public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, PeptideSpectralMatch[] peptideSpectralMatches,
Ms2ScanWithSpecificMass[] arrayOfSortedMs2Scans, CommonParameters commonParameters)
{
foreach (PeptideSpectralMatch psm in peptideSpectralMatches.Where(p => p != null))
{
Ms2ScanWithSpecificMass scan = arrayOfSortedMs2Scans[psm.ScanIndex];
//TODO: spectral angle could be used to disambiguate PSMs. right now for ambiguous PSMs, the spectral angle for only one peptide option is saved
foreach (var peptide in psm.PeptidesToMatchingFragments)
{
if (spectralLibrary == null || !spectralLibrary.TryGetSpectrum(peptide.Key.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
{
continue;
}
double spectralAngle = CalculateNormalizedSpectralAngle(librarySpectrum.MatchedFragmentIons, scan.TheScan, commonParameters);
psm.SpectralAngle = spectralAngle;
}
}
}
public void DisplaySpectrumMatch(PlotView plotView, Canvas canvas, PsmFromTsv psm, ParentChildScanPlotsView parentChildScanPlotsView, out List <string> errors)
{
errors = null;
// clear old parent/child scans
parentChildScanPlotsView.Plots.Clear();
CurrentlyDisplayedPlots.Clear();
// get the scan
if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out DynamicDataConnection spectraFile))
{
errors = new List <string>();
errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
return;
}
MsDataScan scan = spectraFile.GetOneBasedScanFromDynamicConnection(psm.Ms2ScanNumber);
LibrarySpectrum librarySpectrum = null;
// plot the annotated spectrum match
PeptideSpectrumMatchPlot plot;
if (psm.BetaPeptideBaseSequence == null)
{
// get the library spectrum if relevant
if (SpectralLibrary != null)
{
SpectralLibrary.TryGetSpectrum(psm.FullSequence, psm.PrecursorCharge, out var librarySpectrum1);
librarySpectrum = librarySpectrum1;
}
plot = new PeptideSpectrumMatchPlot(plotView, canvas, psm, scan, psm.MatchedIons, librarySpectrum: librarySpectrum);
}
else
{
plot = new CrosslinkSpectrumMatchPlot(plotView, canvas, psm, scan);
}
CurrentlyDisplayedPlots.Add(plot);
// plot parent/child scans
if (psm.ChildScanMatchedIons != null)
{
// draw parent scan
string parentAnnotation = "Scan: " + scan.OneBasedScanNumber
+ " Dissociation Type: " + scan.DissociationType
+ " MsOrder: " + scan.MsnOrder
+ " Selected Mz: " + scan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + scan.RetentionTime.ToString("0.##");
var parentPlotView = new PlotView(); // placeholder
var parentCanvas = new Canvas();
var item = new ParentChildScanPlotTemplate()
{
Plot = new PeptideSpectrumMatchPlot(parentPlotView, parentCanvas, psm, scan, psm.MatchedIons),
SpectrumLabel = parentAnnotation,
TheCanvas = parentCanvas
};
parentChildScanPlotsView.Plots.Add(item);
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
parentPlotView.Model = null;
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psm.ChildScanMatchedIons;
if (psm.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psm.BetaPeptideChildScanMatchedIons)
.GroupBy(p => p.Key)
.ToDictionary(p => p.Key, q => q.SelectMany(p => p.Value).ToList());
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int childScanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(childScanNumber))
{
continue;
}
scansDrawn.Add(childScanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
MsDataScan childScan = spectraFile.GetOneBasedScanFromDynamicConnection(childScanNumber);
string childAnnotation = "Scan: " + childScan.OneBasedScanNumber
+ " Dissociation Type: " + childScan.DissociationType
+ " MsOrder: " + childScan.MsnOrder
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas childCanvas = new Canvas();
PlotView childPlotView = new PlotView(); // placeholder
// make the plot
var childPlot = new PeptideSpectrumMatchPlot(childPlotView, childCanvas, psm, childScan, matchedIons, annotateProperties: false);
childPlot.Model.Title = null;
childPlot.Model.Subtitle = null;
item = new ParentChildScanPlotTemplate()
{
Plot = childPlot, SpectrumLabel = childAnnotation, TheCanvas = childCanvas
};
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
childPlotView.Model = null;
parentChildScanPlotsView.Plots.Add(item);
CurrentlyDisplayedPlots.Add(childPlot);
}
}
}
public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, PeptideSpectralMatch[] psms,
Ms2ScanWithSpecificMass[] arrayOfSortedMs2Scans, CommonParameters commonParameters)
{
if (spectralLibrary != null)
{
// one lock for each MS2 scan; a scan can only be accessed by one thread at a time
var myLocks = new object[psms.Length];
for (int i = 0; i < myLocks.Length; i++)
{
myLocks[i] = new object();
}
int maxThreadsPerFile = commonParameters.MaxThreadsToUsePerFile;
int[] threads = Enumerable.Range(0, maxThreadsPerFile).ToArray();
Parallel.ForEach(threads, (i) =>
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
return;
}
for (; i < psms.Length; i += maxThreadsPerFile)
{
lock (myLocks[i])
{
if (psms[i] != null)
{
Ms2ScanWithSpecificMass scan = arrayOfSortedMs2Scans[psms[i].ScanIndex];
List <(int, PeptideWithSetModifications)> pwsms = new();
List <double> pwsmSpectralAngles = new();
foreach (var(Notch, Peptide) in psms[i].BestMatchingPeptides)
{
//if peptide is target, directly look for the target's spectrum in the spectral library
if (!Peptide.Protein.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
{
SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum, librarySpectrum.XArray, librarySpectrum.YArray, SpectralSimilarity.SpectrumNormalizationScheme.squareRootSpectrumSum, commonParameters.ProductMassTolerance.Value, false);
if (s.SpectralContrastAngle().HasValue)
{
pwsms.Add((Notch, Peptide));
pwsmSpectralAngles.Add((double)s.SpectralContrastAngle());
}
}
//if peptide is decoy, look for the decoy's corresponding target's spectrum in the spectral library and generate decoy spectrum by function GetDecoyLibrarySpectrumFromTargetByRevers
else if (Peptide.Protein.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.PeptideDescription, scan.PrecursorCharge, out var targetlibrarySpectrum))
{
var decoyPeptideTheorProducts = new List <Product>();
Peptide.Fragment(commonParameters.DissociationType, commonParameters.DigestionParams.FragmentationTerminus, decoyPeptideTheorProducts);
var decoylibrarySpectrum = GetDecoyLibrarySpectrumFromTargetByReverse(targetlibrarySpectrum, decoyPeptideTheorProducts);
SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum, decoylibrarySpectrum.Select(x => x.Mz).ToArray(), decoylibrarySpectrum.Select(x => x.Intensity).ToArray(), SpectralSimilarity.SpectrumNormalizationScheme.squareRootSpectrumSum, commonParameters.ProductMassTolerance.Value, false);
if (s.SpectralContrastAngle().HasValue)
{
pwsms.Add((Notch, Peptide));
pwsmSpectralAngles.Add((double)s.SpectralContrastAngle());
}
}
}
if (pwsmSpectralAngles.Count > 0 && !pwsmSpectralAngles.Max().Equals(null))
{
psms[i].SpectralAngle = pwsmSpectralAngles.Max();
}
else
{
psms[i].SpectralAngle = -1;
}
}
}