public TestDataFile(PeptideWithSetModifications pepWithSetMods, int charge, double intensity, double rt) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(charge), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(charge), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(charge) };
var intensities1 = new double[] { intensity, intensity * 10, intensity / 10 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, rt, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(intensity);
intensities2.Add(intensity);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, rt + 0.01, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2");
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
public void Setup()
{
double[] mz = { 328.73795, 329.23935, 447.73849, 448.23987, 482.23792, 482.57089, 482.90393, 500.95358, 501.28732, 501.62131, 611.99377, 612.32806, 612.66187, 722.85217, 723.35345 };
double[] intensities = { 81007096.0, 28604418.0, 78353512.0, 39291696.0, 122781408.0, 94147520.0, 44238040.0, 71198680.0, 54184096.0, 21975364.0, 44514172.0, 43061628.0, 23599424.0, 56022696.0, 41019144.0 };
_mzSpectrumA = new MzmlMzSpectrum(mz, intensities, false);
}
public static void DifferentAnalyzersTest()
{
IMzmlScan[] scans = new IMzmlScan[2];
double[] intensities1 = new double[] { 1 };
double[] mz1 = new double[] { 50 };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");
double[] intensities2 = new double[] { 1 };
double[] mz2 = new double[] { 30 };
MzmlMzSpectrum massSpec2 = new MzmlMzSpectrum(mz2, intensities2, false);
scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.IonTrap3D, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"));
Assert.AreEqual(MZAnalyzerType.Orbitrap, ok.First().MzAnalyzer);
Assert.AreEqual(MZAnalyzerType.IonTrap3D, ok.Last().MzAnalyzer);
}
private MzmlMzSpectrum CreateSpectrum(ChemicalFormula f, double lowerBound, double upperBound, int minCharge)
{
IsotopicDistribution isodist = IsotopicDistribution.GetDistribution(f, 0.1, 0.001);
MzmlMzSpectrum notActuallyMzS = new MzmlMzSpectrum(isodist.Masses.ToArray(), isodist.Intensities.ToArray(), false);
notActuallyMzS.ReplaceXbyApplyingFunction(b => b.X.ToMz(1));
List <double> allMasses = new List <double>();
List <double> allIntensitiess = new List <double>();
while (notActuallyMzS.FirstX > lowerBound)
{
foreach (var thisPeak in notActuallyMzS)
{
if (thisPeak.Mz > lowerBound && thisPeak.Mz < upperBound)
{
allMasses.Add(thisPeak.Mz);
allIntensitiess.Add(thisPeak.Intensity);
}
}
minCharge += 1;
notActuallyMzS = new MzmlMzSpectrum(isodist.Masses.ToArray(), isodist.Intensities.ToArray(), false);
notActuallyMzS.ReplaceXbyApplyingFunction(s => s.X.ToMz(minCharge));
}
var allMassesArray = allMasses.ToArray();
var allIntensitiessArray = allIntensitiess.ToArray();
Array.Sort(allMassesArray, allIntensitiessArray);
return(new MzmlMzSpectrum(allMassesArray, allIntensitiessArray, false));
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, string v) : base(2, new SourceFile(null, null, null, null, null))
{
if (v.Equals("quadratic"))
{
// Add three ms1 peaks with charge 2, exact
var MassSpectrum1 = new MzmlMzSpectrum(new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) }, new double[] { 1, 1, 1 }, false);
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
var t1 = aok.ToMz(1);
var c = 0.0000001;
mz2.Add(t1 + c * Math.Pow(t1, 2));
var t2 = (aok + 1.003).ToMz(1);
mz2.Add(t2 + c * Math.Pow(t2, 2));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2");
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1"),
scan2
};
Scans = ScansHere.ToArray();
}
}
public void FilterByNumberOfMostIntenseRobTest()
{
double[] x = new double[] { 50, 60, 70, 147.0764, 257.1244, 258.127, 275.135 };
double[] y = new double[] { 1, 1, 1, 1, 1, 1, 1 };
MzmlMzSpectrum spectrum = new MzmlMzSpectrum(x, y, false);
Assert.AreEqual(7, spectrum.FilterByNumberOfMostIntense(200).Count());
}
public TestScan(int OneBasedScanNumber, double RetentionTime, MzmlMzSpectrum MassSpectrum, double InjectionTime)
{
MsnOrder = 1;
this.OneBasedScanNumber = OneBasedScanNumber;
this.RetentionTime = RetentionTime;
this.MassSpectrum = MassSpectrum;
this.InjectionTime = InjectionTime;
}
public static void TestVeryCloseExperimentalsModern()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
var thePep = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 };
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1");
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 600, 1, null) };
CommonParameters CommonParameters = new CommonParameters
{
ProductMassTolerance = new PpmTolerance(5),
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
MaxModificationIsoforms = int.MaxValue,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
},
ConserveMemory = false,
ScoreCutoff = 1
};
var indexEngine = new IndexingEngine(new List <Protein> {
prot
}, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType> {
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var cse = new ModernSearchEngine(globalPsms, arrayOfSortedMS2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, false, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void TestIdenticalPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
mods.Add(1, new List <Modification> {
new ModificationWithMass("Hehe", null, motif, TerminusLocalization.NProt, 18.010565, null, null, null, null)
});
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = ye.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 };
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1");
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) };
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
MaxModificationIsoforms = int.MaxValue,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
},
ProductMassTolerance = new PpmTolerance(5),
ConserveMemory = false,
ScoreCutoff = 1
};
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> {
prot
}, new List <ProductType> {
ProductType.B, ProductType.Y
}, new OpenSearchMode(), false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 4);
Assert.Greater(globalPsms[0].Score, 3);
}
public static void WriteEmptyScan()
{
double[] intensities1 = new double[] { };
double[] mz1 = new double[] { };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
IMzmlScan[] scans = new IMzmlScan[] {
new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1")
};
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"));
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan2.mzML"), false);
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
IMzmlScan[] Scans = new IMzmlScan[2];
Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1");
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2");
var myMsDataFile = new FakeMsDataFile(Scans);
var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX;
var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false);
Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML");
okay.GetOneBasedScan(2);
Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1));
Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2));
var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX;
Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);
var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum);
secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44);
Assert.AreEqual(44, secondScan2.MassSpectrum.LastX);
}
public TestDataFile(string slightlyLargerDataFile) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { 50, 60, 70, 80, 90, 630.27216.ToMz(2) };
var intensities1 = new double[] { 1, 1, 1, 1, 1, 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
var mz2 = new double[] { 50, 60, 70, 76.0393, 133.0608, 147.0764, 190.0822, 247.1037, 257.1244, 258.127, 275.1350, 385.1830, 442.2045, 630.27216 };
var intensities2 = new double[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum2 = new MzmlMzSpectrum(mz2, intensities2, false);
ScansHere.Add(new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 630.27216.ToMz(2), 2, 1, 630.27216.ToMz(2), 2, DissociationType.HCD, 1, 630.27216.ToMz(2), 1, "scan=2"));
Scans = ScansHere.ToArray();
}
public TestDataFile(bool emptyScan) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { 50 };
var intensities1 = new double[] { 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
var mz2 = new double[] { 1 };
var intensities2 = new double[] { 1 };
var MassSpectrum2 = new MzmlMzSpectrum(mz2, intensities2, false);
ScansHere.Add(new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 402.18629720155.ToMz(2), 2, 1, 402.18629720155.ToMz(2), 2, DissociationType.HCD, 1, 402.18629720155.ToMz(2), 1, "scan=2"));
Scans = ScansHere.ToArray();
}
public TestDataFile(double closeMassDifference) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { 50, 60, 70, 80, 90, 402.18629720155.ToMz(2) };
var intensities1 = new double[] { 1, 1, 1, 1, 1, 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
var mz2 = new double[] { 50, 60, 70, 147.0764, 258.132 - closeMassDifference - Constants.protonMass, 258.132 - Constants.protonMass, 275.1350 };
var intensities2 = new double[] { 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum2 = new MzmlMzSpectrum(mz2, intensities2, false);
ScansHere.Add(new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 402.18629720155.ToMz(2), 2, 1, 402.18629720155.ToMz(2), 2, DissociationType.HCD, 1, 402.18629720155.ToMz(2), 1, "scan=2"));
Scans = ScansHere.ToArray();
}
public void TestCoIsolationDifferentCharges()
{
Peptide pep1 = new Peptide("AAAAAA");
Peptide pep2 = new Peptide("AAAAAAA[H21]AAAAA");
var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);
var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);
IMzmlScan[] Scans = new IMzmlScan[2];
double[] ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
double[] ms1mzs = dist1.Masses.Select(b => b.ToMz(1)).Concat(dist2.Masses.Select(b => b.ToMz(2))).OrderBy(b => b).ToArray();
double selectedIonMz = ms1mzs[1];
MzmlMzSpectrum MS1 = new MzmlMzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MzmlScan(1, MS1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null);
// Horrible fragmentation, but we don't care about this!
double[] ms2intensities = new double[] { 1000 };
double[] ms2mzs = new double[] { 1000 };
MzmlMzSpectrum MS2 = new MzmlMzSpectrum(ms2mzs, ms2intensities, false);
double isolationMZ = selectedIonMz;
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null, null);
var myMsDataFile = new FakeMsDataFile(Scans);
var cool = myMsDataFile.Last() as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
int maxAssumedChargeState = 2;
Tolerance massTolerance = new Tolerance("10 PPM");
var isolatedMasses = cool.GetIsolatedMassesAndCharges(myMsDataFile.GetOneBasedScan(cool.OneBasedPrecursorScanNumber).MassSpectrum, maxAssumedChargeState, massTolerance, 5).ToList();
Assert.AreEqual(2, isolatedMasses.Count);
Assert.AreEqual(1, isolatedMasses.Count(b => b.Item2 == 1));
Assert.AreEqual(1, isolatedMasses.Count(b => b.Item2 == 2));
Assert.AreEqual(pep1.MonoisotopicMass, isolatedMasses.Select(b => b.Item1.First().Mz.ToMass(b.Item2)).Min(), 1e-9);
Assert.AreEqual(pep2.MonoisotopicMass, isolatedMasses.Select(b => b.Item1.First().Mz.ToMass(b.Item2)).Max(), 1e-9);
}
public TestDataFile(List <PeptideWithSetModifications> pepWithSetModss, bool additionalMasses = false) : base(pepWithSetModss.Count * 2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null))
{
var ScansHere = new List <IMzmlScan>();
for (int i = 0; i < pepWithSetModss.Count; i++)
{
var pepWithSetMods = pepWithSetModss[i];
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(3), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(3), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(3), pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) };
var intensities1 = new double[] { 1, 1, 1, 1, 1, 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
ScansHere.Add(new MzmlScan(2 * i + 1, MassSpectrum1, 1, true, Polarity.Positive, 2 * i, new MzLibUtil.MzRange(0, 10000), "gg", MZAnalyzerType.Orbitrap, 1000, 1, "scan=1"));
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
IEnumerable <double> additionalMassesArray;
if (additionalMasses)
{
additionalMassesArray = new List <double> {
260.08307817722, 397.14199003569, 498.18966850487, 612.23259594625, 683.2697097314, 146.10552769922, 217.14264148437
}
}
;
else
{
additionalMassesArray = new List <double>();
}
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}).Concat(additionalMassesArray))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
ScansHere.Add(new MzmlScanWithPrecursor(2 * i + 2, MassSpectrum2, 2, true, Polarity.Positive, 2 * i + 1, new MzLibUtil.MzRange(0, 10000), "gg", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 2 * i + 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2"));
}
Scans = ScansHere.ToArray();
}
public TestDataFile(int MS3 = 5) : base(MS3, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { 50, 60, 70, 80, 90, 764.1376.ToMz(2) };
var intensities1 = new double[] { 1, 1, 1, 1, 1, 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
var mz2 = new double[] { 52, 62, 72, 147.0764, 257.1244, 258.127, 275.1350, 502 };
var intensities2 = new double[] { 1, 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum2 = new MzmlMzSpectrum(mz2, intensities2, false);
ScansHere.Add(new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 764.1376.ToMz(2), 2, 1, 764.1376.ToMz(2), 2, DissociationType.CID, 1, 764.1376.ToMz(1), 1, "scan=2"));
var mz3 = new double[] { 53, 63, 73, 148.0764, 258.1244, 259.127, 276.1350, 503 };
var intensities3 = new double[] { 1, 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum3 = new MzmlMzSpectrum(mz3, intensities3, false);
ScansHere.Add(new MzmlScanWithPrecursor(3, MassSpectrum3, 2, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 764.1376.ToMz(2), 2, 1, 764.1376.ToMz(2), 2, DissociationType.ETD, 1, 764.1376.ToMz(1), 1, "scan=3"));
var mz4 = new double[] { 54, 64, 74, 149.0764, 259.1244, 260.127, 277.1350, 504 };
var intensities4 = new double[] { 1, 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum4 = new MzmlMzSpectrum(mz4, intensities4, false);
ScansHere.Add(new MzmlScanWithPrecursor(4, MassSpectrum4, 3, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 275.1350.ToMz(1), 1, 1, 275.1350.ToMz(1), 1, DissociationType.HCD, 2, 275.1350.ToMz(1), 1, "scan=4"));
var mz5 = new double[] { 55, 65, 75, 150.0764, 260.1244, 261.127, 278.1350, 505 };
var intensities5 = new double[] { 1, 1, 1, 1, 1, 1, 1, 1 };
var MassSpectrum5 = new MzmlMzSpectrum(mz5, intensities5, false);
ScansHere.Add(new MzmlScanWithPrecursor(5, MassSpectrum5, 3, true, Polarity.Positive, 2,
new MzLibUtil.MzRange(0, 10000), "f", MZAnalyzerType.Unknown, 100000, 257.1244.ToMz(1), 1, 1, 257.1244.ToMz(1), 1, DissociationType.HCD, 2, 257.1244.ToMz(1), 1, "scan=5"));
Scans = ScansHere.ToArray();
}
public static void AnotherMzMLtest()
{
IMzmlScan[] scans = new IMzmlScan[4];
double[] intensities1 = new double[] { 1 };
double[] mz1 = new double[] { 50 };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");
double[] intensities2 = new double[] { 1 };
double[] mz2 = new double[] { 30 };
MzmlMzSpectrum massSpec2 = new MzmlMzSpectrum(mz2, intensities2, false);
scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");
double[] intensities3 = new double[] { 1 };
double[] mz3 = new double[] { 50 };
MzmlMzSpectrum massSpec3 = new MzmlMzSpectrum(mz3, intensities3, false);
scans[2] = new MzmlScan(3, massSpec3, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "3");
double[] intensities4 = new double[] { 1 };
double[] mz4 = new double[] { 30 };
MzmlMzSpectrum massSpec4 = new MzmlMzSpectrum(mz4, intensities4, false);
scans[3] = new MzmlScanWithPrecursor(4, massSpec4, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 3, null, null, "4");
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"));
var scanWithPrecursor = ok.Last(b => b is IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Assert.AreEqual(3, scanWithPrecursor.OneBasedPrecursorScanNumber);
}
public void Setup()
{
Environment.CurrentDirectory = TestContext.CurrentContext.TestDirectory;
UsefulProteomicsDatabases.Loaders.LoadElements(@"elements.dat");
double[] mz = { 328.73795, 329.23935, 447.73849, 448.23987, 482.23792, 482.57089, 482.90393, 500.95358, 501.28732, 501.62131, 611.99377, 612.32806, 612.66187, 722.85217, 723.35345 };
double[] intensities = { 81007096.0, 28604418.0, 78353512.0, 39291696.0, 122781408.0, 94147520.0, 44238040.0, 71198680.0, 54184096.0, 21975364.0, 44514172.0, 43061628.0, 23599424.0, 56022696.0, 41019144.0 };
_mzSpectrumA = new MzmlMzSpectrum(mz, intensities, false);
var peptide = new Peptide("KQEEQMETEQQNKDEGK");
MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
IMzmlScan[] Scans = new IMzmlScan[2];
Scans[0] = new MzmlScan(1, MS1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1);
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 693.9892, 3, .3872, 693.99, 1, DissociationType.Unknown, 1, 693.6550, 1);
myMsDataFile = new FakeMsDataFile(Scans);
}
public void ReplaceFirstScanArrays(double[] mz, double[] intensities)
{
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
Scans[0] = new MzmlScan(Scans[0].OneBasedScanNumber, massSpectrum, Scans[0].MsnOrder, Scans[0].IsCentroid, Scans[0].Polarity, Scans[0].RetentionTime, Scans[0].ScanWindowRange, Scans[0].ScanFilter, Scans[0].MzAnalyzer, massSpectrum.SumOfAllY, Scans[0].InjectionTime, Scans[0].NativeId);
}
public void TestNumPeaksWithinRange()
{
double[] xArray = { 1, 2, 3, 4, 5, 6, 7 };
double[] yArray = { 1, 2, 1, 5, 1, 2, 1 };
var thisSpectrum = new MzmlMzSpectrum(xArray, yArray, false);
Assert.AreEqual(7, thisSpectrum.NumPeaksWithinRange(double.MinValue, double.MaxValue));
Assert.AreEqual(6, thisSpectrum.NumPeaksWithinRange(1, 7));
Assert.AreEqual(0, thisSpectrum.NumPeaksWithinRange(1, 1));
Assert.AreEqual(1, thisSpectrum.NumPeaksWithinRange(1, 2));
Assert.AreEqual(2, thisSpectrum.NumPeaksWithinRange(0.001, 2.999));
Assert.AreEqual(1, thisSpectrum.NumPeaksWithinRange(0, 1.5));
Assert.AreEqual(1, thisSpectrum.NumPeaksWithinRange(6.5, 8));
Assert.AreEqual(2, thisSpectrum.NumPeaksWithinRange(3, 5));
Assert.AreEqual(2, thisSpectrum.NumPeaksWithinRange(3.5, 5.5));
Assert.AreEqual(1, thisSpectrum.NumPeaksWithinRange(7, 8));
Assert.AreEqual(0, thisSpectrum.NumPeaksWithinRange(8, 9));
Assert.AreEqual(0, thisSpectrum.NumPeaksWithinRange(-2, -1));
Assert.AreEqual("[1 to 7] m/z (Peaks 7)", thisSpectrum.ToString());
//Assert.AreEqual(7, thisSpectrum.FilterByNumberOfMostIntense(7).Size);
//Assert.AreEqual(1, thisSpectrum.FilterByNumberOfMostIntense(1).Size);
//Assert.AreEqual(4, thisSpectrum.FilterByNumberOfMostIntense(1).FirstX);
//Assert.AreEqual(2, thisSpectrum.FilterByNumberOfMostIntense(3).FirstX);
//Assert.AreEqual(0, thisSpectrum.FilterByNumberOfMostIntense(0).Size);
//Assert.AreEqual(2, thisSpectrum.WithRangeRemoved(2, 6).Size);
//Assert.AreEqual(0, thisSpectrum.WithRangeRemoved(0, 100).Size);
//Assert.AreEqual(6, thisSpectrum.WithRangeRemoved(7, 100).Size);
//Assert.AreEqual(1, thisSpectrum.WithRangeRemoved(new DoubleRange(double.MinValue, 6)).Size);
List <DoubleRange> xRanges = new List <DoubleRange>
{
new DoubleRange(2, 5),
new DoubleRange(3, 6)
};
//Assert.AreEqual(2, thisSpectrum.WithRangesRemoved(xRanges).Size);
//Assert.AreEqual(3, thisSpectrum.Extract(new DoubleRange(4.5, 10)).Size);
//Assert.AreEqual(2, thisSpectrum.FilterByY(new DoubleRange(1.5, 2.5)).Size);
//Assert.AreEqual(3, thisSpectrum.FilterByY(1.5, double.MaxValue).Size);
//Assert.AreEqual(2, thisSpectrum.ApplyFunctionToX(b => b * 2).FirstX);
Assert.AreEqual(1, thisSpectrum.GetClosestPeak(-100).X);
Assert.AreEqual(7, thisSpectrum.GetClosestPeak(6.6).X);
Assert.AreEqual(7, thisSpectrum.GetClosestPeak(7).X);
Assert.AreEqual(7, thisSpectrum.GetClosestPeak(8).X);
IEnumerable hnm = thisSpectrum;
double dudu = 0;
foreach (var ikik in hnm)
{
dudu += ((Peak)ikik).X;
}
Assert.AreEqual(1 + 2 + 3 + 4 + 5 + 6 + 7, dudu);
}
public static void TestCoIsolation()
{
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
Protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null),
MinPeptideLength = null,
},
ConserveMemory = false,
ScoreCutoff = 1,
DeconvolutionIntensityRatio = 50
};
var variableModifications = new List <ModificationWithMass>();
var fixedModifications = new List <ModificationWithMass>();
var proteinList = new List <Protein> {
new Protein("MNNNKNDNK", null)
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Proteomics.Peptide pep1 = new Proteomics.Peptide("NNNK");
Proteomics.Peptide pep2 = new Proteomics.Peptide("NDNK");
var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);
var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);
IMzmlScan[] Scans = new IMzmlScan[2];
double[] ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
double[] ms1mzs = dist1.Masses.Concat(dist2.Masses).OrderBy(b => b).Select(b => b.ToMz(1)).ToArray();
double selectedIonMz = ms1mzs[1];
MzmlMzSpectrum MS1 = new MzmlMzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MzmlScan(1, MS1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, "scan=1");
double[] ms2intensities = new double[] { 1, 1, 1, 1, 1 };
double[] ms2mzs = new double[] { 146.106.ToMz(1), 228.086.ToMz(1), 229.07.ToMz(1), 260.148.ToMz(1), 342.129.ToMz(1) };
MzmlMzSpectrum MS2 = new MzmlMzSpectrum(ms2mzs, ms2intensities, false);
double isolationMZ = selectedIonMz;
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null, null, "scan=2");
var myMsDataFile = new FakeMsDataFile(Scans);
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 50;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchModes, false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();
// Two matches for this single scan! Corresponding to two co-isolated masses
Assert.AreEqual(2, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[0].Score > 1);
Assert.AreEqual(2, allPsmsArray[0].ScanNumber);
var ojdfkj = (SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(new List <PeptideSpectralMatch> {
allPsmsArray[0], allPsmsArray[1]
}, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, new List <string>()).Run();
foreach (var huh in allPsmsArray)
{
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(ojdfkj.CompactPeptideToProteinPeptideMatching);
}
}
Assert.AreEqual("NNNK", allPsmsArray[0].BaseSequence);
Assert.AreEqual("NDNK", allPsmsArray[1].BaseSequence);
}
//[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());
}
public void CorrectOrder()
{
_mzSpectrumA = new MzmlMzSpectrum(new double[] { 5, 6, 7 }, new double[] { 1, 2, 3 }, false);
Assert.IsTrue(_mzSpectrumA.FilterByNumberOfMostIntense(2).First().Mz < _mzSpectrumA.FilterByNumberOfMostIntense(2).ToList()[1].Mz);
}
