public void DisplaySpectrumMatch(PlotView plotView, Canvas canvas, PsmFromTsv psm, ParentChildScanPlotsView parentChildScanPlotsView, out List <string> errors)
{
errors = null;
// clear old parent/child scans
parentChildScanPlotsView.Plots.Clear();
CurrentlyDisplayedPlots.Clear();
// get the scan
if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out DynamicDataConnection spectraFile))
{
errors = new List <string>();
errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
return;
}
MsDataScan scan = spectraFile.GetOneBasedScanFromDynamicConnection(psm.Ms2ScanNumber);
LibrarySpectrum librarySpectrum = null;
// plot the annotated spectrum match
PeptideSpectrumMatchPlot plot;
//if not crosslinked
if (psm.BetaPeptideBaseSequence == null)
{
// get the library spectrum if relevant
if (SpectralLibrary != null)
{
SpectralLibrary.TryGetSpectrum(psm.FullSequence, psm.PrecursorCharge, out var librarySpectrum1);
librarySpectrum = librarySpectrum1;
}
plot = new PeptideSpectrumMatchPlot(plotView, canvas, psm, scan, psm.MatchedIons, librarySpectrum: librarySpectrum);
}
else //crosslinked
{
plot = new CrosslinkSpectrumMatchPlot(plotView, canvas, psm, scan);
}
CurrentlyDisplayedPlots.Add(plot);
// plot parent/child scans
if (psm.ChildScanMatchedIons != null)
{
// draw parent scan
string parentAnnotation = "Scan: " + scan.OneBasedScanNumber
+ " Dissociation Type: " + scan.DissociationType
+ " MsOrder: " + scan.MsnOrder
+ " Selected Mz: " + scan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + scan.RetentionTime.ToString("0.##");
var parentPlotView = new PlotView(); // placeholder
var parentCanvas = new Canvas();
var item = new ParentChildScanPlotTemplate()
{
Plot = new PeptideSpectrumMatchPlot(parentPlotView, parentCanvas, psm, scan, psm.MatchedIons),
SpectrumLabel = parentAnnotation,
TheCanvas = parentCanvas
};
parentChildScanPlotsView.Plots.Add(item);
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
parentPlotView.Model = null;
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psm.ChildScanMatchedIons;
if (psm.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psm.BetaPeptideChildScanMatchedIons)
.GroupBy(p => p.Key)
.ToDictionary(p => p.Key, q => q.SelectMany(p => p.Value).ToList());
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int childScanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(childScanNumber))
{
continue;
}
scansDrawn.Add(childScanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
MsDataScan childScan = spectraFile.GetOneBasedScanFromDynamicConnection(childScanNumber);
string childAnnotation = "Scan: " + childScan.OneBasedScanNumber
+ " Dissociation Type: " + childScan.DissociationType
+ " MsOrder: " + childScan.MsnOrder
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas childCanvas = new Canvas();
PlotView childPlotView = new PlotView(); // placeholder
// make the plot
var childPlot = new PeptideSpectrumMatchPlot(childPlotView, childCanvas, psm, childScan, matchedIons, annotateProperties: false);
childPlot.Model.Title = null;
childPlot.Model.Subtitle = null;
item = new ParentChildScanPlotTemplate()
{
Plot = childPlot, SpectrumLabel = childAnnotation, TheCanvas = childCanvas
};
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
childPlotView.Model = null;
parentChildScanPlotsView.Plots.Add(item);
CurrentlyDisplayedPlots.Add(childPlot);
}
}
}
public static void SpectralLibraryReaderTestNeutralLoss()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\spectralLibraryNeutralLossTest.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra[0].MatchedFragmentIons[9].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[11].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[13].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[23].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
testLibraryWithoutDecoy.TryGetSpectrum("ASVSELAC[Common Fixed:Carbamidomethyl on C]IYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLIC[Common Fixed:Carbamidomethyl on C]NVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEES[Common Biological:Phosphorylation on S]EES[Common Biological:Phosphorylation on S]DDDMGFGLFD", 11, out var test1);
Assert.AreEqual(test1.ChargeState, 11);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double neutralLoss)>
{
(474.22253552109225, 0.12327031966337068, ProductType.b, 5, 1, 0.0),
(598.2911881692844, 0.17637685313108434, ProductType.y, 5, 1, 0.0),
(587.3078660257297, 0.26448833020105406, ProductType.b, 6, 1, 0.0),
(655.3122852061485, 0.2573965224084584, ProductType.y, 6, 1, 0.0),
(786.3547054957799, 0.5973180470179946, ProductType.y, 7, 1, 0.0),
(901.3828669653562, 0.1394747476004537, ProductType.y, 8, 1, 0.0),
(931.4665832519531, 0.1434341615825174, ProductType.b, 9, 1, 0.0),
(1298.4420166015627, 0.04799051344737827, ProductType.y, 11, 1, 0.0),
(1194.1036493343909, 0.16497897552735782, ProductType.b, 22, 2, 0.0),
(1412.6153999317123, 0.059408140384558945, ProductType.y, 24, 2, 97.976895573),
(1610.16612195462, 0.06598126929193648, ProductType.y, 27, 2, 0.0),
(1561.176395469285, 0.3655719849041352, ProductType.y, 27, 2, 97.976895573),
(1596.6949731527957, 0.1196248007420883, ProductType.y, 28, 2, 97.976895573),
(1632.2140387967154, 0.1134099785167373, ProductType.y, 29, 2, 97.976895573),
(1239.8634635821659, 0.19969145903784855, ProductType.y, 33, 3, 0.0),
(1207.2033996967743, 0.4866798941848081, ProductType.y, 33, 3, 97.976895573),
(1810.301461311722, 0.2822226465462767, ProductType.y, 33, 2, 97.976895573),
(1282.2420159220214, 0.06365769264631967, ProductType.y, 36, 3, 97.976895573),
(1333.9057047796402, 0.04957330666530949, ProductType.y, 37, 3, 0.0),
(1042.7038942258248, 0.10714201465676373, ProductType.y, 39, 4, 0.0),
(1389.9361001454733, 0.20027716863748268, ProductType.y, 39, 3, 0.0),
(1018.2100179729548, 0.23609364592477405, ProductType.y, 39, 4, 97.976895573),
(1357.2775984749799, 1, ProductType.y, 39, 3, 97.976895573),
(1503.354187325224, 0.060227438209151066, ProductType.y, 45, 3, 97.976895573)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
Assert.That(frag.neutralLoss == readFrag.NeutralTheoreticalProduct.NeutralLoss);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 1);
testLibraryWithoutDecoy.TryGetSpectrum("ASVSELAC[Common Fixed:Carbamidomethyl on C]IYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLIC[Common Fixed:Carbamidomethyl on C]NVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEES[Common Biological:Phosphorylation on S]EES[Common Biological:Phosphorylation on S]DDDMGFGLFD", 11, out test1);
Assert.AreEqual(test1.ChargeState, 11);
double maxOfIntensity = frags.Select(p => p.intensity).ToList().Max();
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That((frag.intensity / maxOfIntensity) == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
Assert.That(frag.neutralLoss == readFrag.NeutralTheoreticalProduct.NeutralLoss);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}
public static void SpectralLibraryReaderTest_pDeep()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\yeast2fake_pdeep_lib.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("VGIVPGEVIAPGM[Common Variable:Oxidation on M]R", 3, out var spectrum1));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("C[Common Fixed:Carbamidomethyl on C]TSC[Common Fixed:Carbamidomethyl on C]NGQGIKFVTR", 3, out var spectrum2));
Assert.AreEqual(spectrum2.PrecursorMz, 543.2608252287667);
Assert.AreEqual(spectrum2.RetentionTime, 2789.812255859375);
testLibraryWithoutDecoy.TryGetSpectrum("YHPDKNPSEEAAEK", 3, out var test1);
Assert.AreEqual(test1.PrecursorMz, 538.9179945621);
Assert.AreEqual(test1.RetentionTime, 1361.375244140625);
Assert.AreEqual(test1.ChargeState, 3);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double ppm)>
{
(301.1295080000, 10000.0, ProductType.b, 2, 1, 0.0),
(657.8122378432, 1102.3, ProductType.y, 12, 2, 0.0),
(974.4425296863, 1476.0, ProductType.y, 9, 1, 0.0),
(860.3996026863, 7228.2, ProductType.y, 8, 1, 0.0),
(763.3468386863, 1201.9, ProductType.y, 7, 1, 0.0),
(418.2296246863, 1178.9, ProductType.y, 4, 1, 0.0),
(347.1925106863, 1042.8, ProductType.y, 3, 1, 0.0)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("VGIVPGEVIAPGM[Common Variable:Oxidation on M]R", 3, out var spectrum3));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("C[Common Fixed:Carbamidomethyl on C]TSC[Common Fixed:Carbamidomethyl on C]NGQGIKFVTR", 3, out var spectrum4));
Assert.AreEqual(spectrum4.PrecursorMz, 543.2608252287667);
Assert.AreEqual(spectrum4.RetentionTime, 2789.812255859375);
testLibraryWithoutDecoy.TryGetSpectrum("YHPDKNPSEEAAEK", 3, out test1);
Assert.AreEqual(test1.PrecursorMz, 538.9179945621);
Assert.AreEqual(test1.RetentionTime, 1361.375244140625);
Assert.AreEqual(test1.ChargeState, 3);
double maxOfIntensity = frags.Select(p => p.intensity).ToList().Max();
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That((frag.intensity / maxOfIntensity) == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}
public static void SpectralLibraryReaderTest()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\myPrositLib.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("QSQHM[Common Variable:Oxidation on M]TEVVR", 5, out var spectrum));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("M[Common Variable:Oxidation on M]C[Common Fixed:Carbamidomethyl on C]SDSDGLAPPQHLIR", 2, out spectrum));
testLibraryWithoutDecoy.TryGetSpectrum("ALAVDGAGKPGAEE", 2, out var test1);
Assert.AreEqual(test1.ChargeState, 2);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double ppm)>
{
(148.06044, 0.03711248, ProductType.y, 1, 1, 0.0),
(277.10303, 0.025135221, ProductType.y, 2, 1, 0.0),
(185.12845, 0.8128169, ProductType.b, 2, 1, 0.0),
(348.14014, 0.008474186, ProductType.y, 3, 1, 0.0),
(256.16556, 1.0, ProductType.b, 3, 1, 0.0),
(405.1616, 0.006187536, ProductType.y, 4, 1, 0.0),
(203.08444, 0.00014141058, ProductType.y, 4, 2, 0.0),
(355.23398, 0.1165214, ProductType.b, 4, 1, 0.0),
(178.12064, 0.010349626, ProductType.b, 4, 2, 0.0),
(502.21436, 0.7401104, ProductType.y, 5, 1, 0.0),
(470.26093, 0.055574868, ProductType.b, 5, 1, 0.0),
(235.6341, 0.005631463, ProductType.b, 5, 2, 0.0),
(630.3093, 0.0679749, ProductType.y, 6, 1, 0.0),
(527.2824, 0.02713329, ProductType.b, 6, 1, 0.0),
(264.14484, 0.002669461, ProductType.b, 6, 2, 0.0),
(687.3308, 0.38598263, ProductType.y, 7, 1, 0.0),
(598.3195, 0.016116723, ProductType.b, 7, 1, 0.0),
(758.3679, 0.1706151, ProductType.y, 8, 1, 0.0),
(655.34094, 0.007904499, ProductType.b, 8, 1, 0.0),
(815.3894, 0.5167622, ProductType.y, 9, 1, 0.0),
(408.19833, 0.0012127026, ProductType.y, 9, 2, 0.0),
(783.4359, 0.01972321, ProductType.b, 9, 1, 0.0),
(930.4163, 0.8694488, ProductType.y, 10, 1, 0.0),
(465.7118, 0.026939344, ProductType.y, 10, 2, 0.0),
(1029.4847, 0.27091113, ProductType.y, 11, 1, 0.0),
(515.24603, 0.020846518, ProductType.y, 11, 2, 0.0),
(1100.5219, 0.22043262, ProductType.y, 12, 1, 0.0),
(550.7646, 0.0036459658, ProductType.y, 12, 2, 0.0),
(1008.5473, 0.0029647197, ProductType.b, 12, 1, 0.0),
(1137.5898, 0.009047425, ProductType.b, 13, 1, 0.0),
(569.2986, 7.061393e-05, ProductType.b, 13, 2, 0.0)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("QSQHM[Common Variable:Oxidation on M]TEVVR", 5, out spectrum));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("M[Common Variable:Oxidation on M]C[Common Fixed:Carbamidomethyl on C]SDSDGLAPPQHLIR", 2, out spectrum));
testLibraryWithoutDecoy.TryGetSpectrum("ALAVDGAGKPGAEE", 2, out test1);
Assert.AreEqual(test1.ChargeState, 2);
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}