public void DataFileTest()
{
MsDataScan theSpectrum = new MsDataScan(_mzSpectrumA, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 1000), "fake scan filter", MZAnalyzerType.Unknown, _mzSpectrumA.SumOfAllY, 1, null, "scan=1");
MsDataScan[] theList = new MsDataScan[1];
theList[0] = theSpectrum;
FakeMsDataFile thefile = new FakeMsDataFile(theList);
var theOneBasedScan = thefile.GetOneBasedScan(1);
Assert.AreEqual("Scan #1", theOneBasedScan.ToString());
Assert.AreEqual(15, theOneBasedScan.MassSpectrum.Size);
Assert.AreEqual(15, theOneBasedScan.MassSpectrum.Size);
Assert.AreEqual(1, thefile.NumSpectra);
Assert.AreEqual(1, thefile.NumSpectra);
Assert.IsTrue(thefile.GetOneBasedScan(1).IsCentroid);
foreach (var ok in thefile)
{
Assert.AreEqual(300, ok.ScanWindowRange.Minimum, 1e-9);
Assert.AreEqual(1000, ok.ScanWindowRange.Maximum, 1e-9);
}
int ok1 = 0;
foreach (var i in thefile.GetMsScansInTimeRange(0, 2))
{
ok1 += 1;
}
Assert.AreEqual(1, ok1);
int ok2 = 0;
foreach (var i in thefile.GetMsScansInTimeRange(2, 4))
{
ok2 += 1;
}
Assert.AreEqual(0, ok2);
int ok3 = 0;
foreach (var i in thefile.GetMsScansInTimeRange(-4, -2))
{
ok3 += 1;
}
Assert.AreEqual(0, ok3);
}
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 void TestAMoreRealFile()
{
var theScan = myMsDataFile.GetOneBasedScan(2);
Assert.AreEqual(1, theScan.IsolationRange.Width);
Assert.AreEqual(DissociationType.Unknown, theScan.DissociationType);
Assert.AreEqual(693.99, theScan.IsolationMz);
Assert.AreEqual(1, theScan.IsolationRange.Maximum - theScan.IsolationRange.Minimum);
Assert.AreEqual(1, theScan.OneBasedPrecursorScanNumber);
Assert.AreEqual(3, theScan.SelectedIonChargeStateGuess.Value);
var precursorScan = myMsDataFile.GetOneBasedScan(theScan.OneBasedPrecursorScanNumber.Value);
theScan.RefineSelectedMzAndIntensity(precursorScan.MassSpectrum);
Assert.AreEqual(.32872, theScan.SelectedIonIntensity, 0.01);
Assert.AreEqual(693.9892, theScan.SelectedIonMZ, 0.01);
Assert.AreEqual(693.655, theScan.SelectedIonMonoisotopicGuessMz, 0.001);
Assert.AreNotEqual(0, myMsDataFile.GetOneBasedScan(2).MassSpectrum.FirstX);
Assert.AreEqual(myMsDataFile.GetOneBasedScan(2).MassSpectrum.CopyTo2DArray()[0, 0], myMsDataFile.GetOneBasedScan(2).MassSpectrum.FirstX);
Assert.AreNotEqual(0, myMsDataFile.GetOneBasedScan(2).MassSpectrum.LastX);
theScan.ComputeMonoisotopicPeakIntensity(precursorScan.MassSpectrum);
theScan.TransformMzs(b => 0, b => 0);
Assert.AreEqual("Scan #2", myMsDataFile.GetOneBasedScan(2).ToString());
Assert.AreEqual(0, myMsDataFile.GetOneBasedScan(2).MassSpectrum.FirstX);
Assert.AreEqual(0, myMsDataFile.GetOneBasedScan(2).MassSpectrum.LastX);
Assert.AreEqual(0, theScan.SelectedIonMZ);
List <MsDataScan> a = myMsDataFile.GetAllScansList();
foreach (var b in a)
{
Assert.IsFalse(b.IsCentroid);
}
foreach (var b in myMsDataFile)
{
Assert.AreEqual(Polarity.Positive, b.Polarity);
}
}
public void TestCoIsolation()
{
Peptide pep1 = new Peptide("AAAAAA");
Peptide pep2 = new Peptide("AAA[H]AAA");
var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);
var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);
MsDataScan[] Scans = new MsDataScan[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];
MzSpectrum MS1 = new MzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, null, null);
// Horrible fragmentation, but we don't care about this!
double[] ms2intensities = new double[] { 1000 };
double[] ms2mzs = new double[] { 1000 };
MzSpectrum MS2 = new MzSpectrum(ms2mzs, ms2intensities, false);
double isolationMZ = selectedIonMz;
Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, null, null, null, selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null);
var myMsDataFile = new FakeMsDataFile(Scans);
var cool = myMsDataFile.GetAllScansList().Last();
int maxAssumedChargeState = 1;
Tolerance massTolerance = Tolerance.ParseToleranceString("10 PPM");
var isolatedMasses = cool.GetIsolatedMassesAndCharges(myMsDataFile.GetOneBasedScan(cool.OneBasedPrecursorScanNumber.Value).MassSpectrum, 1, maxAssumedChargeState, 10, 5).ToList();
Assert.AreEqual(2, isolatedMasses.Count);
Assert.AreEqual(2, isolatedMasses.Count(b => b.charge == 1));
Assert.AreEqual(pep1.MonoisotopicMass, isolatedMasses.Select(b => b.peaks.First().Item1.ToMass(b.charge)).Min(), 1e-9);
Assert.AreEqual(pep2.MonoisotopicMass, isolatedMasses.Select(b => b.peaks.First().Item1.ToMass(b.charge)).Max(), 1e-9);
Assert.AreEqual(pep1.MonoisotopicMass, isolatedMasses.Select(b => b.monoisotopicMass.ToMz(b.charge).ToMass(b.charge)).Min(), 1e-9);
Assert.AreEqual(pep2.MonoisotopicMass, isolatedMasses.Select(b => b.monoisotopicMass.ToMz(b.charge).ToMass(b.charge)).Max(), 1e-9);
}
