/// <summary>
/// Compares the modifications indicated in the sequence string to the calculated masses.
/// </summary>
/// <param name="seq">The modified sequence.</param>
/// <param name="calc">Calculator used to calculate the masses.</param>
/// <param name="calcLight">
/// Additional light calculator if necessary to isolate mass changes
/// caused by heavy modifications alone.
/// </param>
/// <returns>
/// True if the given calculators explain the modifications indicated on the sequence,
/// false otherwise.
/// </returns>
private bool EqualsModifications(string seq, IPrecursorMassCalc calc, IPrecursorMassCalc calcLight)
{
var modifications = Settings.PeptideSettings.Modifications;
bool structural = calcLight == null;
string aas = FastaSequence.StripModifications(seq);
foreach (var info in EnumerateSequenceInfos(seq, true))
{
int indexAA = info.IndexAA; // ReSharper
var aa = aas[indexAA];
var roundedTo = info.RoundedTo;
// If the user has indicated the modification by name, find that modification
// and calculate the mass.
double massKey;
if (info.Mass != null)
{
massKey = (double)info.Mass;
}
else
{
var info1 = info;
StaticMod modMatch = null;
int index;
if (structural &&
((index = modifications.StaticModifications.IndexOf(mod => Equals(mod.Name, info1.Name)))
!= -1))
{
modMatch = modifications.StaticModifications[index];
}
if (!structural &&
((index = modifications.HeavyModifications.IndexOf(mod => Equals(mod.Name, info1.Name)))
!= -1))
{
modMatch = modifications.HeavyModifications[index];
}
if (modMatch == null)
{
return(false);
}
roundedTo = DEFAULT_ROUNDING_DIGITS;
massKey = Math.Round(GetDefaultModMass(aa, modMatch), roundedTo);
}
double massMod = Math.Round(calc.GetAAModMass(aas[indexAA], indexAA, aas.Length), roundedTo);
// Subtract the mass difference of the light
// modifications to isolate the masses of the heavy modifications.
if (calcLight != null)
{
massMod -= Math.Round(calcLight.GetAAModMass(aas[indexAA], indexAA, aas.Length), roundedTo);
}
if (!Equals(massKey, massMod))
{
return(false);
}
}
return(true);
}
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));
}
}
}
/// <summary>
/// Compares the modifications indicated in the sequence string to the calculated masses.
/// </summary>
/// <param name="seq">The modified sequence.</param>
/// <param name="calc">Calculator used to calculate the masses.</param>
/// <param name="calcLight">
/// Additional light calculator if necessary to isolate mass changes
/// caused by heavy modifications alone.
/// </param>
/// <returns>
/// True if the given calculators explain the modifications indicated on the sequence,
/// false otherwise.
/// </returns>
private bool EqualsModifications(string seq, IPrecursorMassCalc calc, IPrecursorMassCalc calcLight)
{
var modifications = Settings.PeptideSettings.Modifications;
bool structural = calcLight == null;
string aas = FastaSequence.StripModifications(seq);
foreach (var info in EnumerateSequenceInfos(seq, true))
{
int indexAA = info.IndexAA; // ReSharper
var aa = aas[indexAA];
var roundedTo = info.RoundedTo;
// If the user has indicated the modification by name, find that modification
// and calculate the mass.
double massKey;
if (info.Mass != null)
massKey = (double)info.Mass;
else
{
var info1 = info;
StaticMod modMatch = null;
int index;
if (structural &&
((index = modifications.StaticModifications.IndexOf(mod => Equals(mod.Name, info1.Name)))
!= -1))
modMatch = modifications.StaticModifications[index];
if (!structural &&
((index = modifications.HeavyModifications.IndexOf(mod => Equals(mod.Name, info1.Name)))
!= -1))
modMatch = modifications.HeavyModifications[index];
if (modMatch == null)
return false;
roundedTo = DEFAULT_ROUNDING_DIGITS;
massKey = Math.Round(GetDefaultModMass(aa, modMatch), roundedTo);
}
double massMod = Math.Round(calc.GetAAModMass(aas[indexAA], indexAA, aas.Length), roundedTo);
// Subtract the mass difference of the light
// modifications to isolate the masses of the heavy modifications.
if (calcLight != null)
massMod -= Math.Round(calcLight.GetAAModMass(aas[indexAA], indexAA, aas.Length), roundedTo);
if (!Equals(massKey, massMod))
return false;
}
return true;
}
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));
}
}
}
