private void ProcessTransitionGroup(IDictionary <LibKey, SpectrumMzInfo> spectra,
PeptideGroupDocNode nodePepGroup, PeptideDocNode nodePep, TransitionGroupDocNode nodeTranGroup, int replicateIndex)
{
LibKey key;
if (nodePep.IsProteomic)
{
var sequence = Document.Settings.GetPrecursorCalc(nodeTranGroup.TransitionGroup.LabelType, nodePep.ExplicitMods)
.GetModifiedSequence(nodePep.Peptide.Target, SequenceModFormatType.lib_precision, false);
key = new LibKey(sequence, nodeTranGroup.PrecursorAdduct.AdductCharge);
}
else
{
// For small molecules, the "modification" is expressed in the adduct
key = new LibKey(nodeTranGroup.CustomMolecule.GetSmallMoleculeLibraryAttributes(), nodeTranGroup.PrecursorAdduct);
}
var mi = new List <SpectrumPeaksInfo.MI>();
var rt = 0.0;
var im = IonMobilityAndCCS.EMPTY;
var imGroup = TransitionGroupIonMobilityInfo.EMPTY; // CCS may be available only at group level
var groupChromInfos = nodeTranGroup.GetSafeChromInfo(replicateIndex);
if (!groupChromInfos.IsEmpty)
{
var chromInfo = groupChromInfos.First(info => info.OptimizationStep == 0);
imGroup = chromInfo.IonMobilityInfo;
}
var maxApex = float.MinValue;
var maxApexMs1 = float.MinValue;
string chromFileName = null;
double?mobilityMs1 = null; // Track MS1 ion mobility in order to derive high energy ion mobility offset value
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfos = nodeTran.GetSafeChromInfo(replicateIndex);
if (chromInfos.IsEmpty)
{
continue;
}
var chromInfo = chromInfos.First(info => info.OptimizationStep == 0);
if (chromInfo.Area == 0)
{
continue;
}
if (nodeTran.IsMs1)
{
// Track MS1 ion mobility in order to derive high energy ion mobility offset value
if (chromInfo.Height > maxApexMs1)
{
maxApexMs1 = chromInfo.Height;
mobilityMs1 = chromInfo.IonMobility.IonMobility.Mobility;
}
continue;
}
if (chromFileName == null)
{
var chromFileInfo = Document.Settings.MeasuredResults.Chromatograms[replicateIndex].MSDataFileInfos.FirstOrDefault(file => ReferenceEquals(file.Id, chromInfo.FileId));
if (chromFileInfo != null)
{
chromFileName = chromFileInfo.FilePath.GetFileName();
}
}
List <SpectrumPeakAnnotation> annotations = null;
if (nodeTran.Transition.IsNonReporterCustomIon()) // CONSIDER(bspratt) include annotation for all non-peptide-fragment transitions?
{
var smallMoleculeLibraryAttributes = nodeTran.Transition.CustomIon.GetSmallMoleculeLibraryAttributes();
var ion = new CustomIon(smallMoleculeLibraryAttributes, nodeTran.Transition.Adduct, nodeTran.GetMoleculeMass());
annotations = new List <SpectrumPeakAnnotation> {
SpectrumPeakAnnotation.Create(ion, nodeTran.Annotations.Note)
};
}
mi.Add(new SpectrumPeaksInfo.MI {
Mz = nodeTran.Mz, Intensity = chromInfo.Area, Quantitative = nodeTran.ExplicitQuantitative, Annotations = annotations
});
if (chromInfo.Height > maxApex)
{
maxApex = chromInfo.Height;
rt = chromInfo.RetentionTime;
var mobility = chromInfo.IonMobility.IonMobility;
var mobilityHighEnergyOffset = 0.0;
if (mobilityMs1.HasValue && mobility.HasValue && mobility.Mobility != mobilityMs1)
{
// Note any difference in MS1 and MS2 ion mobilities - the "high energy ion mobility offset"
mobilityHighEnergyOffset = mobility.Mobility.Value - mobilityMs1.Value;
mobility = mobility.ChangeIonMobility(mobilityMs1);
}
im = IonMobilityAndCCS.GetIonMobilityAndCCS(mobility, chromInfo.IonMobility.CollisionalCrossSectionSqA ?? imGroup.CollisionalCrossSection, mobilityHighEnergyOffset);
}
}
if (chromFileName == null)
{
return;
}
SpectrumMzInfo spectrumMzInfo;
if (!spectra.TryGetValue(key, out spectrumMzInfo))
{
spectrumMzInfo = new SpectrumMzInfo
{
SourceFile = DocumentFilePath,
Key = key,
PrecursorMz = nodeTranGroup.PrecursorMz,
SpectrumPeaks = new SpectrumPeaksInfo(mi.ToArray()),
RetentionTimes = new List <SpectrumMzInfo.IonMobilityAndRT>(),
IonMobility = im,
Protein = nodePepGroup.Name,
RetentionTime = rt
};
spectra[key] = spectrumMzInfo;
}
var isBest = replicateIndex == nodePep.BestResult;
if (isBest)
{
spectrumMzInfo.IonMobility = im;
spectrumMzInfo.RetentionTime = rt;
}
spectrumMzInfo.RetentionTimes.Add(new SpectrumMzInfo.IonMobilityAndRT(chromFileName, im, rt, isBest));
}