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);
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);
Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);
var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");
Mzml okay = new Mzml(@"myFakeFile.mzML");
okay.Open();
okay.GetScan(2);
Assert.AreEqual(1, okay.GetSpectrumNumber(1));
Assert.AreEqual(2, okay.GetSpectrumNumber(2));
}
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 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 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);
}
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();
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 MzSpectrum(mz, intensities, false);
var peptide = new Peptide("KQEEQMETEQQNKDEGK");
MzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan[] Scans = new MsDataScan[2];
Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, null, "scan=1");
Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1, null, "scan=2", 693.9892, 3, .3872, 693.99, 1, DissociationType.Unknown, 1, 693.6550);
myMsDataFile = new FakeMsDataFile(Scans);
}
[TestCase(1081.385183, 13, 35454636, 1081.385)] //This is a lesser abundant charge state envelope at the high mz end
public void TestDeconvolutionProteoformMultiChargeState(double selectedIonMz, int selectedIonChargeStateGuess, double selectedIonIntensity, double isolationMz)
{
MsDataScan[] Scans = new MsDataScan[1];
//txt file, not mgf, because it's an MS1. Most intense proteoform has mass of ~14037.9 Da
string Ms1SpectrumPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DataFiles\14kDaProteoformMzIntensityMs1.txt");
string[] spectrumLines = File.ReadAllLines(Ms1SpectrumPath);
int mzIntensityPairsCount = spectrumLines.Length;
double[] ms1mzs = new double[mzIntensityPairsCount];
double[] ms1intensities = new double[mzIntensityPairsCount];
for (int i = 0; i < mzIntensityPairsCount; i++)
{
string[] pair = spectrumLines[i].Split('\t');
ms1mzs[i] = Convert.ToDouble(pair[0]);
ms1intensities[i] = Convert.ToDouble(pair[1]);
}
MzSpectrum spectrum = new MzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MsDataScan(spectrum, 1, 1, false, Polarity.Positive, 1.0, new MzRange(495, 1617), "first spectrum", MZAnalyzerType.Unknown, spectrum.SumOfAllY, null, null, null, selectedIonMz, selectedIonChargeStateGuess, selectedIonIntensity, isolationMz, 4);
var myMsDataFile = new FakeMsDataFile(Scans);
MsDataScan scan = myMsDataFile.GetAllScansList()[0];
List <IsotopicEnvelope> isolatedMasses = scan.GetIsolatedMassesAndCharges(spectrum, 1, 60, 4, 3).ToList();
List <double> monoIsotopicMasses = isolatedMasses.Select(m => m.MonoisotopicMass).ToList();
//The primary monoisotopic mass should be the same regardless of which peak in which charge state was selected for isolation.
//this case is interesting because other monoisotopic mass may have a sodium adduct. The unit test could be expanded to consider this.
Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
}
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);
}