private static ThermoMzPeak GetPeak(PSM psm, double oxoniumIon, ThermoRawFile rawFile)
{
DoubleRange rangeOxonium = DoubleRange.FromPPM(oxoniumIon, 20);
List <ThermoMzPeak> peaks;
ThermoSpectrum spec = rawFile.GetSpectrum(psm.scanNumber);
if (spec.TryGetPeaks(rangeOxonium, out peaks))
{
peaks = peaks.OrderBy(x => x.SignalToNoise).ToList();
}
double diff = double.MaxValue;
ThermoMzPeak returnPeak = null;
foreach (ThermoMzPeak peak in peaks)
{
var currDiff = Math.Abs(peak.MZ - oxoniumIon);
if (currDiff < diff)
{
diff = currDiff;
returnPeak = peak;
}
}
return(returnPeak);
}
public static void GetXICs(ThermoSpectrum currentSpectrum, int specNumber, double rt)
{
List <LFPeptide> donePeptides = targetPeptides.Where(x => x.LastScan < specNumber).ToList();
foreach (var pep in donePeptides)
{
pep.doneBuildingXIC = true;
}
List <LFPeptide> currPeptides = targetPeptides.Where(x => x.FirstScan <= specNumber && x.LastScan >= specNumber).ToList();
foreach (var pep in currPeptides)
{
List <ThermoMzPeak> outPeaks = new List <ThermoMzPeak>();
if (currentSpectrum.TryGetPeaks(pep.lookupRange, out outPeaks))
{
var matchPeak = GetClosestPeak(outPeaks, pep.UserMZ);
var newRTPeak = new RTPeak(matchPeak, rt);
pep.XICLibrary.Add(newRTPeak);
}
else
{
var newRTPeak = new RTPeak(pep.UserMZ, 0, rt);
pep.XICLibrary.Add(newRTPeak);
}
}
}
public static void ThermoSpectrumTest()
{
double[] mz = new double[] { 1 };
double[] intensity = new double[] { 1 };
ThermoSpectrum s1 = new ThermoSpectrum(mz, intensity, false);
ThermoSpectrum s2 = new ThermoSpectrum(mz, intensity, false);
s1.ReplaceXbyApplyingFunction((a) => 4);
Assert.AreEqual(4, s2.XArray[0]);
}
public void MatchIntensities(ThermoSpectrum spectrum, int spectrumNumber)
{
var outputIntensity = 0.0;
spectrum.TryGetIntensities(mzRange, out outputIntensity);
intensities.Add(outputIntensity);
spectrumNumbers.Add(spectrumNumber);
spectrumTICs.Add(spectrum.TotalIonCurrent);
}
public static int GetSpectraCountOxonium(List <int> spectrumList, double oxoniumIon1, double oxoniumIon2, ThermoRawFile rawFile)
{
int count = 0;
foreach (int scan in spectrumList)
{
ThermoSpectrum spectrum = rawFile.GetSpectrum(scan);
bool oxoniumIsPresent = false;
DoubleRange rangeOxonium1 = DoubleRange.FromPPM(oxoniumIon1, 20);
List <ThermoMzPeak> peaks;
if (spectrum.TryGetPeaks(rangeOxonium1, out peaks))
{
peaks = peaks.OrderBy(x => x.SignalToNoise).ToList();
}
if (peaks.Count > 0)
{
if (peaks[0].SignalToNoise > 3)
{
oxoniumIsPresent = true;
}
}
if (oxoniumIon2 > 0)
{
DoubleRange rangeOxonium2 = DoubleRange.FromPPM(oxoniumIon2, 20);
List <ThermoMzPeak> peaks2;
if (spectrum.TryGetPeaks(rangeOxonium2, out peaks2))
{
peaks2 = peaks2.OrderBy(x => x.SignalToNoise).ToList();
}
if (peaks2.Count > 0)
{
if (peaks2[0].SignalToNoise > 3)
{
oxoniumIsPresent = true;
}
}
}
if (oxoniumIsPresent)
{
count++;
}
}
return(count);
}
public static void RecalibrateThermoRawFile()
{
List <ISpectrum> spectra = new List <ISpectrum>();
using (ThermoRawFile rawFile = new ThermoRawFile("Resources/ThermoRawFileMS1MS2.raw"))
{
rawFile.Open();
for (int i = rawFile.FirstSpectrumNumber; i <= rawFile.LastSpectrumNumber; i++)
{
ThermoSpectrum spectrum = rawFile.GetLabeledSpectrum(i);
ThermoSpectrum correctedSpectrum = spectrum.CorrectMasses((mz) => mz - 5); // shift all masses 5 Th lower
spectra.Add(correctedSpectrum);
}
}
}
public void LoadThermoTest2()
{
ThermoRawFile a = new ThermoRawFile(@"05-13-16_cali_MS_60K-res_MS.raw");
a.Open();
Assert.AreEqual(360, a.LastSpectrumNumber);
var ok = a.GetScan(1).MassSpectrum.GetNoises();
Assert.AreEqual(2401.57, ok[0], 0.01);
ThermoSpectrum ok2 = a.GetScan(1).MassSpectrum.newSpectrumExtract(0, 500);
Assert.GreaterOrEqual(1000, a.GetScan(1).MassSpectrum.newSpectrumExtract(0, 500).LastX);
Assert.AreEqual(2, a.GetScan(1).MassSpectrum.newSpectrumFilterByY(5e6).Count);
var ye = a.GetScan(1).MassSpectrum.CopyTo2DArray();
Assert.AreEqual(1, ye[4, 1119]);
Assert.AreEqual("(195.0874,1.0214E+07) z = +1 SN = 4170.38", a.GetScan(1).MassSpectrum.PeakWithHighestY.ToString());
Assert.AreEqual(77561752, a.GetTIC(1));
Assert.AreEqual(144, a.GetSpectrumNumber(2));
Assert.AreEqual(0.98, a.GetElapsedScanTime(100), 0.01);
var cromatogram = a.GetTICChroma();
Assert.AreEqual(360, cromatogram.Count);
Assert.AreEqual(0.01, cromatogram.FirstTime, 0.002);
Assert.AreEqual(2.788433333, cromatogram.PeakWithHighestY.Time, 0.0001);
Assert.AreEqual(2.788433333, cromatogram.GetApex(0, 5).Time, 0.0001);
var newSpectrum = new ThermoSpectrum(a.GetScan(51).MassSpectrum);
Assert.AreEqual(22246 / 5574.8, newSpectrum.GetSignalToNoise(1), 0.01);
Assert.AreEqual(1, newSpectrum.GetCharges()[1]);
Assert.AreEqual(102604, newSpectrum.GetResolutions()[1]);
Assert.AreEqual(181, newSpectrum.newSpectrumExtract(500, 1000).Count);
Assert.AreEqual(0, newSpectrum.newSpectrumExtract(-3, -2).Count);
var hm = newSpectrum.newSpectrumExtract(501, 502);
Assert.AreEqual(0, hm.Count);
}
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().X);
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));
var newSpectrum = new ThermoSpectrum(a.GetOneBasedScan(51).MassSpectrum);
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.First().Polarity, readCovertedMzmlFile.First().Polarity);
}
