public void MatchIsofroms(FragmentTypes type, Tolerance tolerance, double cutoffThreshold, bool phopshoNeutralLoss, params int[] chargeStates)
{
foreach (PeptideIsoform isoform in PeptideIsoforms)
{
isoform.MatchSpectrum(type, tolerance, cutoffThreshold, phopshoNeutralLoss, chargeStates);
}
}
public Fragment(FragmentTypes type, int number, double monoisotopicMass, AminoAcidPolymer parent)
{
Type = type;
Number = number;
Parent = parent;
MonoisotopicMass = monoisotopicMass;
}
public void TestGetIonCapFailFail()
{
FragmentTypes f = FragmentTypes.All;
Assert.That(() => f.GetIonCap(), Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Fragment Type must be a single value to determine the ion cap"));
}
public void TestGetTerminusFail()
{
FragmentTypes f = FragmentTypes.a | FragmentTypes.adot;
Assert.That(() => f.GetTerminus(), Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Fragment Type must be a single value to determine the terminus"));
}
public static ChemicalFormula GetIonCap(this FragmentTypes fragmentType)
{
if (fragmentType == FragmentTypes.None || (fragmentType & (fragmentType - 1)) != FragmentTypes.None)
{
throw new MzLibException("Fragment Type must be a single value to determine the ion cap");
}
return(FragmentIonCaps[fragmentType]);
}
public static Terminus GetTerminus(this FragmentTypes fragmentType)
{
// Super handy: http://stackoverflow.com/questions/4624248/c-logical-riddle-with-bit-operations-only-one-bit-is-set
if (fragmentType == FragmentTypes.None || (fragmentType & (fragmentType - 1)) != FragmentTypes.None)
{
throw new MzLibException("Fragment Type must be a single value to determine the terminus");
}
return(fragmentType >= FragmentTypes.x ? Terminus.C : Terminus.N);
}
public override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return psm;
}
public static IEnumerable <FragmentTypes> GetIndividualFragmentTypes(this FragmentTypes fragmentTypes)
{
foreach (FragmentTypes site in Enum.GetValues(typeof(FragmentTypes)))
{
if (site == FragmentTypes.None || site == FragmentTypes.All || site == FragmentTypes.Internal)
{
continue;
}
if ((fragmentTypes & site) == site)
{
yield return(site);
}
}
}
public void SwitchToFragment(FragmentTypes fragmentType)
{
switch (fragmentType)
{
case FragmentTypes.Home:
ShowFragment(_homeFragment);
break;
case FragmentTypes.Login:
ShowFragment(_loginFragment);
break;
case FragmentTypes.Settings:
ShowFragment(_settingsFragment);
break;
case FragmentTypes.Listoftasks:
ShowFragment(_listOfTasksFragment);
break;
case FragmentTypes.Globaltimelog:
ShowFragment(_globalTimeLogFragment);
break;
case FragmentTypes.Globaltimelogdetails:
ShowFragment(_timeLogDetailFragment);
break;
case FragmentTypes.Listofprojects:
ShowFragment(_listOfProjectFragment);
break;
case FragmentTypes.Taskdetails:
ShowFragment(_taskDetailFragment);
break;
case FragmentTypes.Tasktimelogdetails:
ShowFragment(_taskTimeLogDetailFragment);
break;
}
}
public Lotor(string rawFileDirectory, string inputcsvFile, string outputDirectory, List<Modification> fixedModifications, List<Modification> quantifiedModifications, Tolerance prod_Tolerance, int scoreCutoff, bool separateGroups, double productThreshold,bool ignoreCTerminal,bool reduceSites, FragmentTypes fragType, bool phosphoNeutralLoss = false)
{
_rawFileDirectory = rawFileDirectory;
_csvFile = inputcsvFile;
_outputDirectory = outputDirectory;
_fixedModifications = fixedModifications;
FixedModifications = fixedModifications.OfType<IMass>().ToList();
QuantifiedModifications = quantifiedModifications;
_prodTolerance = prod_Tolerance;
_deltaScoreCutoff = scoreCutoff;
_separateProteinGroups = separateGroups;
_productThreshold = productThreshold;
_fragType = fragType;
_ignoreCTerminal = ignoreCTerminal;
_reduceSites = reduceSites;
//LocalizedHit.AScoreThreshold = ascore_threshold;
LocalizedHit.ScoreThreshold = scoreCutoff;
_phosphoNeutralLoss = phosphoNeutralLoss;
}
public Lotor(string rawFileDirectory, string inputcsvFile, string outputDirectory, List <Modification> fixedModifications, List <Modification> quantifiedModifications, Tolerance prod_Tolerance, int scoreCutoff, bool separateGroups, double productThreshold, bool ignoreCTerminal, bool reduceSites, FragmentTypes fragType, bool phosphoNeutralLoss = false)
{
_rawFileDirectory = rawFileDirectory;
_csvFile = inputcsvFile;
_outputDirectory = outputDirectory;
_fixedModifications = fixedModifications;
FixedModifications = fixedModifications.OfType <IMass>().ToList();
QuantifiedModifications = quantifiedModifications;
_prodTolerance = prod_Tolerance;
_deltaScoreCutoff = scoreCutoff;
_separateProteinGroups = separateGroups;
_productThreshold = productThreshold;
_fragType = fragType;
_ignoreCTerminal = ignoreCTerminal;
_reduceSites = reduceSites;
//LocalizedHit.AScoreThreshold = ascore_threshold;
LocalizedHit.ScoreThreshold = scoreCutoff;
_phosphoNeutralLoss = phosphoNeutralLoss;
}
public DataPointAcquisitionEngine(
List <PeptideSpectralMatch> goodIdentifications,
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile,
Tolerance mzToleranceForMs1Search,
Tolerance mzToleranceForMs2Search,
int numFragmentsNeededForEveryIdentification,
int minMS1isotopicPeaksNeededForConfirmedIdentification,
int minMS2isotopicPeaksNeededForConfirmedIdentification,
FragmentTypes fragmentTypesForCalibration,
List <string> nestedIds) : base(nestedIds)
{
this.goodIdentifications = goodIdentifications;
this.myMsDataFile = myMsDataFile;
this.mzToleranceForMs1Search = mzToleranceForMs1Search;
this.mzToleranceForMs2Search = mzToleranceForMs2Search;
this.numFragmentsNeededForEveryIdentification = numFragmentsNeededForEveryIdentification;
this.minMS1isotopicPeaksNeededForConfirmedIdentification = minMS1isotopicPeaksNeededForConfirmedIdentification;
this.minMS2isotopicPeaksNeededForConfirmedIdentification = minMS2isotopicPeaksNeededForConfirmedIdentification;
this.fragmentTypesForCalibration = fragmentTypesForCalibration;
}
public DataPointAcquisitionEngine(
List <PeptideSpectralMatch> goodIdentifications,
MsDataFile myMsDataFile,
Tolerance mzToleranceForMs1Search,
Tolerance mzToleranceForMs2Search,
int numFragmentsNeededForEveryIdentification,
int minMS1isotopicPeaksNeededForConfirmedIdentification,
int minMS2isotopicPeaksNeededForConfirmedIdentification,
FragmentTypes fragmentTypesForCalibration,
CommonParameters commonParameters,
List <string> nestedIds) : base(commonParameters, nestedIds)
{
GoodIdentifications = goodIdentifications;
MyMsDataFile = myMsDataFile;
MzToleranceForMs1Search = mzToleranceForMs1Search;
MzToleranceForMs2Search = mzToleranceForMs2Search;
NumFragmentsNeededForEveryIdentification = numFragmentsNeededForEveryIdentification;
MinMS1isotopicPeaksNeededForConfirmedIdentification = minMS1isotopicPeaksNeededForConfirmedIdentification;
MinMS2isotopicPeaksNeededForConfirmedIdentification = minMS2isotopicPeaksNeededForConfirmedIdentification;
FragmentTypesForCalibration = fragmentTypesForCalibration;
}
public override SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.TotalIonCurrent;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return results;
}
public void MatchSpectrum(FragmentTypes fragmentTypes, Tolerance tolerance, double cutoffThreshold, bool phosphoNeutralLoss, params int[] chargeStates)
{
Fragments = Fragment(fragmentTypes).OrderBy(f => f.ToString()).ToList();
if (phosphoNeutralLoss)
{
List <Fragment> toAdd = new List <Fragment>();
foreach (Fragment frag in Fragments)
{
List <IMass> mods = frag.GetModifications().ToList();
if (mods.Contains(lotorForm.Phosphorylation))
{
var newFrag = new Fragment(frag.Type, frag.Number, frag.MonoisotopicMass - H3PO4.MonoisotopicMass, frag.Parent);
toAdd.Add(newFrag);
}
}
Fragments.AddRange(toAdd);
}
SpectralMatch = new SpectrumFragmentsMatch(Spectrum);
var matches = SpectralMatch.MatchFragments(Fragments, tolerance, cutoffThreshold, chargeStates);
MatchedFragments = new HashSet <Fragment>(matches);
}
private (List <PeptideSpectralMatch>, DataPointAquisitionResults) GetDataAcquisitionResults(IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile, string currentDataFile, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <Protein> proteinList, string taskId, ICommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode;
if (initPrecTol is PpmTolerance)
{
searchMode = new SinglePpmAroundZeroSearchMode(initPrecTol.Value);
}
else
{
searchMode = new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
}
FragmentTypes fragmentTypesForCalibration = FragmentTypes.None;
if (combinedParameters.BIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.b;
}
if (combinedParameters.YIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.y;
}
if (combinedParameters.CIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.c;
}
if (combinedParameters.ZdotIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.zdot;
}
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters.DoPrecursorDeconvolution, combinedParameters.UseProvidedPrecursorInfo, combinedParameters.DeconvolutionIntensityRatio, combinedParameters.DeconvolutionMaxAssumedChargeState, combinedParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
List <ProductType> lp = new List <ProductType>();
if (combinedParameters.BIons)
{
lp.Add(ProductType.B);
}
if (combinedParameters.YIons)
{
lp.Add(ProductType.Y);
}
if (combinedParameters.CIons)
{
lp.Add(ProductType.C);
}
if (combinedParameters.ZdotIons)
{
lp.Add(ProductType.Zdot);
}
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchMode, false, combinedParameters, initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.ToList();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > compactPeptideToProteinPeptideMatching = ((SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(allPsms, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> {
combinedParameters.DigestionParams
}, combinedParameters.ReportAllAmbiguity, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run()).CompactPeptideToProteinPeptideMatching;
foreach (var huh in allPsms)
{
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
}
allPsms = allPsms.Where(b => b != null).OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(allPsms, searchMode.NumNotches, false, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.01 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
Warn("No PSMs below 1% FDR observed!");
return(new List <PeptideSpectralMatch>(), null);
}
var dissociationTypes = MetaMorpheusEngine.DetermineDissociationType(lp);
foreach (var psm in allPsms)
{
var theScan = myMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
foreach (var huh in lp)
{
var ionMasses = psm.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
huh
});
Array.Sort(ionMasses);
List <double> matchedIonMassesList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
LocalizationEngine.MatchIons(theScan, initProdTol, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, false);
double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray();
psm.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches);
psm.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray());
psm.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray());
}
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
myMsDataFile,
initPrecTol,
initProdTol,
CalibrationParameters.NumFragmentsNeededForEveryIdentification,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CalibrationParameters.MinMS2IsotopicPeaksNeededForConfirmedIdentification,
fragmentTypesForCalibration,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(goodIdentifications, currentResult);
}
private List<LocalizedHit> CalculateBestIsoforms(List<PSM> psms, FragmentTypes fragType, Tolerance prod_tolerance, double productThreshold, bool phosphoNeutralLosses)
{
Log("Localizing Best Isoforms...");
int totalisofromscount = 0;
int count = 0;
int psm_count = 0;
int localized_psm = 0;
List<LocalizedHit> hits = new List<LocalizedHit>();
foreach (PSM psm in psms)
{
psm_count++;
count++;
// Generate all the isoforms for the PSM
int isoformCount = psm.GenerateIsoforms(_ignoreCTerminal);
if(isoformCount == 0)
continue;
totalisofromscount += isoformCount;
// Calculate the probability of success for random matches
//double pvalue = GetPValue(psm, prod_tolerance, productThreshold);
// Match all the isoforms to the spectrum and log the results
psm.MatchIsofroms(fragType, prod_tolerance, productThreshold, phosphoNeutralLosses, 1);
// Perform the localization for all combinations of isoforms
//double[,] res = psm.Calc(pvalue);
Tuple<int, int, double> scores = LocalizedIsoformSimple(psm);
// Check if the localization is above some threshold
//Tuple<int, int, double> scores = LocalizedIsoform(res);
int bestIsoform = scores.Item1;
int secondBestIsoform = scores.Item2;
double ascore = scores.Item3;
//int numSDFs = psm.NumSiteDeterminingFragments[bestIsoform, secondBestIsoform];
List<PeptideIsoform> isoforms = psm.PeptideIsoforms.ToList();
//LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], numSDFs,
// psm.BestSiteDeterminingFragments[bestIsoform, secondBestIsoform],
// psm.BestSiteDeterminingFragments[secondBestIsoform, bestIsoform], pvalue, ascore);
LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], 0,
0,
0, 0, ascore);
hits.Add(hit);
if (hit.IsLocalized)
{
localized_psm++;
}
psm.PeptideIsoforms.Clear();
// Progress Bar Stuff
if (count <= 50)
continue;
count = 0;
ProgressUpdate((double)psm_count / psms.Count);
}
ProgressUpdate(1.0);
Log(string.Format("Total Number of Possible Isoforms Considered: {0:N0}",totalisofromscount));
Log(string.Format("Total Number of PSMs Considered: {0:N0}", psm_count));
Log(string.Format("Total Number of PSMs Localized: {0:N0} ({1:00.00}%)", localized_psm, localized_psm * 100 / psm_count));
ProgressUpdate(0);
return hits;
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int minIndex, int maxIndex, bool calculateChemicalFormula)
{
foreach (FragmentTypes type in types.GetIndividualFragmentTypes())
{
bool isChemicalFormula = calculateChemicalFormula;
ChemicalFormula capFormula = type.GetIonCap();
bool isCTerminal = type.GetTerminus() == Terminus.C;
double monoMass = capFormula.MonoisotopicMass;
ChemicalFormula formula = new ChemicalFormula(capFormula);
IHasChemicalFormula terminus = isCTerminal ? CTerminus : NTerminus;
monoMass += terminus.MonoisotopicMass;
if (isChemicalFormula)
{
formula.Add(terminus);
}
bool first = true;
bool hasMod = _modifications != null;
for (int i = 0; i <= maxIndex; i++)
{
int aaIndex = isCTerminal ? Length - i : i - 1;
// Handle the terminus mods first in a special case
IHasMass mod;
if (first)
{
first = false;
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
continue;
}
monoMass += residues[aaIndex].MonoisotopicMass;
formula.Add(residues[aaIndex]);
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
if (i < minIndex)
{
continue;
}
if (isChemicalFormula)
{
yield return(new ChemicalFormulaFragment(type, i, formula, this));
}
else
{
yield return(new Fragment(type, i, monoMass, this));
}
}
}
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int minIndex, int maxIndex)
{
return(Fragment(types, minIndex, maxIndex, false));
}
public virtual SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return(results);
}
private List <LocalizedHit> CalculateBestIsoforms(List <PSM> psms, FragmentTypes fragType, Tolerance prod_tolerance, double productThreshold, bool phosphoNeutralLosses)
{
Log("Localizing Best Isoforms...");
int totalisofromscount = 0;
int count = 0;
int psm_count = 0;
int localized_psm = 0;
List <LocalizedHit> hits = new List <LocalizedHit>();
foreach (PSM psm in psms)
{
psm_count++;
count++;
// Generate all the isoforms for the PSM
int isoformCount = psm.GenerateIsoforms(_ignoreCTerminal);
if (isoformCount == 0)
{
continue;
}
totalisofromscount += isoformCount;
// Calculate the probability of success for random matches
//double pvalue = GetPValue(psm, prod_tolerance, productThreshold);
// Match all the isoforms to the spectrum and log the results
psm.MatchIsofroms(fragType, prod_tolerance, productThreshold, phosphoNeutralLosses, 1);
// Perform the localization for all combinations of isoforms
//double[,] res = psm.Calc(pvalue);
Tuple <int, int, double> scores = LocalizedIsoformSimple(psm);
// Check if the localization is above some threshold
//Tuple<int, int, double> scores = LocalizedIsoform(res);
int bestIsoform = scores.Item1;
int secondBestIsoform = scores.Item2;
double ascore = scores.Item3;
//int numSDFs = psm.NumSiteDeterminingFragments[bestIsoform, secondBestIsoform];
List <PeptideIsoform> isoforms = psm.PeptideIsoforms.ToList();
//LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], numSDFs,
// psm.BestSiteDeterminingFragments[bestIsoform, secondBestIsoform],
// psm.BestSiteDeterminingFragments[secondBestIsoform, bestIsoform], pvalue, ascore);
LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], 0,
0,
0, 0, ascore);
hits.Add(hit);
if (hit.IsLocalized)
{
localized_psm++;
}
psm.PeptideIsoforms.Clear();
// Progress Bar Stuff
if (count <= 50)
{
continue;
}
count = 0;
ProgressUpdate((double)psm_count / psms.Count);
}
ProgressUpdate(1.0);
Log(string.Format("Total Number of Possible Isoforms Considered: {0:N0}", totalisofromscount));
Log(string.Format("Total Number of PSMs Considered: {0:N0}", psm_count));
Log(string.Format("Total Number of PSMs Localized: {0:N0} ({1:00.00}%)", localized_psm, localized_psm * 100 / psm_count));
ProgressUpdate(0);
return(hits);
}
public IEnumerable <Fragment> Fragment(FragmentTypes types)
{
return(Fragment(types, false));
}
public abstract PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance);
public override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return(psm);
}
public ChemicalFormulaFragment(FragmentTypes type, int number, string chemicalFormula, AminoAcidPolymer parent)
: this(type, number, new ChemicalFormula(chemicalFormula), parent)
{
}
public override SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.GetTotalIonCurrent();
;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return(results);
}
public void MatchIsofroms(FragmentTypes type, Tolerance tolerance, double cutoffThreshold, bool phopshoNeutralLoss, params int[] chargeStates)
{
foreach (PeptideIsoform isoform in PeptideIsoforms)
{
isoform.MatchSpectrum(type, tolerance, cutoffThreshold,phopshoNeutralLoss, chargeStates);
}
}
public abstract PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance);
public virtual SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return results;
}
/// <summary>
/// Calculates all the fragments of the types you specify
/// </summary>
/// <param name="types"></param>
/// <param name="calculateChemicalFormula"></param>
/// <returns></returns>
public IEnumerable <Fragment> Fragment(FragmentTypes types, bool calculateChemicalFormula)
{
return(Fragment(types, 1, Length - 1, calculateChemicalFormula));
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int number)
{
return(Fragment(types, number, false));
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int number, bool calculateChemicalFormula)
{
return(Fragment(types, number, number, calculateChemicalFormula));
}
public ChemicalFormulaFragment(FragmentTypes type, int number, ChemicalFormula formula, AminoAcidPolymer parent)
: base(type, number, formula.MonoisotopicMass, parent)
{
ThisChemicalFormula = ChemicalFormula.ParseFormula(formula.Formula);
}
private DataPointAquisitionResults GetDataAcquisitionResults(MsDataFile myMsDataFile, string currentDataFile, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <Protein> proteinList, string taskId, CommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode = initPrecTol is PpmTolerance ?
(MassDiffAcceptor) new SinglePpmAroundZeroSearchMode(initPrecTol.Value) :
new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
FragmentTypes fragmentTypesForCalibration = FragmentTypes.None;
if (combinedParameters.BIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.b;
}
if (combinedParameters.YIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.y;
}
if (combinedParameters.CIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.c;
}
if (combinedParameters.ZdotIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.zdot;
}
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters.DoPrecursorDeconvolution, combinedParameters.UseProvidedPrecursorInfo, combinedParameters.DeconvolutionIntensityRatio, combinedParameters.DeconvolutionMaxAssumedChargeState, combinedParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
List <ProductType> productTypes = new List <ProductType>();
if (combinedParameters.BIons)
{
productTypes.Add(ProductType.B);
}
if (combinedParameters.YIons)
{
productTypes.Add(ProductType.Y);
}
if (combinedParameters.CIons)
{
productTypes.Add(ProductType.C);
}
if (combinedParameters.ZdotIons)
{
productTypes.Add(ProductType.Zdot);
}
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, productTypes, searchMode, combinedParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.Where(p => p != null).ToList();
var compactPeptideToProteinPeptideMatching = ((SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine
(allPsms, proteinList, fixedModifications, variableModifications, productTypes, new List <DigestionParams> {
combinedParameters.DigestionParams
},
combinedParameters.ReportAllAmbiguity, combinedParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run()).CompactPeptideToProteinPeptideMatching;
foreach (var huh in allPsms)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
allPsms = allPsms.OrderByDescending(b => b.Score)
.ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue)
.GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(allPsms, searchMode.NumNotches, CommonParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.01 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
return(new DataPointAquisitionResults(null, new List <PeptideSpectralMatch>(), new List <LabeledDataPoint>(), new List <LabeledDataPoint>(), 0, 0, 0, 0));
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
myMsDataFile,
initPrecTol,
initProdTol,
CalibrationParameters.NumFragmentsNeededForEveryIdentification,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CalibrationParameters.MinMS2IsotopicPeaksNeededForConfirmedIdentification,
fragmentTypesForCalibration,
CommonParameters,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(currentResult);
}
public ChemicalFormulaFragment(FragmentTypes type, int number, ChemicalFormula formula, AminoAcidPolymer parent)
: base(type, number, formula.MonoisotopicMass, parent)
{
ChemicalFormula = new ChemicalFormula(formula);
}
/// <summary>
/// Returns all fragments that are present in either fragmentation of A or B, but not in both
/// </summary>
public static IEnumerable <Fragment> GetSiteDeterminingFragments(AminoAcidPolymer peptideA, AminoAcidPolymer peptideB, FragmentTypes types)
{
HashSet <Fragment> aFrags = new HashSet <Fragment>(peptideA.Fragment(types));
aFrags.SymmetricExceptWith(peptideB.Fragment(types));
return(aFrags);
}
/// <summary>
/// Calculates the fragments that are different between this and another aminoacidpolymer
/// </summary>
/// <param name="other"></param>
/// <param name="type"></param>
/// <returns></returns>
public IEnumerable <Fragment> GetSiteDeterminingFragments(AminoAcidPolymer other, FragmentTypes type)
{
return(GetSiteDeterminingFragments(this, other, type));
}
public ChemicalFormulaFragment(FragmentTypes type, int number, string chemicalFormula, AminoAcidPolymer parent)
: this(type, number, new ChemicalFormula(chemicalFormula), parent)
{
}
