public void TestFitScoreCalculationEtd()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestTopDownRawFilePathEtd))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestTopDownRawFilePathEtd, 810, 810);
var spec = run.GetSpectrum(810) as ProductSpectrum;
Assert.True(spec != null);
const string suf54 = "ENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK";
var suf54Comp = new AminoAcidSet().GetComposition(suf54);
Assert.True(suf54Comp != null);
var ionType = new IonTypeFactory(10).GetIonType("z6");
var ion = ionType.GetIon(suf54Comp);
//ion.Composition.ComputeApproximateIsotopomerEnvelop();
Console.WriteLine("MonoMz: {0}, MonoMass: {1}", ion.GetMonoIsotopicMz(), ion.Composition.Mass);
var fitScore = spec.GetFitScore(ion, new Tolerance(15), 0.1);
Console.WriteLine("FitScore: {0}", fitScore);
Assert.True(fitScore < 0.15);
}
public void TestReadingDiaRawFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = TestRawFilePath;
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
const int SCAN = 100;
const int MAX_POINTS = 50;
var run = InMemoryLcMsRun.GetLcMsRunScanRange(rawFilePath, SCAN);
var spec = run.GetSpectrum(SCAN);
spec.Display(MAX_POINTS);
// Console.WriteLine("{0}, {1}", spec.Peaks[50].Mz, spec.Peaks[50].Intensity);
// Console.WriteLine("{0}, {1}", spec.Peaks[500].Mz, spec.Peaks[500].Intensity);
// Console.WriteLine("{0}, {1}", spec.Peaks[1000].Mz, spec.Peaks[1000].Intensity);
Assert.IsTrue(Math.Abs(spec.Peaks[50].Mz - 414.75503540039062) < 0.0001, "Invalid m/z for peak at index 50");
Assert.IsTrue(Math.Abs(spec.Peaks[50].Intensity - 1071.5673828125) < 0.01, "Invalid intensity for peak at index 50");
Assert.IsTrue(Math.Abs(spec.Peaks[500].Mz - 578.1298828125) < 0.0001, "Invalid m/z for peak at index 500");
Assert.IsTrue(Math.Abs(spec.Peaks[500].Intensity - 573.02374267578125) < 0.01, "Invalid intensity for peak at index 500");
Assert.IsTrue(Math.Abs(spec.Peaks[1000].Mz - 974.17694091796875) < 0.0001, "Invalid m/z for peak at index 1000");
Assert.IsTrue(Math.Abs(spec.Peaks[1000].Intensity - 678.13824462890625) < 0.01, "Invalid intensity for peak at index 1000");
}
public void TestReadingScanNums()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestRawFilePath, 20000, 20100);
var msLevel = new Dictionary <int, int>();
//for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
foreach (var scanNum in run.AllScanNumbers)
{
msLevel[scanNum] = run.GetMsLevel(scanNum);
}
//for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
foreach (var scanNum in run.AllScanNumbers)
{
var spec = run.GetSpectrum(scanNum);
Assert.True(spec.MsLevel == msLevel[scanNum]);
if (spec.MsLevel == 2)
{
var precursorScanNum = 0;
for (var prevScan = scanNum - 1; prevScan >= run.MinLcScan; prevScan--)
{
if (run.GetMsLevel(prevScan) == 1)
{
precursorScanNum = prevScan;
break;
}
}
Assert.True(run.GetPrecursorScanNum(scanNum) == precursorScanNum);
var nextScanNum = run.MaxLcScan + 1;
//for (var nextScan = scanNum + 1; nextScan <= run.MaxLcScan; nextScan++)
foreach (var nextScan in run.AllScanNumbers.Where(x => x > scanNum))
{
if (run.GetMsLevel(nextScan) == 1)
{
nextScanNum = nextScan;
break;
}
}
if (run.GetNextScanNum(scanNum) != nextScanNum)
{
Console.WriteLine("{0}\t{1}\t{2}", scanNum, run.GetNextScanNum(scanNum), nextScanNum);
}
Assert.True(run.GetNextScanNum(scanNum) == nextScanNum);
}
}
Assert.True(run.GetNextScanNum(20025) == 20032);
Console.WriteLine(run.GetNextScanNum(20025));
}
public void TestFitScoreCalculationCid()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestTopDownRawFilePathCid, 5743, 5743);
var spec = run.GetSpectrum(5743);
Assert.True(spec != null);
const string protein = "MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG";
var protComp = new AminoAcidSet().GetComposition(protein) + Composition.H2O;
Assert.True(protComp != null);
Assert.True(protComp.C == 1035);
Assert.True(protComp.H == 1683);
Assert.True(protComp.N == 289);
Assert.True(protComp.O == 318);
Assert.True(protComp.P == 0);
Assert.True(protComp.S == 7);
Assert.True(Math.Abs(protComp.Mass - 23473.245267145) < 0.0000001);
Assert.True(protComp.NominalMass == 23461);
var ion = new Ion(protComp, 20);
// ion.Composition.ComputeApproximateIsotopomerEnvelop();
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine(@"MonoMz: {0}, MonoMass: {1}", ion.GetMonoIsotopicMz(), ion.Composition.Mass);
var matchedPeaks = spec.GetAllIsotopePeaks(ion, new Tolerance(15), 0.1);
for (var i = 0; i < matchedPeaks.Length; i++)
{
var intensity = matchedPeaks[i] == null ? 0 : matchedPeaks[i].Intensity;
Console.WriteLine(@"{0,3} {1,10:F4} {2,10:F3} {3,10:F3}", i, ion.GetIsotopeMz(i), isotopomerEnvelope[i], intensity);
}
var fitScore = spec.GetFitScore(ion, new Tolerance(15), 0.1);
var cosine = spec.GetConsineScore(ion, new Tolerance(15), 0.1);
var corr = spec.GetCorrScore(ion, new Tolerance(15), 0.1);
Console.WriteLine(@"FitScore: {0}", fitScore);
Console.WriteLine(@"Cosine: {0}", cosine);
Console.WriteLine(@"Corr: {0}", corr);
Assert.True(Math.Abs(fitScore - 0.181194589537041) < 0.0001);
Assert.True(Math.Abs(cosine - 0.917609346566222) < 0.0001);
Assert.True(Math.Abs(corr - 0.808326778009839) < 0.0001);
}
public void TestReadingIsolationWindows()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestLcMsRun.TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestLcMsRun.TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestRawFilePath, 10000, 10100);
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var isolationWindow = run.GetIsolationWindow(scanNum);
if (isolationWindow != null)
{
Console.WriteLine("{0}\t{1}\t{2}", scanNum, isolationWindow.MonoisotopicMz ?? 0.0, isolationWindow.Charge ?? 0.0);
}
}
}
public void TestParsingSpectrumFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
if (!File.Exists(TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestTopDownRawFilePathCid);
}
const int SCAN = 425;
const int MAX_POINTS = 50;
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestTopDownRawFilePathCid, SCAN, SCAN);
const int scanNum = SCAN;
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
if (spec != null)
{
spec.Display(MAX_POINTS);
var precursorInfo = spec.IsolationWindow;
Console.WriteLine("ActivationMethod: {0}", spec.ActivationMethod);
Console.WriteLine("Rt: {0}", spec.ElutionTime);
Console.WriteLine("PrecursorScan: {0}", run.GetPrecursorScanNum(spec.ScanNum));
Console.WriteLine("IsolationWindowTargetMz: {0}", precursorInfo.IsolationWindowTargetMz);
Console.WriteLine("IsolationWindowLowerOffset: {0}", precursorInfo.IsolationWindowLowerOffset);
Console.WriteLine("IsolationWindowUpperOffset: {0}", precursorInfo.IsolationWindowUpperOffset);
Console.WriteLine("MsLevel: {0}", run.GetMsLevel(scanNum));
}
Console.WriteLine(@"Done. {0:f4} sec", sw.Elapsed.TotalSeconds);
}
