#", rt),
CreateHead(@"AA", rt),
CreateHead(@"#", rt)
};
foreach (var charge in charges)
{
string plusSub = Transition.GetChargeIndicator(charge);
foreach (IonType type in types)
{
CellDesc cell = CreateHead(type.ToString().ToLower() + plusSub, rt);
if (Transition.IsNTerminal(type))
{
headers.Insert(0, cell);
}
else
{
headers.Add(cell);
}
}
}
table.Add(headers);
int len = aa.Length;
for (int i = 0; i < len; i++)
{
CellDesc cellAA = CreateRowLabel(aa.Substring(i, 1), rt);
cellAA.Align = StringAlignment.Center;
var row = new RowDesc
{
CreateRowLabel(i == len - 1 ? string.Empty : (i + 1).ToString(CultureInfo.InvariantCulture), rt),
cellAA,
CreateRowLabel(i == 0 ? string.Empty : (len - i).ToString(CultureInfo.InvariantCulture), rt)
};
foreach (var charge in charges)
{
foreach (IonType type in types)
{
CellDesc cell;
if (Transition.IsNTerminal(type))
{
if (i == len - 1)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i];
cell = CreateIon(type, i + 1, massH, charge, choices, chosen, tranSelected, rt);
}
row.Insert(0, cell);
}
else
{
if (i == 0)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i - 1];
cell = CreateIon(type, len - i, massH, charge, choices, chosen, tranSelected, rt);
}
row.Add(cell);
}
}
}
table.Add(row);
}
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
SizeF size = table.CalcDimensions(g);
if (draw)
{
tableDetails.Draw(g);
g.TranslateTransform(0, sizeDetails.Height);
table.Draw(g);
g.TranslateTransform(0, -sizeDetails.Height);
}
int width = (int)Math.Round(Math.Max(sizeDetails.Width, size.Width));
int height = (int)Math.Round(sizeDetails.Height + size.Height);
return(new Size(width + 2, height + 2));
}
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcFilterPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
if (IsCustomIon)
{
var ionMz =
BioMassCalc.CalculateIonMz(
CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType),
PrecursorCharge);
if (!useFilter ||
!libraryFilter ||
IsMatched(transitionRanks,
ionMz, IonType.precursor,
PrecursorCharge, null))
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i);
ionMz = BioMassCalc.CalculateIonMz(precursorMS1Mass, PrecursorCharge);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks, CustomIon));
}
}
else
{
var transition = new Transition(this, PrecursorCharge, null, CustomIon, IonType.precursor);
double massH = CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType);
yield return(new TransitionDocNode(transition, null, massH, null, null));
}
}
yield break;
}
string sequence = Peptide.Sequence;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
tranSettings.Filter.IonTypes.Count == 1 && tranSettings.Filter.IonTypes[0] == IonType.precursor;
double precursorMassPredict = calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorCharge);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorCharge);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorCharge, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null));
}
}
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcPredictPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter,
bool ensureMassesAreMeasurable)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
MassType massType = tranSettings.Prediction.FragmentMassType;
MassType massTypeIon = precursorMS1 ? tranSettings.Prediction.PrecursorMassType : massType;
var sequence = Peptide.Target;
var ionTypes = IsProteomic ? tranSettings.Filter.PeptideIonTypes : tranSettings.Filter.SmallMoleculeIonTypes;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
ionTypes.Count == 1 && ionTypes[0] == IonType.precursor;
var precursorMassPredict = precursorMS1
? calcPredictPre.GetPrecursorMass(sequence)
: calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
Adduct productAdduct;
if (losses == null)
{
productAdduct = PrecursorAdduct;
}
else
{
productAdduct = losses.GetProductAdduct(PrecursorAdduct);
if (productAdduct == null)
{
continue;
}
}
double ionMz = IsProteomic ?
SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorAdduct) :
PrecursorAdduct.MzFromNeutralMass(CustomMolecule.GetMass(massTypeIon), massTypeIon);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null && ensureMassesAreMeasurable)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
var precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorAdduct);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks, productAdduct));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (ensureMassesAreMeasurable && minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorAdduct, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null, productAdduct));
}
}
}
