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 static List <MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass scan, List <Product> theoreticalProducts, CommonParameters commonParameters)
{
var matchedFragmentIons = new List <MatchedFragmentIon>();
// if the spectrum has no peaks
if (!scan.ExperimentalFragments.Any())
{
return(matchedFragmentIons);
}
if (scan.TheScan.MassSpectrum.XcorrProcessed)
{
foreach (Product product in theoreticalProducts)
{
// unknown fragment mass; this only happens rarely for sequences with unknown amino acids
if (double.IsNaN(product.NeutralMass))
{
continue;
}
double theoreticalFragmentMz = Math.Round(product.NeutralMass.ToMz(1) / 1.0005079, 0) * 1.0005079;
var closestMzIndex = scan.TheScan.MassSpectrum.GetClosestPeakIndex(theoreticalFragmentMz).Value;
if (commonParameters.ProductMassTolerance.Within(scan.TheScan.MassSpectrum.XArray[closestMzIndex], theoreticalFragmentMz))
{
matchedFragmentIons.Add(new MatchedFragmentIon(product, theoreticalFragmentMz, scan.TheScan.MassSpectrum.YArray[closestMzIndex], 1));
}
}
return(matchedFragmentIons);
}
// search for ions in the spectrum
foreach (Product product in theoreticalProducts)
{
// unknown fragment mass; this only happens rarely for sequences with unknown amino acids
if (double.IsNaN(product.NeutralMass))
{
continue;
}
// get the closest peak in the spectrum to the theoretical peak
var closestExperimentalMass = scan.GetClosestExperimentalFragmentMass(product.NeutralMass);
// is the mass error acceptable?
if (commonParameters.ProductMassTolerance.Within(closestExperimentalMass.monoisotopicMass, product.NeutralMass) && closestExperimentalMass.charge <= scan.PrecursorCharge)
{
matchedFragmentIons.Add(new MatchedFragmentIon(product, closestExperimentalMass.monoisotopicMass.ToMz(closestExperimentalMass.charge),
closestExperimentalMass.peaks.First().intensity, closestExperimentalMass.charge));
}
}
if (commonParameters.AddCompIons)
{
double protonMassShift = complementaryIonConversionDictionary[commonParameters.DissociationType].ToMass(1);
foreach (Product product in theoreticalProducts)
{
// unknown fragment mass or diagnostic ion or precursor; skip those
if (double.IsNaN(product.NeutralMass) || product.ProductType == ProductType.D || product.ProductType == ProductType.M)
{
continue;
}
double compIonMass = scan.PrecursorMass + protonMassShift - product.NeutralMass;
// get the closest peak in the spectrum to the theoretical peak
var closestExperimentalMass = scan.GetClosestExperimentalFragmentMass(compIonMass);
// is the mass error acceptable?
if (commonParameters.ProductMassTolerance.Within(closestExperimentalMass.monoisotopicMass, compIonMass) && closestExperimentalMass.charge <= scan.PrecursorCharge)
{
matchedFragmentIons.Add(new MatchedFragmentIon(product, closestExperimentalMass.monoisotopicMass.ToMz(closestExperimentalMass.charge),
closestExperimentalMass.totalIntensity, closestExperimentalMass.charge));
}
}
}
return(matchedFragmentIons);
}
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;
}
}
}