public static void XlTestGenerateIntensityRanks()
{
double[] intensity = new double[] { 1.1, 1.1, 0.5, 3.2, 0.5, 6.0 };
int[] rank = PsmCross.GenerateIntensityRanks(intensity);
int[] Rank = new int[] { 4, 3, 6, 2, 5, 1 };
Assert.AreEqual(rank, Rank);
}
private void UpdateModel(int x)
{
Ms2ScanWithSpecificMass msScanForDraw = arrayOfMs2ScansSortedByMass.Where(p => p.OneBasedScanNumber == x).First();
//mainViewModel.UpdateScanModel(msScanForDraw);
PsmCross psmCross = PSMs.Where(p => p.ScanNumber == x).First();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Tolerance productMassTolerance = new PpmTolerance(20);
var pmm = PsmCross.XlCalculateTotalProductMassesForSingle(psmCross, lp, false);
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(msScanForDraw.TheScan, productMassTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
matchedIonMassesListPositiveIsMatch.PredictedIonName = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp).ProductName;
matchedIonMassesListPositiveIsMatch.PredictedIonMZ = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp).ProductMz;
matchedIonMassesListPositiveIsMatch.PredictedIonIntensity = predictedIntensities[psmCross.ScanNumber];
psmCross.MatchedIonInfo = matchedIonMassesListPositiveIsMatch;
mainViewModel.UpdateCrosslinkModelForSingle(msScanForDraw, psmCross);
pdeepModelView.UpdataModelForPdeep(psmCross);
}
//Calculate the FDR of crosslinked peptide (D - 2DD) / T
private static List <PsmCross> CrosslinkFDRAnalysis(List <PsmCross> items)
{
var ids = new List <PsmCross>();
foreach (var item in items)
{
ids.Add(item);
}
int cumulative_target = 0;
int cumulative_decoy = 0;
int cumulative_decoy_decoy = 0;
for (int i = 0; i < ids.Count; i++)
{
var item1 = ids[i]; var item2 = ids[i].BetaPsmCross;
var isDecoy1 = item1.IsDecoy; var isDecoy2 = item2.IsDecoy;
if (isDecoy1 || isDecoy2)
{
cumulative_decoy++;
}
else
{
cumulative_target++;
}
if (isDecoy1 && isDecoy2)
{
cumulative_decoy_decoy++;
}
double temp_q_value = (double)(cumulative_decoy - 2 * cumulative_decoy_decoy) / (cumulative_target + cumulative_decoy);
item1.SetFdrValues(cumulative_target, cumulative_decoy, temp_q_value, 0, 0, 0, 0, 0, 0, false);
// item2.SetFdrValues(cumulative_target, cumulative_decoy, temp_q_value, 0, 0, 0);
}
double min_q_value = double.PositiveInfinity;
for (int i = ids.Count - 1; i >= 0; i--)
{
PsmCross id = ids[i];
if (id.FdrInfo.QValue < 0)
{
id.FdrInfo.QValue = 0;
}
if (id.FdrInfo.QValue > min_q_value)
{
id.FdrInfo.QValue = min_q_value;
}
else if (id.FdrInfo.QValue < min_q_value)
{
min_q_value = id.FdrInfo.QValue;
}
}
return(ids);
}
public static void XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
Protease protease = new Protease("New Custom Protease", new List <Tuple <string, TerminusType> > {
new Tuple <string, TerminusType>("K", TerminusType.C)
}, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
Assert.AreEqual(crosslinker.CrosslinkerModSites, "K");
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses;
var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c[0], 128.09496301518999, 1e-6);
var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x[0], 4);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses;
var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6);
var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x2[0], 4);
//Test crosslinker with multiple types of mod
var protSTC = new Protein("GASTACK", null);
var peps = protSTC.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pepSTC = peps[0];
Assert.AreEqual(pepSTC.BaseSequence, "GASTACK");
CrosslinkerTypeClass crosslinker2 = new CrosslinkerTypeClass("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0);
string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
Assert.AreEqual(crosslinkerModSitesAll, "STC");
}
public static void XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
DigestionParams digestionParams = new DigestionParams
{
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
MaxMissedCleavages = 2,
Protease = protease,
MinPeptideLength = 1
};
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
Assert.AreEqual(crosslinker.CrosslinkerModSite, 'K');
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSite).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses;
var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c[0], 128.09496301518999, 1e-6);
var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker).ToArray();
Assert.AreEqual(x[0], 4);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses;
var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6);
var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker).ToArray();
Assert.AreEqual(x2[0], 4);
}
//Calculate the FDR of single peptide FP/TP
private static List <PsmCross> SingleFDRAnalysis(List <PsmCross> items)
{
var ids = new List <PsmCross>();
foreach (var item in items)
{
ids.Add(item);
}
int cumulative_target = 0;
int cumulative_decoy = 0;
for (int i = 0; i < ids.Count; i++)
{
var item1 = ids[i];
var isDecoy1 = item1.IsDecoy;
if (isDecoy1)
{
cumulative_decoy++;
}
else
{
cumulative_target++;
}
double temp_q_value = (double)cumulative_decoy / cumulative_target;
item1.SetFdrValues(cumulative_target, cumulative_decoy, temp_q_value, 0, 0, 0, 0, 0, 0, false);
}
double min_q_value = double.PositiveInfinity;
for (int i = ids.Count - 1; i >= 0; i--)
{
PsmCross id = ids[i];
if (id.FdrInfo.QValue > min_q_value)
{
id.FdrInfo.QValue = min_q_value;
}
else if (id.FdrInfo.QValue < min_q_value)
{
min_q_value = id.FdrInfo.QValue;
}
}
return(ids);
}
public void TestMods()
{
PsmCross PSM = new PsmCross();
PSM.BaseSequence = "DMHGDSEYNIMFGPDICGPGTK";
PSM.FullSequence = "DM[Common Variable:Oxidation of M]HGDSEYNIM[Common Variable:Oxidation of M]FGPDIC[Common Fixed:Carbamidomethyl of C]GPGTK";
PSM.PeptideMonisotopicMass = 2472.0032;
var mods = TsvResultReader.GetMods(PSM);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus = new Dictionary <int, ModificationWithMass>();
foreach (var item in mods)
{
ModificationMotif.TryGetMotif(item.Value, out ModificationMotif modificationMotif);
ModificationWithMass mod = new ModificationWithMass("mod", null, modificationMotif, TerminusLocalization.Any, 10);
allModsOneIsNterminus.Add(item.Key, mod);
}
PepWithSetModForCompactPep pepWithSetModForCompactPep = new PepWithSetModForCompactPep();
pepWithSetModForCompactPep.allModsOneIsNterminus = allModsOneIsNterminus;
pepWithSetModForCompactPep.BaseSequence = PSM.BaseSequence;
pepWithSetModForCompactPep.Length = PSM.BaseSequence.Length;
pepWithSetModForCompactPep.MonoisotopicMass = (double)PSM.PeptideMonisotopicMass;
var compactPeptide = new CompactPeptide(pepWithSetModForCompactPep, TerminusType.None);
PSM.CompactPeptide = compactPeptide;
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Tolerance productMassTolerance = new PpmTolerance(10);
var pmm = PsmCross.XlCalculateTotalProductMassesForSingle(PSM, lp, false);
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
//double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, productMassTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
}
public static void XlTest_BSA_DSSO()
{
//Generate parameters
var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, cIons: true, zDotIons: true, scoreCutoff: 2, digestionParams: new DigestionParams(minPeptideLength: 5));
var xlSearchParameters = new XlSearchParameters {
XlCharge_2_3_PrimeFragment = true
};
//Create databases contain two protein.
var proteinList = new List <Protein> {
new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02")
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994);
var variableModifications = new List <ModificationWithMass>()
{
mod1
};
var fixedModifications = new List <ModificationWithMass>()
{
mod2
};
var localizeableModifications = new List <ModificationWithMass>();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y, ProductType.C, ProductType.Zdot
};
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
//Generate digested peptide lists.
List <PeptideWithSetModifications> digestedList = new List <PeptideWithSetModifications>();
foreach (var item in proteinList)
{
var digested = item.Digest(commonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
digestedList.AddRange(digested);
}
foreach (var fdfd in digestedList)
{
fdfd.CompactPeptide(TerminusType.None);
}
//Run index engine
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <DigestionParams>
{
commonParameters.DigestionParams
}, commonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var fragmentIndexCount = indexResults.FragmentIndex.Count(p => p != null);
var fragmentIndexAll = indexResults.FragmentIndex.Select((s, j) => new { j, s }).Where(p => p.s != null).Select(t => t.j).ToList();
Assert.IsTrue(fragmentIndexAll.Count() > 0);
//Get MS2 scans.
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, commonParameters.DoPrecursorDeconvolution, commonParameters.UseProvidedPrecursorInfo, commonParameters.DeconvolutionIntensityRatio, commonParameters.DeconvolutionMaxAssumedChargeState, commonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Generate crosslinker, which is DSSO here.
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(xlSearchParameters.CrosslinkerType);
//TwoPassCrosslinkSearchEngine.Run().
List <PsmCross> newPsms = new List <PsmCross>();
new TwoPassCrosslinkSearchEngine(newPsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, lp, 0, commonParameters, false, xlSearchParameters.XlPrecusorMsTl, crosslinker, xlSearchParameters.CrosslinkSearchTop, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, xlSearchParameters.XlCharge_2_3, xlSearchParameters.XlCharge_2_3_PrimeFragment, new List <string> {
}).Run();
var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
new CrosslinkAnalysisEngine(newPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, lp, null, crosslinker, TerminusType.None, commonParameters, new List <string> {
}).Run();
foreach (var item in newPsms)
{
item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
}
//Test newPsms
Assert.AreEqual(newPsms.Count(), 3);
//Test Output
var task = new XLSearchTask();
task.WriteAllToTsv(newPsms, TestContext.CurrentContext.TestDirectory, "allPsms", new List <string> {
});
task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> {
});
task.WriteSingleToTsv(newPsms.Where(p => p.CrossType == PsmCrossType.Singe).ToList(), TestContext.CurrentContext.TestDirectory, "singlePsms", new List <string> {
});
//Test PsmCross.XlCalculateTotalProductMasses.
var psmCrossAlpha = new PsmCross(digestedList[1].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var psmCrossBeta = new PsmCross(digestedList[2].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites);
var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, true, false, linkPos);
Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 99);
}
public void UpdateCrosslinkModelForSingle(Ms2ScanWithSpecificMass MsScanForDraw, PsmCross psmParentsForDraw)
{
var x = MsScanForDraw.TheScan.MassSpectrum.XArray;
var y = MsScanForDraw.TheScan.MassSpectrum.YArray;
string scanNum = psmParentsForDraw.ScanNumber.ToString();
string sequence1 = psmParentsForDraw.FullSequence;
var matchedIonDic1 = psmParentsForDraw.MatchedIonInfo;
PlotModel model = new PlotModel {
Title = "Spectrum anotation of Scan " + scanNum + " for Crosslinked Peptide", DefaultFontSize = 15
};
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Bottom, Title = "m/z", Minimum = 0, Maximum = x.Max() * 1.02
});
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Left, Title = "Intensity(counts)", Minimum = 0, Maximum = y.Max() * 1.2
});
var textAnnoSeq1 = new TextAnnotation()
{
};
textAnnoSeq1.FontSize = 9; textAnnoSeq1.TextColor = OxyColors.Red; textAnnoSeq1.StrokeThickness = 0; textAnnoSeq1.TextPosition = new DataPoint(x.Max() / 2, y.Max() * 1.15); textAnnoSeq1.Text = sequence1;
model.Annotations.Add(textAnnoSeq1);
LineSeries[] s0 = new LineSeries[x.Length];
LineSeries[] s1 = new LineSeries[x.Length];
//Draw the ms/ms scan peaks
for (int i = 0; i < x.Length; i++)
{
s0[i] = new LineSeries();
s0[i].Color = OxyColors.DimGray;
s0[i].StrokeThickness = 0.15;
s0[i].Points.Add(new DataPoint(x[i], 0));
s0[i].Points.Add(new DataPoint(x[i], y[i]));
model.Series.Add(s0[i]);
}
//Draw the ms/ms scan matched peaks
for (int i = 0; i < matchedIonDic1.MatchedIonMz.Length; i++)
{
OxyColor ionColor = OxyColors.Red;
if (matchedIonDic1.MatchedIonMz[i] > 0)
{
s1[i] = new LineSeries();
s1[i].Color = ionColor;
s1[i].StrokeThickness = 0.2;
s1[i].Points.Add(new DataPoint(matchedIonDic1.MatchedIonMz[i] + 1.007277, 0));
s1[i].Points.Add(new DataPoint(matchedIonDic1.MatchedIonMz[i] + 1.007277, matchedIonDic1.MatchedIonIntensity[i]));
var textAnno1 = new TextAnnotation();
textAnno1.FontSize = 6;
textAnno1.TextColor = ionColor;
textAnno1.StrokeThickness = 0;
textAnno1.TextPosition = s1[i].Points[1];
textAnno1.Text = matchedIonDic1.MatchedIonMz[i].ToString("f3");
var textAnno2 = new TextAnnotation();
textAnno2.FontSize = 6;
textAnno2.TextColor = ionColor;
textAnno2.StrokeThickness = 0;
textAnno2.TextPosition = new DataPoint(s1[i].Points[1].X, s1[i].Points[1].Y + y.Max() * 0.02);
textAnno2.Text = matchedIonDic1.MatchedIonName[i];
model.Annotations.Add(textAnno1);
model.Annotations.Add(textAnno2);
model.Series.Add(s1[i]);
}
}
// Axes are created automatically if they are not defined
// Set the Model property, the INotifyPropertyChanged event will make the WPF Plot control update its content
this.Model = model;
}
public static List <PsmCross> ReadTsv(string filePath)
{
List <PsmCross> PSMs = new List <PsmCross>();
Dictionary <string, int> ids = new Dictionary <string, int>();
//Empty array. Is this correct?
string[][] resultArray = new string[][] { };
try
{
resultArray = File.ReadLines(filePath).Select(p => p.Split('\t')).ToArray();
}
catch (Exception)
{
MessageBox.Show("Please check the file.");
return(null);
}
for (int i = 0; i < resultArray[0].Length; i++)
{
ids.Add(resultArray[0][i], i);
}
for (int i = 1; i < resultArray.Length; i++)
{
PsmCross PSM = new PsmCross();
PSM.ScanNumber = Convert.ToInt32(resultArray[i][ids["Scan Number"]]);
var baseSeq = resultArray[i][ids["Base Sequence"]];
var chargeState = resultArray[i][ids["Precursor Charge"]];
var fullSeq = resultArray[i][ids["Full Sequence"]];
if (baseSeq.Contains("|"))
{
baseSeq = baseSeq.Split('|').First();
fullSeq = fullSeq.Split('|').First();
}
PSM.BaseSequence = baseSeq;
PSM.ScanPrecursorCharge = Convert.ToInt32(chargeState);
PSM.FullSequence = fullSeq;
PSM.IsDecoy = (resultArray[i][ids["Decoy"]] == "N" ? false :true);
PSM.PeptideMonisotopicMass = Convert.ToDouble(resultArray[i][ids["Precursor Mass"]]);
var mods = GetMods(PSM);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus = new Dictionary <int, ModificationWithMass>();
foreach (var item in mods)
{
//I don't really know why use as here.
var theMod = GlobalVariables.AllModsKnown.Where(p => p.id == item.Value).First() as ModificationWithMass;
allModsOneIsNterminus.Add(item.Key, theMod);
}
PepWithSetModForCompactPep pepWithSetModForCompactPep = new PepWithSetModForCompactPep();
pepWithSetModForCompactPep.allModsOneIsNterminus = allModsOneIsNterminus;
pepWithSetModForCompactPep.BaseSequence = PSM.BaseSequence;
pepWithSetModForCompactPep.Length = PSM.BaseSequence.Length;
pepWithSetModForCompactPep.MonoisotopicMass = (double)PSM.PeptideMonisotopicMass;
var compactPeptide = new CompactPeptide(pepWithSetModForCompactPep, TerminusType.None);
PSM.CompactPeptide = compactPeptide;
PSMs.Add(PSM);
}
return(PSMs);
}
// TODO: Draw to pdf file
public void XLDrawMSMatchToPdf(Ms2ScanWithSpecificMass MsScanForDraw, PsmCross psmParentsForDraw, int order, string OutputFolder)
{
var x = MsScanForDraw.TheScan.MassSpectrum.XArray;
var y = MsScanForDraw.TheScan.MassSpectrum.YArray;
string scanNum = psmParentsForDraw.ScanNumber.ToString();
string sequence1 = psmParentsForDraw.FullSequence + "-" + psmParentsForDraw.XlPos.ToString();
string sequence2 = psmParentsForDraw.BetaPsmCross.FullSequence + "-" + psmParentsForDraw.BetaPsmCross.XlPos.ToString();
var matchedIonDic1 = psmParentsForDraw.MatchedIonInfo;
var matchedIonDic2 = psmParentsForDraw.BetaPsmCross.MatchedIonInfo;
PlotModel model = new PlotModel {
Title = "Spectrum anotation of Scan " + scanNum + " for Crosslinked Peptide", DefaultFontSize = 15
};
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Bottom, Title = "m/z", Minimum = 0, Maximum = x.Max() * 1.02, AbsoluteMinimum = 0
});
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Left, Title = "Intensity(counts)", Minimum = 0, Maximum = y.Max() * 1.2, AbsoluteMinimum = 0
});
var textAnnoSeq1 = new TextAnnotation()
{
};
//textAnnoSeq1.TextRotation=90;
textAnnoSeq1.FontSize = 12; textAnnoSeq1.TextColor = OxyColors.Red; textAnnoSeq1.StrokeThickness = 0; textAnnoSeq1.TextPosition = new DataPoint(x.Max() / 2, y.Max() * 1.15); textAnnoSeq1.Text = sequence1;
var textAnnoSeq2 = new TextAnnotation()
{
};
//textAnnoSeq2.TextRotation=90;
textAnnoSeq2.FontSize = 12; textAnnoSeq2.TextColor = OxyColors.Blue; textAnnoSeq2.StrokeThickness = 0; textAnnoSeq2.TextPosition = new DataPoint(x.Max() / 2, y.Max() * 1.1); textAnnoSeq2.Text = sequence2;
model.Annotations.Add(textAnnoSeq1);
model.Annotations.Add(textAnnoSeq2);
LineSeries[] s0 = new LineSeries[x.Length];
LineSeries[] s1 = new LineSeries[x.Length];
LineSeries[] s2 = new LineSeries[x.Length];
//Draw the ms/ms scan peaks
for (int i = 0; i < x.Length; i++)
{
s0[i] = new LineSeries();
s0[i].Color = OxyColors.DimGray;
s0[i].StrokeThickness = STROKE_THICKNESS_UNANNOTATED;
s0[i].Points.Add(new DataPoint(x[i], 0));
s0[i].Points.Add(new DataPoint(x[i], y[i]));
model.Series.Add(s0[i]);
}
//Draw the ms/ms scan matched peaks
for (int i = 0; i < matchedIonDic1.MatchedIonMz.Length; i++)
{
OxyColor ionColor = OxyColors.Red;
if (matchedIonDic1.MatchedIonMz[i] > 0)
{
s1[i] = new LineSeries();
s1[i].Color = ionColor;
s1[i].StrokeThickness = STROKE_THICKNESS_ANNOTATED;
s1[i].Points.Add(new DataPoint(matchedIonDic1.MatchedIonMz[i] + 1.007277, 0));
s1[i].Points.Add(new DataPoint(matchedIonDic1.MatchedIonMz[i] + 1.007277, matchedIonDic1.MatchedIonIntensity[i]));
var textAnno1 = new TextAnnotation();
//textAnno1.TextRotation=90;
textAnno1.FontSize = 12;
textAnno1.TextColor = ionColor;
textAnno1.StrokeThickness = 0;
textAnno1.TextPosition = s1[i].Points[1];
textAnno1.Text = matchedIonDic1.MatchedIonMz[i].ToString("f3");
var textAnno2 = new TextAnnotation();
//textAnno2.TextRotation=90;
textAnno2.FontSize = 12;
textAnno2.TextColor = ionColor;
textAnno2.StrokeThickness = 0;
textAnno2.TextPosition = new DataPoint(s1[i].Points[1].X, s1[i].Points[1].Y + y.Max() * 0.02);
textAnno2.Text = matchedIonDic1.MatchedIonName[i];
model.Annotations.Add(textAnno1);
model.Annotations.Add(textAnno2);
model.Series.Add(s1[i]);
}
}
for (int i = 0; i < matchedIonDic2.MatchedIonMz.Length; i++)
{
OxyColor ionColor = OxyColors.Blue;
if (matchedIonDic2.MatchedIonMz[i] > 0)
{
s2[i] = new LineSeries();
s2[i].Color = ionColor;
s2[i].StrokeThickness = STROKE_THICKNESS_ANNOTATED;
s2[i].Points.Add(new DataPoint(matchedIonDic2.MatchedIonMz[i] + 1.007277, 0));
s2[i].Points.Add(new DataPoint(matchedIonDic2.MatchedIonMz[i] + 1.007277, matchedIonDic2.MatchedIonIntensity[i]));
var textAnno1 = new TextAnnotation();
//textAnno1.TextRotation=90;
textAnno1.FontSize = 12;
textAnno1.TextColor = ionColor;
textAnno1.StrokeThickness = 0;
textAnno1.TextPosition = s2[i].Points[1];
textAnno1.Text = matchedIonDic2.MatchedIonMz[i].ToString("f3");
var textAnno2 = new TextAnnotation();
//textAnno2.TextRotation=90;
textAnno2.FontSize = 12;
textAnno2.TextColor = ionColor;
textAnno2.StrokeThickness = 0;
textAnno2.TextPosition = new DataPoint(s2[i].Points[1].X, s2[i].Points[1].Y + y.Max() * 0.02);
textAnno2.Text = matchedIonDic2.MatchedIonName[i];
model.Annotations.Add(textAnno1);
model.Annotations.Add(textAnno2);
model.Series.Add(s2[i]);
}
}
using (var stream = File.Create(OutputFolder + "\\" + order.ToString() + "_Scan" + scanNum + ".pdf"))
{
PdfExporter pdf = new PdfExporter {
Width = 500, Height = 210
};
pdf.Export(model, stream);
}
}
public static void XlTestLocalization()
{
var CommonParameters = new CommonParameters();
var proteinList = new List <Protein> {
new Protein("CASIQKFGERLCVLHEKTPVSEK", null)
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994);
var variableModifications = new List <ModificationWithMass>()
{
mod1
};
var fixedModifications = new List <ModificationWithMass>()
{
mod2
};
var localizeableModifications = new List <ModificationWithMass>();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var results = (IndexingResults)engine.Run();
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
foreach (var fdfd in digestedList)
{
fdfd.CompactPeptide(TerminusType.None);
//Assert.Contains(fdfd.CompactPeptide(TerminusType.None), results.PeptideIndex);
}
var productMasses = digestedList[3].CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
var x = PsmCross.XlPosCal(digestedList[3].CompactPeptide(TerminusType.None), crosslinker).ToArray();
Assert.AreEqual(x[0], 5);
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, CommonParameters.DoPrecursorDeconvolution, CommonParameters.UseProvidedPrecursorInfo, CommonParameters.DeconvolutionIntensityRatio, CommonParameters.DeconvolutionMaxAssumedChargeState, CommonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
var psmCrossAlpha = new PsmCross(digestedList[3].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]);
var psmCrossBeta = new PsmCross(digestedList[5].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]);
var modMassAlpha1 = psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass;
//Another method to calculate modification mass of cross-linked peptides
//var modMassAlpha2 = listOfSortedms2Scans[0].PrecursorMass - psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods;
var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker);
var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, modMassAlpha1, crosslinker, lp, true, false, linkPos);
Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 35);
Assert.AreEqual(productMassesAlphaList[0].ProductMz[26], 2312.21985342336);
}
public void UpdataModelForPdeep(PsmCross psmParentsForDraw)
{
var x = psmParentsForDraw.MatchedIonInfo.PredictedIonMZ;
var y = psmParentsForDraw.MatchedIonInfo.PredictedIonIntensity;
var xM = psmParentsForDraw.MatchedIonInfo.MatchedIonMz;
var yM = psmParentsForDraw.MatchedIonInfo.MatchedIonIntensity;
string scanNum = psmParentsForDraw.ScanNumber.ToString();
string sequence1 = psmParentsForDraw.FullSequence + "-" + psmParentsForDraw.XlPos.ToString();
PlotModel model = new PlotModel {
Title = "pDeep Spectrum anotation of Scan " + scanNum + " for Peptide", DefaultFontSize = 15
};
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Bottom, Title = "m/z", Minimum = 0, Maximum = x.Max() * 1.02
});
model.Axes.Add(new LinearAxis {
Position = AxisPosition.Left, Title = "Intensity(counts)", Minimum = -y.Max() * 1.2, Maximum = y.Max() * 1.2
});
var textAnnoSeq1 = new TextAnnotation()
{
};
textAnnoSeq1.FontSize = 12; textAnnoSeq1.TextColor = OxyColors.Red; textAnnoSeq1.StrokeThickness = 0; textAnnoSeq1.TextPosition = new DataPoint(x.Max() / 2, y.Max() * 1.15); textAnnoSeq1.Text = sequence1;
model.Annotations.Add(textAnnoSeq1);
LineSeries s0 = new LineSeries();
s0.Color = OxyColors.Black;
s0.StrokeThickness = 1;
s0.Points.Add(new DataPoint(0, 0));
s0.Points.Add(new DataPoint(x.Max(), 0));
model.Series.Add(s0);
LineSeries[] s1 = new LineSeries[x.Length];
for (int i = 0; i < x.Length; i++)
{
OxyColor ionColor = OxyColors.Red;
if (x[i] > 0)
{
s1[i] = new LineSeries();
s1[i].Color = ionColor;
s1[i].StrokeThickness = 0.75;
s1[i].Points.Add(new DataPoint(x[i] + 1.007277, 0));
s1[i].Points.Add(new DataPoint(x[i] + 1.007277, y[i]));
var textAnno1 = new TextAnnotation();
textAnno1.FontSize = 9;
textAnno1.TextColor = ionColor;
textAnno1.StrokeThickness = 0;
textAnno1.TextPosition = s1[i].Points[1];
textAnno1.Text = x[i].ToString("f3");
var textAnno2 = new TextAnnotation();
textAnno2.FontSize = 9;
textAnno2.TextColor = ionColor;
textAnno2.StrokeThickness = 0;
textAnno2.TextPosition = new DataPoint(s1[i].Points[1].X, s1[i].Points[1].Y + y.Max() * 0.02);
textAnno2.Text = psmParentsForDraw.MatchedIonInfo.PredictedIonName[i];
model.Annotations.Add(textAnno1);
model.Annotations.Add(textAnno2);
model.Series.Add(s1[i]);
}
}
//Matched fragment ions
LineSeries[] s2 = new LineSeries[xM.Length];
for (int i = 0; i < xM.Length; i++)
{
OxyColor ionColor = OxyColors.Blue;
if (xM[i] > 0)
{
s2[i] = new LineSeries();
s2[i].Color = ionColor;
s2[i].StrokeThickness = 0.75;
s2[i].Points.Add(new DataPoint(xM[i] + 1.007277, 0));
s2[i].Points.Add(new DataPoint(xM[i] + 1.007277, -yM[i] / yM.Max()));
var textAnno1 = new TextAnnotation();
textAnno1.FontSize = 9;
textAnno1.TextColor = ionColor;
textAnno1.StrokeThickness = 0;
textAnno1.TextPosition = s2[i].Points[1];
textAnno1.Text = xM[i].ToString("f3");
var textAnno2 = new TextAnnotation();
textAnno2.FontSize = 9;
textAnno2.TextColor = ionColor;
textAnno2.StrokeThickness = 0;
textAnno2.TextPosition = new DataPoint(s2[i].Points[1].X, s2[i].Points[1].Y - yM.Max() / yM.Max() * 0.02);
textAnno2.Text = psmParentsForDraw.MatchedIonInfo.PredictedIonName[i];
model.Annotations.Add(textAnno1);
model.Annotations.Add(textAnno2);
model.Series.Add(s2[i]);
}
}
// Axes are created automatically if they are not defined
// Set the Model property, the INotifyPropertyChanged event will make the WPF Plot control update its content
this.PdeepModel = model;
}
