public static void ThermoDynamicTest()
{
ThermoDynamicData dynamicThermo = ThermoDynamicData.InitiateDynamicConnection(@"testFileWMS2.raw");
var ms1scan = dynamicThermo.GetOneBasedScan(1);
MsDataScan ms2scan = dynamicThermo.GetOneBasedScan(651);
Assert.That(ms1scan.OneBasedScanNumber == 1);
Assert.That(ms2scan.OneBasedScanNumber == 651);
Assert.That(Math.Round(ms2scan.RetentionTime, 2) == 12.16);
Assert.That(ms2scan.OneBasedPrecursorScanNumber == 650);
Assert.That(ms2scan.SelectedIonMZ == 442.67);
var t = dynamicThermo.ThermoGlobalParams.MsOrderByScan;
Assert.That(t[0] == 1);
Assert.That(t[5] == 1);
Assert.That(t[649] == 1);
Assert.That(t[650] == 2);
Assert.That(!t.Where(v => v == 0).Any());
}
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 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);
}