public static void TestLookingForAcceptableIsotopicEnvelopes()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("AAAHSSLK", ""), new Protein("RQPAQPR", ""), new Protein("EKAEAEAEK", "")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
var ms2ScanTest = listOfSortedms2Scans[0];
//test when all the masses are not in the given range
//test1 when all the masses are too small
var test1 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(50, 95);
Assert.AreEqual(test1, null);
//test2 when all the masses are too big
var test2 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(582, 682);
Assert.AreEqual(test2, null);
//test3 when the mass which is bigger than given min mass is bigger than the mass which is smaller than the given max mass
//for example: the mass array is [1,2,3,4,5], the given min mass is 2.2, the given max mass is 2.8
var test3 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(110, 111);
Assert.AreEqual(test3, null);
//test normal conditions:look for IsotopicEnvelopes which are in the range of acceptable mass
var test4 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(120, 130);
IsotopicEnvelope[] expected4 = ms2ScanTest.ExperimentalFragments.Skip(15).Take(9).ToArray();
Assert.That(ms2ScanTest.ExperimentalFragments[15].MonoisotopicMass > 120 && ms2ScanTest.ExperimentalFragments[14].MonoisotopicMass < 120);
Assert.That(ms2ScanTest.ExperimentalFragments[23].MonoisotopicMass < 130 && ms2ScanTest.ExperimentalFragments[24].MonoisotopicMass > 130);
Assert.AreEqual(test4, expected4);
var test5 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(400, 500);
IsotopicEnvelope[] expected5 = ms2ScanTest.ExperimentalFragments.Skip(150).Take(7).ToArray();
Assert.That(ms2ScanTest.ExperimentalFragments[150].MonoisotopicMass > 400 && ms2ScanTest.ExperimentalFragments[149].MonoisotopicMass < 400);
Assert.That(ms2ScanTest.ExperimentalFragments[156].MonoisotopicMass < 500 && ms2ScanTest.ExperimentalFragments[157].MonoisotopicMass > 500);
Assert.AreEqual(test5, expected5);
}
public static void TestXicExtraction()
{
string dataFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "SmallCalibratibleYeast.mzml");
var data = Mzml.LoadAllStaticData(dataFilePath);
var peptide = new PeptideWithSetModifications("KAPAGGAADAAAK", new Dictionary <string, Modification>());
var xic = data.ExtractIonChromatogram(peptide.MonoisotopicMass, 2, new PpmTolerance(10), 24.806);
Assert.That(xic.Data.Count(p => p.Y > 0) == 4);
}
public static void Test_ChargeDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
Stopwatch stopwatch0 = new Stopwatch();
stopwatch0.Start();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
stopwatch0.Stop();
Stopwatch stopwatch_iso = new Stopwatch();
stopwatch_iso.Start();
var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
stopwatch_iso.Stop();
Stopwatch stopwatch1 = new Stopwatch();
stopwatch1.Start();
var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
stopwatch1.Stop();
//Stopwatch stopwatch2 = new Stopwatch();
//stopwatch2.Start();
var stopwatch2 = Stopwatch.StartNew();
var x2 = ChargeDecon.QuickFindChargesForScan(spectrum, deconvolutionParameter);
stopwatch2.Stop();
// Stopwatch stopwatch3 = new Stopwatch();
// stopwatch3.Start();
// int indUp = spectrum.ExtractIndicesByY().First();
// double mass_up = spectrum.XArray[indUp];
// var highest = ChargeDecon.FindChargesForPeak(spectrum, indUp, new DeconvolutionParameter());
// stopwatch3.Stop();
// var Parameters = Program.AddParametersFromFile("");
// List<double> masses = highest.Select(p => p.Value.Mz).ToList();
// string dynamicTargets;
// string dynamicMaxITs;
// Stopwatch stopwatch4 = new Stopwatch();
// stopwatch4.Start();
// var test = BoxCarScan.BuildDynamicBoxString(Parameters, masses, out dynamicTargets, out dynamicMaxITs);
// stopwatch4.Stop();
// Assert.That(test == "[(400.0,522.8),(524.8,542.2),(544.2,563.1),(565.1,585.6),(587.6,610.0),(612.0,636.5),(638.5,665.4),(667.4,697.1),(699.1,732.0),(734.0,770.5),(772.5,813.3),(815.3,861.1),(863.1,915.0),(917.0,976.0),(978.0,1045.7),(1047.7,1126.1),(1128.1,1200.0)]");
}
public static void TestSummedMsDataFile()
{
ThermoStaticData rawFile = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
// 3 scans
SummedMsDataFile summed3 = new SummedMsDataFile(rawFile, 3, 10);
Assert.AreEqual(rawFile.NumSpectra - 2, summed3.NumSpectra);
var resultingTic = summed3.GetOneBasedScan(1).TotalIonCurrent;
var mySummedTic = rawFile.GetOneBasedScan(1).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(2).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(3).MassSpectrum.SumOfAllY;
var instrumentSummedTic = rawFile.GetOneBasedScan(1).TotalIonCurrent + rawFile.GetOneBasedScan(2).TotalIonCurrent + rawFile.GetOneBasedScan(3).TotalIonCurrent;
// Tics are approximately what they should be
Assert.IsTrue(Math.Abs(resultingTic - mySummedTic) / mySummedTic < 1e-4);
Assert.IsTrue(Math.Abs(resultingTic - instrumentSummedTic) / instrumentSummedTic < 1e-1);
// Equal to representative
Assert.AreEqual(summed3.GetOneBasedScan(1).RetentionTime, rawFile.GetOneBasedScan(2).RetentionTime);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size <= rawFile.GetOneBasedScan(1).MassSpectrum.Size + rawFile.GetOneBasedScan(2).MassSpectrum.Size + rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(1).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(2).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY == rawFile.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY);
// Interval of 893-899 mz
Assert.AreEqual(2, rawFile.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(2, rawFile.GetOneBasedScan(2).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(1, rawFile.GetOneBasedScan(3).MassSpectrum.NumPeaksWithinRange(893, 899));
// One peak persists across the three scans! So instead of 5 see three peaks in summed
Assert.AreEqual(3, summed3.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.FirstX, Math.Min(Math.Min(rawFile.GetOneBasedScan(1).MassSpectrum.FirstX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.FirstX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.FirstX.Value));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.LastX, Math.Max(Math.Max(rawFile.GetOneBasedScan(1).MassSpectrum.LastX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.LastX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.LastX.Value));
// 5 scans
SummedMsDataFile summed5 = new SummedMsDataFile(rawFile, 5, 10);
Assert.AreEqual(rawFile.NumSpectra - 4, summed5.NumSpectra);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(summed5, "testSummed.mzML", false);
var ok = Mzml.LoadAllStaticData("testSummed.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, "testSummed2.mzML", false);
Mzml.LoadAllStaticData("testSummed2.mzML");
}
public static void WriteIndexedMzmlFromThermoTest()
{
var smallThermo = ThermoStaticData.LoadAllStaticData(@"small.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(smallThermo, Path.Combine(TestContext.CurrentContext.TestDirectory, "Hi.mzML"), true);
var smallMzml = Mzml.LoadAllStaticData(@"Hi.mzML");
Assert.AreEqual(smallMzml.NumSpectra, 48);
Assert.AreEqual(smallMzml.GetOneBasedScan(8).OneBasedScanNumber, 8);
Assert.AreEqual(smallThermo.GetOneBasedScan(5).RetentionTime, smallMzml.GetOneBasedScan(5).RetentionTime);
}
public static void Test_RealDataDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var test = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var ms1scans = scans.Where(p => p.MsnOrder == 1).ToList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
}
public static void Test_FragmentMesh()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var CEs = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
var mesh = CEs.First().mzs_box;
Assert.That(mesh.Count() == 3);
}
public static void BU_dynamicBoxCarRange()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
Parameters parameters = Program.AddParametersFromFile("");
var isos = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, parameters.DeconvolutionParameter);
List <List <Tuple <double, double, double> > > Boxes = new List <List <Tuple <double, double, double> > >();
BoxCarScan.GenerateDynamicBoxes_BU(isos, parameters, Boxes);
Assert.That(Boxes.Count == 2);
}
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 LoadMzmlAnotherTest()
{
Mzml a = Mzml.LoadAllStaticData(@"small.pwiz.1.1.mzML");
Assert.AreEqual(19914, a.First().MassSpectrum.Size);
//a = new Mzml(@"small.pwiz.1.1.mzML", 400);
//a.Open();
//Assert.AreEqual(400, a.First().MassSpectrum.Size);
//var cool = a.GetOneBasedScan(6) as MzmlScanWithPrecursor;
//Assert.AreEqual(1, cool.IsolationWidth);
//a.Close();
}
/// <summary>
/// Tests peak filtering for ThermoRawFileReader
/// </summary>
public static void TestPeakFilteringRawFileReader(string infile)
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var filterParams = new FilteringParams(200, 0.01, 0, 1, false, true, true);
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
var a = ThermoRawFileReader.LoadAllStaticData(path, filterParams, maxThreads: 1);
var rawScans = a.GetAllScansList();
foreach (var scan in rawScans)
{
Assert.That(scan.MassSpectrum.XArray.Length <= 200);
}
string outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", Path.GetFileNameWithoutExtension(infile) + ".mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var mzml = Mzml.LoadAllStaticData(outfile1, filterParams, maxThreads: 1);
var mzmlScans = mzml.GetAllScansList();
for (int i = 0; i < mzmlScans.Count; i++)
{
var mzmlScan = mzmlScans[i];
var rawScan = rawScans[i];
for (int j = 0; j < mzmlScan.MassSpectrum.XArray.Length; j++)
{
double roundedMzmlMz = Math.Round(mzmlScan.MassSpectrum.XArray[j], 2);
double roundedRawMz = Math.Round(rawScan.MassSpectrum.XArray[j], 2);
Assert.AreEqual(roundedMzmlMz, roundedRawMz);
double roundedMzmlIntensity = Math.Round(mzmlScan.MassSpectrum.XArray[j], 0);
double roundedRawIntensity = Math.Round(rawScan.MassSpectrum.XArray[j], 0);
Assert.AreEqual(roundedMzmlIntensity, roundedRawIntensity);
}
}
Console.WriteLine($"Analysis time for TestPeakFilteringRawFileReader: {stopwatch.Elapsed.Hours}h " +
$"{stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
public static void LoadCompressedMzml()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.RAW");
Mzml b = Mzml.LoadAllStaticData(@"smallCentroid.mzML");
Assert.AreEqual(a.NumSpectra, b.NumSpectra);
Assert.AreEqual(a.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
}
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 static void ProcessXcorrInMzSpectrum()
{
Dictionary <string, MsDataFile> MyMsDataFiles = new Dictionary <string, MsDataFile>();
string origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "BinGenerationTest.mzML");
FilteringParams filter = new FilteringParams(200, 0.01, null, 1, false, false, true);
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, 1);
var scans = MyMsDataFiles[origDataFile].GetAllScansList();
foreach (MsDataScan scan in scans.Where(s => s.MsnOrder > 1))
{
scan.MassSpectrum.XCorrPrePreprocessing(0, 1968 * 1.0005079, scan.IsolationMz.Value);
}
Assert.AreEqual(6, scans[0].MassSpectrum.XArray.Count());
Assert.AreEqual(20, scans[1].MassSpectrum.XArray.Count());
}
/// <summary>
/// Tests LoadAllStaticData for ThermoRawFileReader
/// </summary>
public static void TestLoadAllStaticDataRawFileReader(string infile, string outfile1, string outfile2)
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile1);
outfile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile2);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var a = ThermoRawFileReader.LoadAllStaticData(path, maxThreads: 1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var aa = Mzml.LoadAllStaticData(outfile1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, outfile2, true);
Mzml.LoadAllStaticData(outfile2);
Console.WriteLine($"Analysis time for TestLoadAllStaticDataRawFileReader({infile}): {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
public void LoadMzmlTest()
{
Mzml a = Mzml.LoadAllStaticData(@"tiny.pwiz.1.1.mzML");
var ya = a.GetOneBasedScan(1).MassSpectrum;
Assert.AreEqual(15, ya.Size);
var ya2 = a.GetOneBasedScan(2).MassSpectrum;
Assert.AreEqual(10, ya2.Size);
var ya3 = a.GetOneBasedScan(3).MassSpectrum;
Assert.AreEqual(0, ya3.Size);
var ya4 = a.GetOneBasedScan(4).MassSpectrum;
Assert.AreEqual(15, ya4.Size);
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > ok = a;
Assert.AreEqual(1, ok.GetClosestOneBasedSpectrumNumber(5));
}
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 LoadMzmlFromConvertedMGFTest()
{
Mzml a = Mzml.LoadAllStaticData(@"tester.mzML");
var ya = a.GetOneBasedScan(1).MassSpectrum;
Assert.AreEqual(192, ya.Size);
var ya2 = a.GetOneBasedScan(3).MassSpectrum;
Assert.AreEqual(165, ya2.Size);
var ya3 = a.GetOneBasedScan(5).MassSpectrum;
Assert.AreEqual(551, ya3.Size);
var ya4 = a.GetOneBasedScan(975).MassSpectrum;
Assert.AreEqual(190, ya4.Size);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "CreateFileFromConvertedMGF.mzML", false);
Mzml b = Mzml.LoadAllStaticData(@"CreateFileFromConvertedMGF.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(b, "CreateFileFromConvertedMGF2.mzML", false);
}
public static void TestClassicSearchEngineTopDown()
{
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: "top-down"),
scoreCutoff: 1,
assumeOrphanPeaksAreZ1Fragments: false);
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
// test output file name (should be proteoform and not peptide)
Assert.That(GlobalVariables.AnalyteType == "Proteoform");
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("MPKVYSYQEVAEHNGPENFWIIIDDKVYDVSQFKDEHPGGDEIIMDLGGQDATESFVDIGHSDEALRLLKGLYIGDVDKTSERVSVEKVSTSENQSKGSGTLVVILAILMLGVAYYLLNE", "P40312")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TopDownTestData\slicedTDYeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpetralLibrary = false;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), writeSpetralLibrary).Run();
var psm = allPsmsArray.Where(p => p != null).FirstOrDefault();
Assert.That(psm.MatchedFragmentIons.Count == 47);
}
public static List <ScanHeaderInfo> FileScanHeaderInfo(string fullFilePathWithExtension)
{
string filename = Path.GetFileName(fullFilePathWithExtension);
List <ScanHeaderInfo> scanHeaderInfoList = new();
switch (GetDataFileType(fullFilePathWithExtension))
{
case DataFileType.Thermo:
ThermoRawFileReader staticRaw = ThermoRawFileReader.LoadAllStaticData(fullFilePathWithExtension);
foreach (MsDataScan item in staticRaw)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.mzML:
List <MsDataScan> mzmlDataScans = Mzml.LoadAllStaticData(fullFilePathWithExtension).GetAllScansList();
foreach (MsDataScan item in mzmlDataScans)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.mgf:
List <MsDataScan> mgfDataScans = Mgf.LoadAllStaticData(fullFilePathWithExtension).GetAllScansList();
foreach (MsDataScan item in mgfDataScans)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.unknown:
default:
break;
}
return(scanHeaderInfoList);
}
public MsDataFile LoadFile(string origDataFile, int?topNpeaks, double?minRatio, bool trimMs1Peaks, bool trimMsMsPeaks, CommonParameters commonParameters)
{
FilteringParams filter = new FilteringParams(topNpeaks, minRatio, null, 1, false, trimMs1Peaks, trimMsMsPeaks);
if (commonParameters.DissociationType == DissociationType.LowCID || commonParameters.ChildScanDissociationType == DissociationType.LowCID)
{
filter = null;
}
if (MyMsDataFiles.TryGetValue(origDataFile, out MsDataFile value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (FileLoadingLock) // Lock because reading is sequential
{
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
else if (Path.GetExtension(origDataFile).Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mgf.LoadAllStaticData(origDataFile, filter);
}
else
{
#if NETFRAMEWORK
MyMsDataFiles[origDataFile] = ThermoStaticData.LoadAllStaticData(origDataFile, filter);
#else
Warn("No capability for reading " + origDataFile);
#endif
}
return(MyMsDataFiles[origDataFile]);
}
}
public MsDataFile LoadFile(string origDataFile, CommonParameters commonParameters)
{
FilteringParams filter = new FilteringParams(commonParameters.NumberOfPeaksToKeepPerWindow, commonParameters.MinimumAllowedIntensityRatioToBasePeak, commonParameters.WindowWidthThomsons, commonParameters.NumberOfWindows, commonParameters.NormalizePeaksAccrossAllWindows, commonParameters.TrimMs1Peaks, commonParameters.TrimMsMsPeaks);
if (commonParameters.DissociationType == DissociationType.LowCID || commonParameters.ChildScanDissociationType == DissociationType.LowCID)
{
filter = null;
}
if (MyMsDataFiles.TryGetValue(origDataFile, out MsDataFile value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (FileLoadingLock) // Lock because reading is sequential
{
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
else if (Path.GetExtension(origDataFile).Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mgf.LoadAllStaticData(origDataFile, filter);
}
else
{
#if NETFRAMEWORK
MyMsDataFiles[origDataFile] = ThermoStaticData.LoadAllStaticData(origDataFile, filter);
#else
Warn("No capability for reading " + origDataFile);
#endif
}
return(MyMsDataFiles[origDataFile]);
}
}
public static void LoadThermoTest2()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
Assert.AreEqual(360, a.NumSpectra);
Assert.GreaterOrEqual(1000, a.GetOneBasedScan(1).MassSpectrum.Extract(0, 500).Last().Mz);
Assert.AreEqual(2, a.GetOneBasedScan(1).MassSpectrum.FilterByY(5e6, double.MaxValue).Count());
var ye = a.GetOneBasedScan(1).MassSpectrum.CopyTo2DArray();
Assert.AreEqual(77561752, a.GetOneBasedScan(1).TotalIonCurrent);
Assert.AreEqual(144, a.GetClosestOneBasedSpectrumNumber(2));
MzSpectrum newSpectrum = new MzSpectrum(a.GetOneBasedScan(51).MassSpectrum.XArray, a.GetOneBasedScan(51).MassSpectrum.YArray, true);
Assert.AreEqual(1120, a.GetOneBasedScan(1).MassSpectrum.Size);
var newDeconvolution = a.GetOneBasedScan(1).MassSpectrum.Deconvolute(new MzRange(double.MinValue, double.MaxValue), 1, 10, 1, 4).ToList();
Assert.IsTrue(newDeconvolution.Any(b => Math.Abs(b.peaks.First().mz.ToMass(b.charge) - 523.257) < 0.001));
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"), false);
var sdafaf = a.Deconvolute(null, null, 1, 30, 10, 3, 10, b => true).OrderByDescending(b => b.NumPeaks).First();
Assert.IsTrue(Math.Abs(262.64 - sdafaf.Mass.ToMz(2)) <= 0.01);
using (ThermoDynamicData dynamicThermo = ThermoDynamicData.InitiateDynamicConnection(@"05-13-16_cali_MS_60K-res_MS.raw"))
{
Assert.AreEqual(136, dynamicThermo.GetClosestOneBasedSpectrumNumber(1.89));
dynamicThermo.ClearCachedScans();
}
Mzml readCovertedMzmlFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"));
Assert.AreEqual(a.GetAllScansList().First().Polarity, readCovertedMzmlFile.GetAllScansList().First().Polarity);
}
public static void ReadWriteReadEtc()
{
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"testFileWMS2.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
}
public static void TestReverseDecoyGenerationDuringSearch()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("KKAEDGINK", ""), new Protein("AVNSISLK", ""), new Protein("EKAEAEAEK", ""), new Protein("DITANLR", ""), new Protein("QNAIGTAK", ""),
new Protein("FHKSQLNK", ""), new Protein("KQVAQWNK", ""), new Protein("NTRIEELK", ""), new Protein("RQPAQPR", ""),
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\myPrositLib.msp");
var testLibrary = new SpectralLibrary(new List <string> {
path
});
//test when doing spectral library search without generating library
PeptideSpectralMatch[] allPsmsArray1 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray1, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, testLibrary, new List <string>(), false).Run();
var psm1 = allPsmsArray1.Where(p => p != null).ToList();
Assert.That(psm1[0].IsDecoy == false && psm1[0].FullSequence == "DITANLR");
Assert.That(psm1[1].IsDecoy == true && psm1[1].FullSequence == "LSISNVAK");
Assert.That(psm1[2].IsDecoy == true && psm1[2].FullSequence == "LSISNVAK");
Assert.That(psm1[3].IsDecoy == false && psm1[3].FullSequence == "RQPAQPR");
Assert.That(psm1[4].IsDecoy == false && psm1[4].FullSequence == "KKAEDGINK");
Assert.That(psm1[5].IsDecoy == false && psm1[5].FullSequence == "EKAEAEAEK");
Assert.That(psm1[6].IsDecoy == false && psm1[6].FullSequence == "EKAEAEAEK");
proteinList.Add(new Protein("LSISNVAK", "", isDecoy: true));
//test when doing spectral library search with generating library; non spectral search won't generate decoy by "decoy on the fly" , so proteinlist used by non spectral library search would contain decoys
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, testLibrary, new List <string>(), true).Run();
var psm2 = allPsmsArray2.Where(p => p != null).ToList();
Assert.That(psm2[0].IsDecoy == false && psm2[0].FullSequence == "DITANLR");
Assert.That(psm2[1].IsDecoy == true && psm2[1].FullSequence == "LSISNVAK");
Assert.That(psm2[2].IsDecoy == true && psm2[2].FullSequence == "LSISNVAK");
Assert.That(psm2[3].IsDecoy == false && psm2[3].FullSequence == "RQPAQPR");
Assert.That(psm2[4].IsDecoy == false && psm2[4].FullSequence == "KKAEDGINK");
Assert.That(psm2[5].IsDecoy == false && psm2[5].FullSequence == "EKAEAEAEK");
Assert.That(psm2[6].IsDecoy == false && psm2[6].FullSequence == "EKAEAEAEK");
//test when doing non spectral library search without generating library
PeptideSpectralMatch[] allPsmsArray3 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray3, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm3 = allPsmsArray3.Where(p => p != null).ToList();
Assert.That(psm3[0].IsDecoy == false && psm3[0].FullSequence == "DITANLR");
Assert.That(psm3[1].IsDecoy == true && psm3[1].FullSequence == "LSISNVAK");
Assert.That(psm3[2].IsDecoy == true && psm3[2].FullSequence == "LSISNVAK");
Assert.That(psm3[3].IsDecoy == false && psm3[3].FullSequence == "RQPAQPR");
Assert.That(psm3[4].IsDecoy == false && psm3[4].FullSequence == "KKAEDGINK");
Assert.That(psm3[5].IsDecoy == false && psm3[5].FullSequence == "EKAEAEAEK");
Assert.That(psm3[6].IsDecoy == false && psm3[6].FullSequence == "EKAEAEAEK");
//test when doing non spectral library search with generating library
PeptideSpectralMatch[] allPsmsArray4 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray4, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm4 = allPsmsArray4.Where(p => p != null).ToList();
Assert.That(psm4[0].IsDecoy == false && psm4[0].FullSequence == "DITANLR");
Assert.That(psm4[1].IsDecoy == true && psm4[1].FullSequence == "LSISNVAK");
Assert.That(psm4[2].IsDecoy == true && psm4[2].FullSequence == "LSISNVAK");
Assert.That(psm4[3].IsDecoy == false && psm4[3].FullSequence == "RQPAQPR");
Assert.That(psm4[4].IsDecoy == false && psm4[4].FullSequence == "KKAEDGINK");
Assert.That(psm4[5].IsDecoy == false && psm4[5].FullSequence == "EKAEAEAEK");
Assert.That(psm4[6].IsDecoy == false && psm4[6].FullSequence == "EKAEAEAEK");
//compare psm's target/decoy results in 4 conditions. they should be same as new decoy methods shouldn't change the t/d results
for (int i = 0; i < psm1.Count; i++)
{
Assert.That(psm1[i].FullSequence == psm2[i].FullSequence && psm3[i].FullSequence == psm3[i].FullSequence && psm2[i].FullSequence == psm3[i].FullSequence);
Assert.That(psm1[i].IsDecoy == psm2[i].IsDecoy && psm3[i].IsDecoy == psm3[i].IsDecoy && psm2[i].IsDecoy == psm3[i].IsDecoy);
}
//compare MetaMorpheus scores in 4 conditions; for some psms, they should have a little higher score when "generating library" as they switch to all charges ions matching function
for (int j = 0; j < psm1.Count; j++)
{
if (psm1[j].FullSequence == psm2[j].FullSequence && psm1[j].MatchedFragmentIons.Count != psm2[j].MatchedFragmentIons.Count)
{
Assert.That(psm1[j].Score < psm2[j].Score);
}
}
}
public static void TestMatchIonsOfAllChargesBottomUp()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("AAAHSSLK", ""), new Protein("RQPAQPR", ""), new Protein("EKAEAEAEK", "")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//search by new method of looking for all charges
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm = allPsmsArray.Where(p => p != null).ToList();
Assert.That(psm[1].MatchedFragmentIons.Count == 14);
//there are ions with same product type and same fragment number but different charges
Assert.That(psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.ProductType == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.ProductType &&
psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.FragmentNumber == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.FragmentNumber &&
psm[1].MatchedFragmentIons[8].Charge != psm[1].MatchedFragmentIons[9].Charge);
Assert.That(psm[2].MatchedFragmentIons.Count == 14);
Assert.That(psm[4].MatchedFragmentIons.Count == 16);
//search by old method of looking for only one charge
PeptideSpectralMatch[] allPsmsArray_oneCharge = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray_oneCharge, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm_oneCharge = allPsmsArray_oneCharge.Where(p => p != null).ToList();
//compare 2 scores , they should have same integer part but new search has a little higher score than old search
Assert.That(psm[1].Score > psm_oneCharge[1].Score);
Assert.AreEqual(Math.Truncate(psm[1].Score), 12);
Assert.AreEqual(Math.Truncate(psm_oneCharge[1].Score), 12);
//compare 2 results and evaluate the different matched ions
var peptideTheorProducts = new List <Product>();
Assert.That(psm_oneCharge[1].MatchedFragmentIons.Count == 12);
var differences = psm[1].MatchedFragmentIons.Except(psm_oneCharge[1].MatchedFragmentIons);
psm[1].BestMatchingPeptides.First().Peptide.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
foreach (var ion in differences)
{
foreach (var product in peptideTheorProducts)
{
if (product.Annotation.ToString().Equals(ion.NeutralTheoreticalProduct.Annotation.ToString()))
{
//to see if the different matched ions are qualified
Assert.That(CommonParameters.ProductMassTolerance.Within(ion.Mz.ToMass(ion.Charge), product.NeutralMass));
}
}
}
//test specific condition: unknown fragment mass; this only happens rarely for sequences with unknown amino acids
var myMsDataFile1 = new TestDataFile();
var variableModifications1 = new List <Modification>();
var fixedModifications1 = new List <Modification>();
var proteinList1 = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance1 = new PpmTolerance(5);
var listOfSortedms2Scans1 = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters1 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray1 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = true;
new ClassicSearchEngine(allPsmsArray1, listOfSortedms2Scans1, variableModifications1, fixedModifications1, null, null, null,
proteinList1, searchModes, CommonParameters1, fsp, null, new List <string>(), writeSpectralLibrary).Run();
var psm1 = allPsmsArray1.Where(p => p != null).ToList();
Assert.AreEqual(psm1.Count, 222);
}
public static void TestMatchIonsOfAllChargesTopDown()
{
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: "top-down"),
scoreCutoff: 1,
assumeOrphanPeaksAreZ1Fragments: false);
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
// test output file name (should be proteoform and not peptide)
Assert.That(GlobalVariables.AnalyteType == "Proteoform");
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("MPKVYSYQEVAEHNGPENFWIIIDDKVYDVSQFKDEHPGGDEIIMDLGGQDATESFVDIGHSDEALRLLKGLYIGDVDKTSERVSVEKVSTSENQSKGSGTLVVILAILMLGVAYYLLNE", "P40312")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TopDownTestData\slicedTDYeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//search by new method of looking for all charges
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm = allPsmsArray.Where(p => p != null).FirstOrDefault();
Assert.That(psm.MatchedFragmentIons.Count == 62);
//search by old method of looking for only one charge
PeptideSpectralMatch[] allPsmsArray_oneCharge = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray_oneCharge, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm_oneCharge = allPsmsArray_oneCharge.Where(p => p != null).FirstOrDefault();
Assert.That(psm_oneCharge.MatchedFragmentIons.Count == 47);
//compare 2 scores , they should have same integer but new search has a little higher score than old search
Assert.That(psm.Score > psm_oneCharge.Score);
Assert.AreEqual(Math.Truncate(psm.Score), 47);
Assert.AreEqual(Math.Truncate(psm_oneCharge.Score), 47);
//compare 2 results and evaluate the different matched ions
var peptideTheorProducts = new List <Product>();
var differences = psm.MatchedFragmentIons.Except(psm_oneCharge.MatchedFragmentIons);
psm.BestMatchingPeptides.First().Peptide.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
foreach (var ion in differences)
{
foreach (var product in peptideTheorProducts)
{
if (product.Annotation.ToString().Equals(ion.NeutralTheoreticalProduct.Annotation.ToString()))
{
//to see if the different matched ions are qualified
Assert.That(CommonParameters.ProductMassTolerance.Within(ion.Mz.ToMass(ion.Charge), product.NeutralMass));
}
}
}
}
private static void Main(string[] args)
{
Loaders.LoadElements("elements.dat");
var p = new FluentCommandLineParser <ApplicationArguments>();
p.Setup(arg => arg.DeconvolutionTolerancePpm)
.As("DeconvolutionTolerancePpm");
p.Setup(arg => arg.MinScan)
.As("MinScan");
p.Setup(arg => arg.MaxScan)
.As("MaxScan");
p.Setup(arg => arg.MinAssumedChargeState)
.As("MinAssumedChargeState");
p.Setup(arg => arg.MaxAssumedChargeState)
.As("MaxAssumedChargeState");
p.Setup(arg => arg.IntensityRatioLimit)
.As("IntensityRatioLimit");
p.Setup(arg => arg.FilePath)
.As("FilePath").
Required();
var result = p.Parse(args);
Console.WriteLine("Running deconvolution using the following parameters:");
Console.WriteLine(p.Object);
if (result.HasErrors == false)
{
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile;
if (Path.GetExtension(p.Object.FilePath).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
myMsDataFile = Mzml.LoadAllStaticData(p.Object.FilePath);
}
else
{
myMsDataFile = ThermoStaticData.LoadAllStaticData(p.Object.FilePath);
}
using (StreamWriter output = new StreamWriter(@"MS2DeconvolutionOutput-" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss", CultureInfo.InvariantCulture) + ".tsv"))
{
output.WriteLine("Mass\tNumPeaks\tNumScans\tMinScan\tMaxScan\tAverageElutionTime\tIntensity\tObservedCharges\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope");
foreach (var ok in myMsDataFile.OfType <IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > >())
{
if ((!p.Object.MinScan.HasValue || ok.OneBasedScanNumber >= p.Object.MinScan) && (!p.Object.MaxScan.HasValue || ok.OneBasedScanNumber <= p.Object.MaxScan))
{
var hmm = ok.MassSpectrum.Deconvolute(new MzRange(0, double.PositiveInfinity), p.Object.MinAssumedChargeState, p.Object.MaxAssumedChargeState, p.Object.DeconvolutionTolerancePpm, p.Object.IntensityRatioLimit).ToList();
List <DeconvolutionFeatureWithMassesAndScans> currentListOfGroups = new List <DeconvolutionFeatureWithMassesAndScans>();
foreach (var isotopicEnvelope in hmm)
{
DeconvolutionFeatureWithMassesAndScans matchingGroup = null;
var mass = isotopicEnvelope.monoisotopicMass;
foreach (var possibleGroup in currentListOfGroups)
{
var possibleGroupMass = possibleGroup.Mass;
if (Math.Abs(mass - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass + 1.002868314 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass + 2.005408917 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass + 3.007841294 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass - 1.002868314 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass - 2.005408917 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm ||
Math.Abs(mass - 3.007841294 - possibleGroupMass) / possibleGroupMass * 1e6 <= p.Object.AggregationTolerancePpm)
{
matchingGroup = possibleGroup;
matchingGroup.AddEnvelope(isotopicEnvelope, ok.OneBasedScanNumber, ok.RetentionTime);
break;
}
}
if (matchingGroup == null)
{
var newGroupScans = new DeconvolutionFeatureWithMassesAndScans();
newGroupScans.AddEnvelope(isotopicEnvelope, ok.OneBasedScanNumber, ok.RetentionTime);
currentListOfGroups.Add(newGroupScans);
}
}
foreach (var ook in currentListOfGroups)
{
output.WriteLine(ook.OneLineString());
}
}
}
}
}
else
{
Console.WriteLine("BAD PARAMETERS");
Console.WriteLine(result.ErrorText);
}
}
public static void TestFlashLFQWithPassedFile()
{
// read periodic table - needed to open the raw files
PeriodicTableLoader.Load(Path.Combine(TestContext.CurrentContext.TestDirectory, @"elements.dat"));
// get the raw files
string rawPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"sliced-raw.raw");
string mzmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"sliced-mzml.mzml");
var rawFile = ThermoDynamicData.InitiateDynamicConnection(rawPath);
var mzmlFile = Mzml.LoadAllStaticData(mzmlPath);
RawFileInfo raw = new RawFileInfo(rawPath, rawFile);
RawFileInfo mzml = new RawFileInfo(mzmlPath, mzmlFile);
// create some PSMs
Identification id1 = new Identification(raw, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.12193, 2, new List <string> {
"MyProtein"
});
Identification id2 = new Identification(raw, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.05811, 2, new List <string> {
"MyProtein"
});
Identification id3 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.12193, 2, new List <string> {
"MyProtein"
});
Identification id4 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.05811, 2, new List <string> {
"MyProtein"
});
// create the FlashLFQ engine
FlashLFQEngine engine = new FlashLFQEngine(new List <Identification> {
id1, id2, id3, id4
});
// run the engine
var results = engine.Run();
// check raw results
Assert.That(results.peaks[raw].Count == 1);
Assert.That(results.peaks[raw].First().intensity > 0);
Assert.That(!results.peaks[raw].First().isMbrFeature);
Assert.That(results.peptideBaseSequences["EGFQVADGPLYR"].intensities[raw] > 0);
Assert.That(results.peptideModifiedSequences["EGFQVADGPLYR"].intensities[raw] > 0);
Assert.That(results.proteinGroups["MyProtein"].intensities[raw] > 0);
// check mzml results
Assert.That(results.peaks[mzml].Count == 1);
Assert.That(results.peaks[mzml].First().intensity > 0);
Assert.That(!results.peaks[mzml].First().isMbrFeature);
Assert.That(results.peptideBaseSequences["EGFQVADGPLYR"].intensities[mzml] > 0);
Assert.That(results.peptideModifiedSequences["EGFQVADGPLYR"].intensities[mzml] > 0);
Assert.That(results.proteinGroups["MyProtein"].intensities[mzml] > 0);
// test peak output
List <string> output = new List <string>()
{
FlashLFQ.ChromatographicPeak.TabSeparatedHeader
};
foreach (var peak in results.peaks.SelectMany(p => p.Value))
{
output.Add(peak.ToString());
}
Assert.That(output.Count == 3);
// test peptide base sequence output
output = new List <string>()
{
Peptide.TabSeparatedHeader
};
foreach (var pep in results.peptideBaseSequences)
{
output.Add(pep.Value.ToString());
}
Assert.That(output.Count == 2);
// test peptide mod sequence output
output = new List <string>()
{
Peptide.TabSeparatedHeader
};
foreach (var pep in results.peptideModifiedSequences)
{
output.Add(pep.Value.ToString());
}
Assert.That(output.Count == 2);
// test protein output
output = new List <string>()
{
ProteinGroup.TabSeparatedHeader
};
foreach (var protein in results.proteinGroups)
{
output.Add(protein.Value.ToString());
}
Assert.That(output.Count == 2);
}
public bool Run_TdMzCal(InputFile raw_file, List <SpectrumMatch> topdown_hits)
{
all_topdown_hits = topdown_hits.Where(h => h.score > 0).ToList();
//need to reset m/z in case same td hits used for multiple calibration raw files...
Parallel.ForEach(all_topdown_hits, h => h.mz = h.reported_mass.ToMz(h.charge));
high_scoring_topdown_hits = all_topdown_hits.Where(h => h.score >= 40).ToList();
this.raw_file = raw_file;
if (high_scoring_topdown_hits.Count < 5)
{
return(false);
}
myMsDataFile = Path.GetExtension(raw_file.complete_path) == ".raw" ?
ThermoStaticData.LoadAllStaticData(raw_file.complete_path) :
null;
if (myMsDataFile == null)
{
myMsDataFile = Mzml.LoadAllStaticData(raw_file.complete_path);
}
if (myMsDataFile == null)
{
return(false);
}
DataPointAquisitionResults dataPointAcquisitionResult = GetDataPoints();
if (dataPointAcquisitionResult.Ms1List.Count < 10)
{
return(false);
}
if (Sweet.lollipop.mass_calibration)
{
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
//x values
var explanatoryVariables = new double[4];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].mz;
explanatoryVariables[1] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
explanatoryVariables[2] = dataPointAcquisitionResult.Ms1List[i].logTotalIonCurrent;
explanatoryVariables[3] = dataPointAcquisitionResult.Ms1List[i].logInjectionTime;
//yvalue
double mzError = dataPointAcquisitionResult.Ms1List[i].massError;
myMs1DataPoints.Add((explanatoryVariables, mzError));
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
CalibrateHitsAndComponents(ms1Model);
if (Sweet.lollipop.calibrate_raw_files)
{
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile,
raw_file.directory + "\\" + raw_file.filename + "_calibrated.mzML", false);
}
}
if (Sweet.lollipop.retention_time_calibration)
{
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
List <SpectrumMatch> firstElutingTopDownHit = new List <SpectrumMatch>();
List <string> PFRs = high_scoring_topdown_hits.Select(h => h.pfr_accession).Distinct().ToList();
foreach (var PFR in PFRs)
{
var firstHitWithPFR = high_scoring_topdown_hits
.Where(h => h.pfr_accession == PFR).OrderBy(h => h.ms2_retention_time).First();
firstElutingTopDownHit.Add(firstHitWithPFR);
}
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
if (firstElutingTopDownHit.Contains(dataPointAcquisitionResult.Ms1List[i].identification))
{
//x values
var explanatoryVariables = new double[1];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
//yvalue
double RTError = dataPointAcquisitionResult.Ms1List[i].RTError;
myMs1DataPoints.Add((explanatoryVariables, RTError));
}
}
if (myMs1DataPoints.Count < 10)
{
return(false);
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
foreach (Component c in Sweet.lollipop.calibration_components.Where(h => h.input_file.lt_condition == raw_file.lt_condition && h.input_file.biological_replicate == raw_file.biological_replicate && h.input_file.fraction == raw_file.fraction && h.input_file.technical_replicate == raw_file.technical_replicate))
{
c.rt_apex = c.rt_apex - ms1Model.Predict(new double[] { c.rt_apex });
}
}
return(true);
}
