protected override MetaMorpheusEngineResults RunSpecific()
{
// don't try to localize mass differences for ambiguous peptides
foreach (PeptideSpectralMatch psm in AllResultingIdentifications.Where(b => b.FullSequence != null))
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
MsDataScan scan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
Ms2ScanWithSpecificMass scanWithSpecificMass = new Ms2ScanWithSpecificMass(scan, psm.ScanPrecursorMonoisotopicPeakMz, psm.ScanPrecursorCharge, psm.FullFilePath, CommonParameters);
PeptideWithSetModifications peptide = psm.BestMatchingPeptides.First().Peptide;
double massDifference = psm.ScanPrecursorMass - peptide.MonoisotopicMass;
// this section will iterate through all residues of the peptide and try to localize the mass-diff at each residue and report a score for each residue
var localizedScores = new List <double>();
for (int r = 0; r < peptide.Length; r++)
{
// create new PeptideWithSetMods with unidentified mass difference at the given residue
PeptideWithSetModifications peptideWithLocalizedMassDiff = peptide.Localize(r, massDifference);
// this is the list of theoretical products for this peptide with mass-difference on this residue
List <Product> productsWithLocalizedMassDiff = peptideWithLocalizedMassDiff.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus).ToList();
var matchedIons = MatchFragmentIons(scanWithSpecificMass, productsWithLocalizedMassDiff, CommonParameters);
// score when the mass-diff is on this residue
double localizedScore = CalculatePeptideScore(scan, matchedIons);
localizedScores.Add(localizedScore);
}
psm.LocalizedScores = localizedScores;
}
return(new LocalizationEngineResults(this));
}
protected override MetaMorpheusEngineResults RunSpecific()
{
TerminusType terminusType = ProductTypeMethods.IdentifyTerminusType(ProductTypes);
foreach (PeptideSpectralMatch psm in AllResultingIdentifications)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
psm.MatchedIonSeriesDict = new Dictionary <ProductType, int[]>();
psm.MatchedIonMassToChargeRatioDict = new Dictionary <ProductType, double[]>();
psm.ProductMassErrorDa = new Dictionary <ProductType, double[]>();
psm.ProductMassErrorPpm = new Dictionary <ProductType, double[]>();
psm.MatchedIonIntensitiesDict = new Dictionary <ProductType, double[]>();
var theScan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
foreach (ProductType productType in ProductTypes)
{
var sortedTheoreticalProductMasses = psm.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
productType
});
Array.Sort(sortedTheoreticalProductMasses);
List <int> matchedIonSeriesList = new List <int>();
List <double> matchedIonMassToChargeRatioList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
List <double> matchedIonIntensityList = new List <double>();
//populate the above lists
MatchIonsOld(theScan, commonParameters.ProductMassTolerance, sortedTheoreticalProductMasses, matchedIonSeriesList, matchedIonMassToChargeRatioList, productMassErrorDaList, productMassErrorPpmList, matchedIonIntensityList, thePrecursorMass, productType, commonParameters.AddCompIons);
psm.MatchedIonSeriesDict.Add(productType, matchedIonSeriesList.ToArray());
psm.MatchedIonMassToChargeRatioDict.Add(productType, matchedIonMassToChargeRatioList.ToArray());
psm.ProductMassErrorDa.Add(productType, productMassErrorDaList.ToArray());
psm.ProductMassErrorPpm.Add(productType, productMassErrorPpmList.ToArray());
psm.MatchedIonIntensitiesDict.Add(productType, matchedIonIntensityList.ToArray());
}
}
foreach (PeptideSpectralMatch psm in AllResultingIdentifications.Where(b => b.NumDifferentCompactPeptides == 1))
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
var theScan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
if (psm.FullSequence == null)
{
continue;
}
PeptideWithSetModifications representative = psm.CompactPeptides.First().Value.Item2.First();
var localizedScores = new List <double>();
for (int indexToLocalize = 0; indexToLocalize < representative.Length; indexToLocalize++)
{
PeptideWithSetModifications localizedPeptide = representative.Localize(indexToLocalize, psm.ScanPrecursorMass - representative.MonoisotopicMass);
var gg = localizedPeptide.CompactPeptide(terminusType).ProductMassesMightHaveDuplicatesAndNaNs(ProductTypes);
Array.Sort(gg);
var score = CalculatePeptideScoreOld(theScan, commonParameters.ProductMassTolerance, gg, thePrecursorMass, DissociationTypes, commonParameters.AddCompIons, 0);
localizedScores.Add(score);
}
psm.LocalizedScores = localizedScores;
}
return(new LocalizationEngineResults(this));
}
protected override MetaMorpheusEngineResults RunSpecific()
{
// don't try to localize mass differences for ambiguous peptides
PeptideSpectralMatch[] unambiguousPsms = AllResultingIdentifications.Where(b => b.FullSequence != null).ToArray();
double psmsSearched = 0;
int oldPercentProgress = 0;
ReportProgress(new ProgressEventArgs(oldPercentProgress, "Localizing mass-differences... ", NestedIds));
Parallel.ForEach(Partitioner.Create(0, unambiguousPsms.Length),
new ParallelOptions {
MaxDegreeOfParallelism = CommonParameters.MaxThreadsToUsePerFile
},
(range, loopState) =>
{
for (int i = range.Item1; i < range.Item2; i++)
{
PeptideSpectralMatch psm = unambiguousPsms[i];
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
MsDataScan scan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
Ms2ScanWithSpecificMass scanWithSpecificMass = new Ms2ScanWithSpecificMass(scan, psm.ScanPrecursorMonoisotopicPeakMz, psm.ScanPrecursorCharge, psm.FullFilePath, CommonParameters);
PeptideWithSetModifications peptide = psm.BestMatchingPeptides.First().Peptide;
double massDifference = psm.ScanPrecursorMass - peptide.MonoisotopicMass;
// this section will iterate through all residues of the peptide and try to localize the mass-diff at each residue and report a score for each residue
var localizedScores = new List <double>();
for (int r = 0; r < peptide.Length; r++)
{
// create new PeptideWithSetMods with unidentified mass difference at the given residue
PeptideWithSetModifications peptideWithLocalizedMassDiff = peptide.Localize(r, massDifference);
// this is the list of theoretical products for this peptide with mass-difference on this residue
List <Product> productsWithLocalizedMassDiff = peptideWithLocalizedMassDiff.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus).ToList();
var matchedIons = MatchFragmentIons(scanWithSpecificMass, productsWithLocalizedMassDiff, CommonParameters);
// score when the mass-diff is on this residue
double localizedScore = CalculatePeptideScore(scan, matchedIons);
localizedScores.Add(localizedScore);
}
psm.LocalizedScores = localizedScores;
// report search progress (PSM mass differences localized so far out of total)
psmsSearched++;
var percentProgress = (int)((psmsSearched / unambiguousPsms.Length) * 100);
if (percentProgress > oldPercentProgress)
{
oldPercentProgress = percentProgress;
ReportProgress(new ProgressEventArgs(percentProgress, "Localizing mass-differences... ", NestedIds));
}
}
});
return(new LocalizationEngineResults(this));
}