public static void TestCompIons_MatchIonsScore()
{
TestDataFile t = new TestDataFile();
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 300;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { precursorMass + (2 * Constants.ProtonMass) - 275.1350, precursorMass + (2 * Constants.ProtonMass) - 258.127, precursorMass + (2 * Constants.ProtonMass) - 257.1244, 50, 60, 70, 147.0764, precursorMass + (2 * Constants.ProtonMass) - 147.0764, precursorMass + (2 * Constants.ProtonMass) - 70, precursorMass + (2 * Constants.ProtonMass) - 60, precursorMass + (2 * Constants.ProtonMass) - 50, 257.1244, 258.127, 275.1350 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <Product> productsWithLocalizedMassDiff = new List <Product>();
foreach (double d in sorted_theoretical_product_masses_for_this_peptide)
{
productsWithLocalizedMassDiff.Add(new Product(ProductType.b, FragmentationTerminus.Both, d, 1, 1, 0));
}
CommonParameters commonParametersNoComp = new CommonParameters {
ProductMassTolerance = new AbsoluteTolerance(0.01)
};
CommonParameters commonParametersWithComp = new CommonParameters(productMassTolerance: new AbsoluteTolerance(0.01), addCompIons: true);
MsDataScan scan = t.GetOneBasedScan(2);
var scanWithMass = new Ms2ScanWithSpecificMass(scan, precursorMass.ToMz(1), 1, "", new CommonParameters());
List <MatchedFragmentIon> matchedIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersNoComp);
List <MatchedFragmentIon> matchedCompIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersWithComp);
matchedCompIons.AddRange(matchedIons);
// score when the mass-diff is on this residue
double localizedScore = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreNormal = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreComp = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedCompIons);
Assert.IsTrue(scoreNormal * 2 == scoreComp && scoreComp > scoreNormal + 1);
}
//[Test]
public static void TestGetCombinedMs2Scans()
{
var myMsDataFile = new TestDataFile(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//Write prime code to combine MS2MS3
Dictionary <int, double> listOfScanPrecusor = new Dictionary <int, double>();
List <MsDataScan> ListOfSortedMsScans = new List <MsDataScan>();
List <Ms2ScanWithSpecificMass> test = new List <Ms2ScanWithSpecificMass>();
foreach (var ms2scan in myMsDataFile.GetAllScansList().Where(x => x.MsnOrder != 1))
{
if (ms2scan.MsnOrder == 2 && !listOfScanPrecusor.Contains(new KeyValuePair <int, double>(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ.Value)))
{
if (ms2scan.OneBasedPrecursorScanNumber.HasValue)
{
listOfScanPrecusor.Add(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ.Value);
List <int> currentScanMS2OneBasedScanNumber = new List <int>
{
ms2scan.OneBasedScanNumber
};
var mz2 = ms2scan.MassSpectrum.XArray.ToList();
var intensities2 = ms2scan.MassSpectrum.YArray.ToList();
for (int i = 1; i < 7; i++)
{
if (ms2scan.OneBasedScanNumber + i <= myMsDataFile.NumSpectra)
{
var x = myMsDataFile.GetOneBasedScan(ms2scan.OneBasedScanNumber + i);
//var x = myMsDataFile.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().ElementAt(i);
if (x.MsnOrder == 2 && x.SelectedIonMZ == ms2scan.SelectedIonMZ)
{
currentScanMS2OneBasedScanNumber.Add(x.OneBasedScanNumber);
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
if (x.MsnOrder == 3 && currentScanMS2OneBasedScanNumber.Contains(x.OneBasedPrecursorScanNumber.Value))
{
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
}
}
var MassSpectrum2 = new MzSpectrum(mz2.ToArray(), intensities2.ToArray(), false);
ListOfSortedMsScans.Add(new MsDataScan(MassSpectrum2, ms2scan.OneBasedScanNumber, ms2scan.MsnOrder, ms2scan.IsCentroid, Polarity.Positive, ms2scan.RetentionTime,
ms2scan.ScanWindowRange, ms2scan.ScanFilter, ms2scan.MzAnalyzer, ms2scan.TotalIonCurrent, ms2scan.InjectionTime, null, "", ms2scan.SelectedIonMZ, ms2scan.SelectedIonChargeStateGuess, ms2scan.SelectedIonIntensity, ms2scan.IsolationMz, null, ms2scan.DissociationType, ms2scan.OneBasedPrecursorScanNumber, ms2scan.SelectedIonMonoisotopicGuessMz));
}
}
}
foreach (var ms2scan in ListOfSortedMsScans.Where(x => x.MsnOrder != 1))
{
test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
}
var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
}
public static void TestPsmHeader()
{
DigestionParams digestionParams = new DigestionParams();
PeptideWithSetModifications pepWithSetMods = new Protein(
"MQQQQQQQ",
"accession1",
"org",
new List <Tuple <string, string> > {
new Tuple <string, string>("geneNameType", "geneName")
},
new Dictionary <int, List <Modification> > {
{ 2, new List <Modification> {
new Modification("mod", "mod")
} }
},
name: "name",
full_name: "fullName",
sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(2, "P", "Q", "changed this sequence")
})
.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
MsDataFile myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
MsDataScan scann = myMsDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null);
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods.CompactPeptide(TerminusType.None), 1, 2, 3, scan, digestionParams);
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pepWithSetMods.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pepWithSetMods
} }
};
psm.MatchToProteinLinkedPeptides(matching);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
List <ProductType> lp = new List <ProductType> {
ProductType.B
};
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, lp, myMsDataFile, new CommonParameters(productMassTolerance: fragmentTolerance), new List <string>()).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 6, 0, 0, 0, true);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
public static void TestCompIons_MatchIons()
{
TestDataFile t = new TestDataFile(0.0001);
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 402.18629720155;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { 50, 60, 70, 147.0764 - Constants.ProtonMass, 200, 215, 230, 245, precursorMass + Constants.ProtonMass - 147.0764, 258.127, 275.1350, precursorMass + (2 * Constants.ProtonMass) - 70, precursorMass + (2 * Constants.ProtonMass) - 60, precursorMass + (2 * Constants.ProtonMass) - 50 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <double> matchedIonMassesT = new List <double>();
List <double> matchedDaErrorT = new List <double>();
List <double> matchedPpmErrorT = new List <double>();
List <double> matchedIonIntensityT = new List <double>();
List <double> matchedIonMassesF = new List <double>();
List <double> matchedDaErrorF = new List <double>();
List <double> matchedPpmErrorF = new List <double>();
List <double> matchedIonIntensityF = new List <double>();
List <int> matchedIonSeriesT = new List <int>();
List <int> matchedIonSeriesF = new List <int>();
MetaMorpheusEngine.MatchIonsOld(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, matchedIonSeriesT, matchedIonMassesT, matchedDaErrorT, matchedPpmErrorT, matchedIonIntensityT, precursorMass, ProductType.BnoB1ions, true);
MetaMorpheusEngine.MatchIonsOld(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, matchedIonSeriesF, matchedIonMassesF, matchedDaErrorF, matchedPpmErrorF, matchedIonIntensityF, precursorMass, ProductType.BnoB1ions, false);
//Test the number of series is doubled
Assert.IsTrue(matchedIonSeriesT.Count == matchedIonSeriesF.Count * 2);
//Test the number of ions is doubled
Assert.IsTrue(matchedIonMassesT.Count == matchedIonMassesF.Count * 2);
//Test the number of da errors is doubled
Assert.IsTrue(matchedDaErrorT.Count == matchedDaErrorF.Count * 2);
//test the number of ppm errors is doubled
Assert.IsTrue(matchedPpmErrorT.Count == matchedPpmErrorF.Count * 2);
//test the number of the intensity values is doubled
Assert.IsTrue(matchedIonIntensityT.Count == matchedIonIntensityF.Count * 2);
foreach (double d in matchedDaErrorF)
{
Assert.IsTrue(d <= 0.01);
}
foreach (double d in matchedDaErrorT)
{
Assert.IsTrue(d <= 0.01);
}
}
public static void TestCompIons_MatchIonsScore()
{
TestDataFile t = new TestDataFile();
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 300;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { precursorMass + (2 * Constants.protonMass) - 275.1350, precursorMass + (2 * Constants.protonMass) - 258.127, precursorMass + (2 * Constants.protonMass) - 257.1244, 50, 60, 70, 147.0764, precursorMass + (2 * Constants.protonMass) - 147.0764, precursorMass + (2 * Constants.protonMass) - 70, precursorMass + (2 * Constants.protonMass) - 60, precursorMass + (2 * Constants.protonMass) - 50, 257.1244, 258.127, 275.1350 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
double scoreT = MetaMorpheusEngine.CalculatePeptideScore(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, precursorMass, new List <DissociationType> {
DissociationType.HCD
}, true, 0);
double scoreF = MetaMorpheusEngine.CalculatePeptideScore(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, precursorMass, new List <DissociationType> {
DissociationType.HCD
}, false, 0);
Assert.IsTrue(scoreT == scoreF * 2 && scoreT > scoreF + 1);
}
public static void TestPsmHeader()
{
CommonParameters commonParameters = new CommonParameters();
PeptideWithSetModifications pepWithSetMods = new Protein(
"MQQQQQQQ",
"accession1",
"org",
new List <Tuple <string, string> > {
new Tuple <string, string>("geneNameType", "geneName")
},
new Dictionary <int, List <Modification> > {
{ 2, new List <Modification> {
new Modification("mod", "mod")
} }
},
name: "name",
fullName: "fullName",
sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(2, "P", "Q", "changed this sequence")
})
.Digest(commonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).First();
MsDataFile myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
MsDataScan scann = myMsDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null, new CommonParameters());
var theoreticalIons = new List <Product>();
pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalIons);
var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalIons, new CommonParameters());
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods, 1, 2, 3, scan, commonParameters, matchedIons);
psm.ResolveAllAmbiguities();
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, myMsDataFile, new CommonParameters(productMassTolerance: fragmentTolerance), null, new List <string>()).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 0, 0, 0);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
public static void TestPsmHeader()
{
DigestionParams digestionParams = new DigestionParams();
PeptideWithSetModifications pepWithSetMods = new Protein("MQQQQQQQ", "accession1").Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scann = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null);
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods.CompactPeptide(TerminusType.None), 1, 2, 3, scan);
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pepWithSetMods.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pepWithSetMods
} }
};
psm.MatchToProteinLinkedPeptides(matching);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
List <ProductType> lp = new List <ProductType> {
ProductType.B
};
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 6, 0, 0, 0, false);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
private static Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase> GetInfo(bool localizeable)
{
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: 2, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain, maxModsForPeptides: 1), scoreCutoff: 1);
// Alanine = Glycine + CH2
Protein protein1 = new Protein("MA", "protein1");
Protein protein2 = new Protein("MG", "protein2");
Protein protein3;
double monoisotopicMass = Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass;
ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
ModificationMotif.TryGetMotif("A", out ModificationMotif motif2);
TerminusLocalization modificationSites = TerminusLocalization.Any;
List <ModificationWithMass> allKnownFixedModifications = new List <ModificationWithMass>
{
new ModificationWithMass("CH2 on Glycine", null, motif1, modificationSites, monoisotopicMass)
};
List <ModificationWithMass> variableModifications;
ModificationWithMass alanineMod = new ModificationWithMass("CH2 on Alanine", null, motif2, modificationSites, monoisotopicMass);
if (localizeable)
{
variableModifications = new List <ModificationWithMass>();
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
alanineMod
} }
};
protein3 = new Protein("MA", "protein3", oneBasedModifications: oneBasedModifications);
}
else
{
variableModifications = new List <ModificationWithMass>();
variableModifications = new List <ModificationWithMass> {
alanineMod
};
protein3 = new Protein("MA", "protein3");
}
var pepWithSetModifications1 = protein1.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications2 = protein2.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications3 = protein3.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).Last();
CompactPeptide compactPeptide1 = new CompactPeptide(pepWithSetModifications1, TerminusType.None);
CompactPeptide compactPeptideDuplicate = new CompactPeptide(pepWithSetModifications2, TerminusType.None);
Assert.AreEqual(compactPeptide1, compactPeptideDuplicate);
CompactPeptide compactPeptide2 = new CompactPeptide(pepWithSetModifications3, TerminusType.None);
string fullFilePath = null;
int precursorCharge = 0;
TestDataFile testDataFile = new TestDataFile();
MsDataScan mzLibScan = testDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(mzLibScan, 0, precursorCharge, fullFilePath);
int scanIndex = 0;
double score = 0;
int notch = 0;
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(compactPeptide2, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
var newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3
};
MassDiffAcceptor massDiffAcceptors = new SinglePpmAroundZeroSearchMode(5);
SequencesToActualProteinPeptidesEngine stappe = new SequencesToActualProteinPeptidesEngine(newPsms, new List <Protein> {
protein1, protein2, protein3
},
allKnownFixedModifications, variableModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());
var haha = (SequencesToActualProteinPeptidesEngineResults)stappe.Run();
var compactPeptideToProteinPeptideMatching = haha.CompactPeptideToProteinPeptideMatching;
Assert.AreEqual(2, compactPeptideToProteinPeptideMatching.Count);
psm1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
bool noOneHitWonders = false;
return(new Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase>
(
newPsms, compactPeptideToProteinPeptideMatching, massDiffAcceptors, noOneHitWonders, compactPeptide1, compactPeptide2
));
}
public static void FdrTestMethod()
{
MassDiffAcceptor searchModes = new DotMassDiffAcceptor(null, new List <double> {
0, 1.0029
}, new PpmTolerance(5));
List <string> nestedIds = new List <string>();
Protein p = new Protein("MNKNNKNNNKNNNNK", null);
DigestionParams digestionParams = new DigestionParams();
var digested = p.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
PeptideWithSetModifications pep1 = digested[0];
PeptideWithSetModifications pep2 = digested[1];
PeptideWithSetModifications pep3 = digested[2];
PeptideWithSetModifications pep4 = digested[3];
TestDataFile t = new TestDataFile(new List <PeptideWithSetModifications> {
pep1, pep2, pep3
});
MsDataScan mzLibScan1 = t.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan1 = new Ms2ScanWithSpecificMass(mzLibScan1, pep1.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(pep1, 0, 3, 0, scan1, digestionParams, new List <MatchedFragmentIon>());
MsDataScan mzLibScan2 = t.GetOneBasedScan(4);
Ms2ScanWithSpecificMass scan2 = new Ms2ScanWithSpecificMass(mzLibScan2, pep2.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(pep2, 1, 2, 1, scan2, digestionParams, new List <MatchedFragmentIon>());
MsDataScan mzLibScan3 = t.GetOneBasedScan(6);
Ms2ScanWithSpecificMass scan3 = new Ms2ScanWithSpecificMass(mzLibScan3, pep3.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(pep3, 0, 1, 2, scan3, digestionParams, new List <MatchedFragmentIon>());
psm3.AddOrReplace(pep4, 1, 1, true, new List <MatchedFragmentIon>(), 0);
var newPsms = new List <PeptideSpectralMatch> {
psm1, psm2, psm3
};
foreach (PeptideSpectralMatch psm in newPsms)
{
psm.ResolveAllAmbiguities();
}
FdrAnalysisEngine fdr = new FdrAnalysisEngine(newPsms, searchModes.NumNotches, new CommonParameters(), nestedIds);
fdr.Run();
Assert.AreEqual(2, searchModes.NumNotches);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[1].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[2].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoy);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoy);
Assert.AreEqual(2, newPsms[1].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoy);
Assert.AreEqual(3, newPsms[2].FdrInfo.CumulativeTarget);
}
public static void FdrTestMethod()
{
MassDiffAcceptor searchModes = new DotMassDiffAcceptor(null, new List <double> {
0, 1.0029
}, new PpmTolerance(5));
List <string> nestedIds = new List <string>();
Protein p = new Protein("MNKNNKNNNKNNNNK", null);
DigestionParams digestionParams = new DigestionParams();
var digested = p.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).ToList();
PeptideWithSetModifications pep1 = digested[0];
PeptideWithSetModifications pep2 = digested[1];
PeptideWithSetModifications pep3 = digested[2];
PeptideWithSetModifications pep4 = digested[3];
TestDataFile t = new TestDataFile(new List <PeptideWithSetModifications> {
pep1, pep2, pep3
});
CompactPeptide peptide1 = new CompactPeptide(pep1, TerminusType.None);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > mzLibScan1 = t.GetOneBasedScan(2) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan1 = new Ms2ScanWithSpecificMass(mzLibScan1, peptide1.MonoisotopicMassIncludingFixedMods.ToMz(1), 1, null);
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(peptide1, 0, 3, 0, scan1);
CompactPeptide peptide2 = new CompactPeptide(pep2, TerminusType.None);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > mzLibScan2 = t.GetOneBasedScan(4) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan2 = new Ms2ScanWithSpecificMass(mzLibScan2, peptide2.MonoisotopicMassIncludingFixedMods.ToMz(1), 1, null);
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(peptide2, 1, 2, 1, scan2);
CompactPeptide peptide3 = new CompactPeptide(pep3, TerminusType.None);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > mzLibScan3 = t.GetOneBasedScan(6) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan3 = new Ms2ScanWithSpecificMass(mzLibScan3, peptide3.MonoisotopicMassIncludingFixedMods.ToMz(1), 1, null);
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(peptide3, 0, 1, 2, scan3);
CompactPeptide peptide4 = new CompactPeptide(pep4, TerminusType.None);
psm3.AddOrReplace(peptide4, 1, 1, true);
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{
peptide1, new HashSet <PeptideWithSetModifications> {
pep1
}
},
{
peptide2, new HashSet <PeptideWithSetModifications> {
pep2
}
},
{
peptide3, new HashSet <PeptideWithSetModifications> {
pep3
}
},
{
peptide4, new HashSet <PeptideWithSetModifications> {
pep4
}
},
};
psm1.MatchToProteinLinkedPeptides(matching);
psm2.MatchToProteinLinkedPeptides(matching);
psm3.MatchToProteinLinkedPeptides(matching);
var newPsms = new List <PeptideSpectralMatch> {
psm1, psm2, psm3
};
FdrAnalysisEngine fdr = new FdrAnalysisEngine(newPsms, searchModes.NumNotches, true, nestedIds);
fdr.Run();
Assert.AreEqual(2, searchModes.NumNotches);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[1].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[2].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoy);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoy);
Assert.AreEqual(2, newPsms[1].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoy);
Assert.AreEqual(3, newPsms[2].FdrInfo.CumulativeTarget);
}
//[Test]
public static void TestGetCombinedMs2Scans()
{
var myMsDataFile = new TestDataFile(5);
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Write prime code to combine MS2MS3
Dictionary <int, double> listOfScanPrecusor = new Dictionary <int, double>();
List <IMzmlScan> ListOfSortedMsScans = new List <IMzmlScan>();
List <Ms2ScanWithSpecificMass> test = new List <Ms2ScanWithSpecificMass>();
foreach (var ms2scan in myMsDataFile.OfType <IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > >())
{
if (ms2scan.MsnOrder == 2 && !listOfScanPrecusor.Contains(new KeyValuePair <int, double>(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ)))
{
if (ms2scan.OneBasedPrecursorScanNumber.HasValue)
{
listOfScanPrecusor.Add(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ);
List <int> currentScanMS2OneBasedScanNumber = new List <int>();
currentScanMS2OneBasedScanNumber.Add(ms2scan.OneBasedScanNumber);
var mz2 = ms2scan.MassSpectrum.XArray.ToList();
var intensities2 = ms2scan.MassSpectrum.YArray.ToList();
for (int i = 1; i < 7; i++)
{
if (ms2scan.OneBasedScanNumber + i <= myMsDataFile.NumSpectra)
{
var x = myMsDataFile.GetOneBasedScan(ms2scan.OneBasedScanNumber + i) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
//var x = myMsDataFile.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().ElementAt(i);
if (x.MsnOrder == 2 && x.SelectedIonMZ == ms2scan.SelectedIonMZ)
{
currentScanMS2OneBasedScanNumber.Add(x.OneBasedScanNumber);
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
if (x.MsnOrder == 3 && currentScanMS2OneBasedScanNumber.Contains(x.OneBasedPrecursorScanNumber.Value))
{
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
}
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.ToArray(), intensities2.ToArray(), false);
ListOfSortedMsScans.Add(new MzmlScanWithPrecursor(ms2scan.OneBasedScanNumber, MassSpectrum2, ms2scan.MsnOrder, ms2scan.IsCentroid, Polarity.Positive, ms2scan.RetentionTime,
ms2scan.ScanWindowRange, ms2scan.ScanFilter, ms2scan.MzAnalyzer, ms2scan.TotalIonCurrent, ms2scan.SelectedIonMZ, ms2scan.SelectedIonChargeStateGuess, ms2scan.SelectedIonIntensity, ms2scan.IsolationMz, null, ms2scan.DissociationType, ms2scan.OneBasedPrecursorScanNumber, ms2scan.SelectedIonMonoisotopicGuessMz, ms2scan.InjectionTime, ""));
}
}
}
foreach (var ms2scan in ListOfSortedMsScans.OfType <IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > >())
{
test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, ""));
}
var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
//Using function to combine MS2MS3
//var listOfSortedms2Scans2 = MetaMorpheusTask.GetCombinedMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Assert.AreEqual(5, myMsDataFile.NumSpectra);
//Assert.AreEqual(1, listOfSortedms2Scans2.Count());
}