public void GetIsoProfile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O() - Composition.Hydrogen;
//Console.WriteLine(neutral);
for (var charge = 22; charge <= 60; charge++)
{
var ion = new Ion(neutral, charge);
Console.WriteLine("{0}\t{1}", charge, ion.GetMostAbundantIsotopeMz());
}
var ion27 = new Ion(neutral, 29);
var isotopes = ion27.GetIsotopes(0.1);
foreach (var isotope in isotopes)
{
Console.WriteLine("{0}\t{1}", ion27.GetIsotopeMz(isotope.Index), isotope.Ratio);
}
}
/// <summary>
/// Calculate M/Z error of peaks in isotope envelope.
/// </summary>
/// <param name="peaks">The peaks to calculate error for.</param>
/// <param name="ion">The ion to calculate theoretical isotope envelope for.</param>
/// <param name="relativeIntensityThreshold">Relative intensity threshold for calculating isotopes</param>
/// <param name="deconvoluted"></param>
/// <returns>Array of ppm errors for each peak.</returns>
public static double?[] GetIsotopePpmError(Peak[] peaks, Ion ion, double relativeIntensityThreshold, bool deconvoluted = false)
{
double?[] ppmErrors;
if (!deconvoluted)
{
var isotopes = ion.GetIsotopes(relativeIntensityThreshold).ToArray();
ppmErrors = new double?[isotopes.Max(i => i.Index) + 1];
foreach (var isotope in isotopes)
{
var isotopeIndex = isotope.Index;
if (peaks[isotopeIndex] == null)
{
ppmErrors[isotopeIndex] = null;
}
else
{
ppmErrors[isotopeIndex] = GetPeakPpmError(peaks[isotopeIndex], ion.GetIsotopeMz(isotopeIndex));
}
}
}
else
{
var mz = ion.Composition.Mass;
ppmErrors = new double?[1];
ppmErrors[0] = GetPeakPpmError(peaks[0], mz);
}
return(ppmErrors);
}
public void TestIsoProfile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string sequence = "MWYMISAQDVENSLEKRLAARPAHLARLQELADEGRLLVAGPHPAIDSENPGDAGFSGSLVVADFDSLATAQAWADADPYFAAGVYQSVVVKPFKRVLP";
var aaSet = new AminoAcidSet();
var comp = aaSet.GetComposition(sequence) + Composition.H2O;
var ion = new Ion(comp, 9);
foreach (var i in ion.GetIsotopes(0.1))
{
Console.WriteLine(ion.GetIsotopeMz(i.Index) + "\t" + i.Ratio);
}
}
public void TestIsoProfile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
var composition = Composition.Parse("C(82) H(149) N(23) O(24) S(3)");
const int charge = 3;
var ion = new Ion(composition, charge);
foreach (var isotope in ion.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}\t{2}", isotope.Index, ion.GetIsotopeMz(isotope.Index), isotope.Ratio);
}
Console.WriteLine(composition.Mass);
}
public void TestXicGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
// Test
var tolerance = new Tolerance(30);
const string peptide = "AIANGQVDGFPTQEECR";
const int targetScanNum = 37633;
const int charge = 2;
//const string peptide = "IVDTNGAGDAFAGGFMAGLTK";
//const int targetScanNum = 67513;
//const int charge = 3;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
Console.WriteLine("Theoretical isotopomer profile:");
foreach (var p in precursorIon.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}", precursorIon.GetIsotopeMz(p.Index), p.Ratio);
}
var xicArr = new Dictionary <int, Xic>();
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
for (var i = -1; i < 3; i++)
{
xicArr[i] = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetIsotopeMz(i), tolerance, targetScanNum);
}
for (var i = -1; i < 3; i++)
{
Console.WriteLine("\nIndex: {0}", i);
Console.WriteLine("m/z: {0}", precursorIon.GetIsotopeMz(i));
Console.WriteLine("#XicPeaks: {0}", xicArr[i].Count);
Console.WriteLine("Intensity: {0}", xicArr[i].GetSumIntensities() / xicArr[basePeakIndex].GetSumIntensities());
Console.WriteLine("Correlation: {0}", xicArr[i].GetCorrelation(xicArr[basePeakIndex]));
}
}
public void TestPeptide()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
//const string sequence = "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
const string sequence = "IRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
//const string sequence = "MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG";
//const string sequence = "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK";
//const string sequence =
// "METTKPSFQDVLEFVRLFRRKNKLQREIQDVEKKIRDNQKRVLLLDNLSDYIKPGMSVEAIQGIIASMKGDYEDRVDDYIIKNAELSKERRDISKKLKAMGEMKNGEAK";
var aaSet = new AminoAcidSet();
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
Console.WriteLine(composition);
Console.WriteLine(composition.Mass);
Console.WriteLine(composition.NominalMass);
// 2nd isotope
Console.WriteLine(composition.GetIsotopeMass(0));
Console.WriteLine(composition.GetIsotopeMass(1));
Console.WriteLine(composition.GetIsotopeMass(2));
//Assert.AreEqual(composition.ToPlainString(), "C34H51N7O14");
Console.WriteLine("Isotopomer Envelope:");
foreach (var e in composition.GetIsotopomerEnvelopeRelativeIntensities())
{
Console.WriteLine(e);
}
Console.WriteLine();
Console.WriteLine("Isotope ions:");
var ion = new Ion(composition + Composition.H2O, 13);
foreach (var p in ion.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}", ion.GetIsotopeMz(p.Index), p.Ratio);
}
Console.WriteLine();
}
public void TestGetAllIsotopePeaks()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string specFilePath = @"H:\Research\GlycoTopDown\raw\User_sample_test_02252015.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
//const int scanNum = 17338;
const double relativeIntensity = 0.1;
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
var spec = run.GetSpectrum(17338);
var comp = Composition.Parse("C(610) H(945) N(172) O(189) S(3)");
var ion = new Ion(comp + BaseIonType.B.OffsetComposition, 9); // b127(9+)
Console.WriteLine("Composition: " + comp + " " + comp.Mass);
Console.WriteLine("b127(9+): " + ion.GetMonoIsotopicMz());
Console.WriteLine("b127(9+) 0th isotope: " + ion.GetIsotopeMz(0));
Console.WriteLine("b127(9+) 6th isotope: " + ion.GetIsotopeMz(6));
var peaks = spec.GetAllIsotopePeaks(ion, new Tolerance(10), relativeIntensity);
var isotopes = ion.GetIsotopes(relativeIntensity).ToArray();
for (var i = 0; i < isotopes.Length; i++)
{
if (peaks[i] == null)
{
continue;
}
var isotopeIndex = isotopes[i].Index;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", isotopeIndex, peaks[isotopeIndex].Mz, ion.GetIsotopeMz(isotopeIndex), GetPeakPpmError(peaks[isotopeIndex], ion.GetIsotopeMz(isotopeIndex)));
}
}
private bool IsValid(MsGfMatch match)
{
var specFileKey = Path.GetFileNameWithoutExtension(match.SpecFile);
if (specFileKey == null)
{
return(false);
}
var precursorIon = new Ion(match.Formula, match.Charge);
var prevMs1ScanNum = Run[specFileKey].GetPrecursorScanNum(match.ScanNum);
var nextMs1ScanNum = Run[specFileKey].GetNextScanNum(prevMs1ScanNum, 1);
//var isotopeMzs =
// precursorIon.GetIsotopes(NumIsotopesToCheckForValidation)
// .Select(isotope => precursorIon.GetIsotopeMz(isotope.Index)).ToArray();
var isotopes = precursorIon.GetIsotopes(NumIsotopesToCheckForValidation).ToArray();
Array.Sort(isotopes); // sort by indices
var prevMs1Spec = Run[specFileKey].GetSpectrum(prevMs1ScanNum);
if (prevMs1Spec != null)
{
//if (prevMs1Spec.ContainsIon(precursorIon, ToleranceForBaseXic, 0.9)) return true;
var isPrevIsotopeValid = false;
foreach (var isotope in isotopes)
{
var mz = precursorIon.GetIsotopeMz(isotope.Index);
if (prevMs1Spec.FindPeak(mz, ToleranceForBaseXic) != null) // match
{
if (isPrevIsotopeValid)
{
return(true);
}
isPrevIsotopeValid = true;
}
}
}
var nextMs1Spec = Run[specFileKey].GetSpectrum(nextMs1ScanNum);
if (nextMs1Spec != null)
{
var isPrevIsotopeValid = false;
foreach (var isotope in isotopes)
{
var mz = precursorIon.GetIsotopeMz(isotope.Index);
if (nextMs1Spec.FindPeak(mz, ToleranceForBaseXic) != null) // match
{
if (isPrevIsotopeValid)
{
return(true);
}
isPrevIsotopeValid = true;
}
}
}
return(false);
}
public void AnalyizeFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
//const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
const double fdrThreshold = 0.01;
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
Console.WriteLine("IsDecoy\tPeptide\tScanNum\tCharge\tSpecEValue\tQValue\tPrecursorMz" +
"\tTheo0\tTheo1\tTheo2\tTheo3" +
"\tObs0\tCorr0\tObs1\tCorr1\tObs2\tCorr2\tObs3\tCorr3\tObs-1\tCorr-1\tObs0.5\tCorr0.5");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var specEValue = Convert.ToDouble(token[12]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
Console.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", (isDecoy ? 1 : 0), peptide, scanNum, charge, specEValue, qValue, precursorIon.GetMonoIsotopicMz());
var isotopeIndices = new double[] { 0, 1, 2, 3, -1, 0.5 };
var theoIsotopes = precursorIon.GetIsotopes(0.01);
var numIsotopes = 0;
foreach (var theoIsotope in theoIsotopes)
{
Console.Write("\t" + theoIsotope.Ratio);
if (++numIsotopes == 4)
{
break;
}
}
foreach (var isotopeIndex in isotopeIndices)
{
var isotopeMz = precursorIon.GetIsotopeMz(isotopeIndex);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
var relativeIntensity = xic.GetSumIntensities() / baseIntensity;
var correlation = xic.GetCorrelation(baseXic);
Console.Write("\t{0}\t{1}", relativeIntensity, correlation);
}
Console.WriteLine();
}
}
public void TestFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
//const double isotopeRatioTolerance = 2;
//const double correlationThreshold = 0.3;
const double fdrThreshold = 0.01;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\oldResult\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
var numTargets = 0;
var numValidTargets = 0;
var numDecoys = 0;
var numValidDecoys = 0;
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
if (isDecoy)
{
numDecoys++;
}
else
{
numTargets++;
}
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
var isValid = true;
foreach (var isotope in precursorIon.GetIsotopes(relativeIntensityThreshold))
{
if (isotope.Index == basePeakIndex)
{
continue;
}
var isotopeMz = precursorIon.GetIsotopeMz(isotope.Index);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
if (xic.Count == 0)
{
isValid = false;
break;
}
//if (xic.Count > 0)
//{
// var isotopeRatio = xic.GetSumIntensities() / baseIntensity / isotope.Item2;
// var correlation = xic.GetCorrelation(baseXic);
// if (isotopeRatio > 0.8 && isotopeRatio < 1.2
// && correlation > 0.8)
// {
// isValid = true;
// }
//}
// Check if isotope ratio is within tolerance
//if (isotopeRatio > isotopeRatioTolerance || isotopeRatio < 1 / isotopeRatioTolerance)
//{
// isValid = false;
// //Console.WriteLine("Off ratio\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, isotopeRatio);
// break;
//}
// Check if correlation is high
//if (correlation < correlationThreshold)
//{
// isValid = false;
// //Console.WriteLine("Low correlation\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, correlation);
// break;
//}
}
if (isValid && !isDecoy)
{
numValidTargets++;
}
else if (isValid)
{
numValidDecoys++;
}
//Console.WriteLine("{0}\t{1}\t{2}", peptide, scanNum, charge);
}
Console.WriteLine("#Targets: {0}", numTargets);
Console.WriteLine("#ValidTargets: {0}\t{1}", numValidTargets, numValidTargets / (double)numTargets);
Console.WriteLine("#Decoys: {0}", numDecoys);
Console.WriteLine("#ValidDecoys: {0}\t{1}", numValidDecoys, numValidDecoys / (double)numDecoys);
sw.Stop();
Console.WriteLine(@"TimeForPrecursorValidation {0:f4} sec", sw.Elapsed.TotalSeconds);
}