public IEnumerable <TransitionGroup> GetTransitionGroups(SrmSettings settings, PeptideDocNode nodePep, ExplicitMods mods, bool useFilter)
{
if (IsCustomIon)
{
// We can't generate nodes as we do with peptides, so just filter what we do have on instrument mz range
foreach (var group in nodePep.TransitionGroups.Where(tranGroup => tranGroup.TransitionGroup.IsCustomIon))
{
if (!useFilter || settings.TransitionSettings.IsMeasurablePrecursor(group.PrecursorMz))
{
yield return(group.TransitionGroup);
}
}
}
else
{
IList <int> precursorCharges = settings.TransitionSettings.Filter.PrecursorCharges;
if (!useFilter)
{
precursorCharges = new List <int>();
for (int i = TransitionGroup.MIN_PRECURSOR_CHARGE; i < TransitionGroup.MAX_PRECURSOR_CHARGE; i++)
{
precursorCharges.Add(i);
}
}
var modSettings = settings.PeptideSettings.Modifications;
double precursorMassLight = settings.GetPrecursorMass(IsotopeLabelType.light, Sequence, mods);
var listPrecursorMasses = new List <KeyValuePair <IsotopeLabelType, double> >
{
new KeyValuePair <IsotopeLabelType, double>(IsotopeLabelType.light, precursorMassLight)
};
foreach (var typeMods in modSettings.GetHeavyModifications())
{
IsotopeLabelType labelType = typeMods.LabelType;
double precursorMass = precursorMassLight;
if (settings.HasPrecursorCalc(labelType, mods))
{
precursorMass = settings.GetPrecursorMass(labelType, Sequence, mods);
}
listPrecursorMasses.Add(new KeyValuePair <IsotopeLabelType, double>(labelType, precursorMass));
}
foreach (int charge in precursorCharges)
{
if (useFilter && !settings.Accept(settings, this, mods, charge))
{
continue;
}
for (int i = 0; i < listPrecursorMasses.Count; i++)
{
var pair = listPrecursorMasses[i];
IsotopeLabelType labelType = pair.Key;
double precursorMass = pair.Value;
// Only return a heavy group, if the precursor masses differ
// between the light and heavy calculators
if (i == 0 || precursorMass != precursorMassLight)
{
if (settings.TransitionSettings.IsMeasurablePrecursor(SequenceMassCalc.GetMZ(precursorMass, charge)))
{
yield return(new TransitionGroup(this, null, charge, labelType));
}
}
}
}
}
}
public IEnumerable <TransitionGroup> GetTransitionGroups(SrmSettings settings, PeptideDocNode nodePep, ExplicitMods mods, bool useFilter)
{
if (IsCustomMolecule)
{
// TODO(bspratt) WHY NOT USING TRANSITION SETTINGS FILTER PRECURSOR ADDUCTS?
// We can't generate precursors as we do with peptides, so just filter what we do have on instrument mz range
//var precursorAdducts = settings.TransitionSettings.Filter.SmallMoleculePrecursorAdducts;
// TODO(bspratt) generate precursor transitions if doc has no fragments
// CONSIDER(bspratt) could we reasonably reuse fragments with proposed precursors of suitable charge and polarity (say, add an M+Na node that mimics an existing M+H node and children)
foreach (var group in nodePep.TransitionGroups.Where(tranGroup => tranGroup.TransitionGroup.IsCustomIon))
{
if (!useFilter || settings.TransitionSettings.IsMeasurablePrecursor(group.PrecursorMz))
{
yield return(group.TransitionGroup);
}
}
}
else
{
var precursorCharges = settings.TransitionSettings.Filter.PeptidePrecursorCharges;
if (!useFilter)
{
precursorCharges = new List <Adduct>();
for (int i = TransitionGroup.MIN_PRECURSOR_CHARGE; i < TransitionGroup.MAX_PRECURSOR_CHARGE; i++)
{
precursorCharges.Add(Adduct.FromChargeProtonated(i));
}
}
var modSettings = settings.PeptideSettings.Modifications;
var precursorMassLight = settings.GetPrecursorMass(IsotopeLabelType.light, Target, mods);
var listPrecursorMasses = new List <KeyValuePair <IsotopeLabelType, TypedMass> >
{
new KeyValuePair <IsotopeLabelType, TypedMass>(IsotopeLabelType.light, precursorMassLight)
};
foreach (var typeMods in modSettings.GetHeavyModifications())
{
IsotopeLabelType labelType = typeMods.LabelType;
var precursorMass = precursorMassLight;
if (settings.HasPrecursorCalc(labelType, mods))
{
precursorMass = settings.GetPrecursorMass(labelType, Target, mods);
}
listPrecursorMasses.Add(new KeyValuePair <IsotopeLabelType, TypedMass>(labelType, precursorMass));
}
foreach (var adduct in precursorCharges)
{
if (useFilter && !settings.Accept(settings, this, mods, adduct))
{
continue;
}
for (int i = 0; i < listPrecursorMasses.Count; i++)
{
var pair = listPrecursorMasses[i];
IsotopeLabelType labelType = pair.Key;
var precursorMass = pair.Value;
// Only return a heavy group, if the precursor masses differ
// between the light and heavy calculators
if (i == 0 || precursorMass != precursorMassLight)
{
if (settings.TransitionSettings.IsMeasurablePrecursor(SequenceMassCalc.GetMZ(precursorMass, adduct)))
{
yield return(new TransitionGroup(this, adduct, labelType));
}
}
}
}
}
}