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 precursor mass-to-charge ratio of sequence.
/// </summary>
/// <param name="sequence">Sequence to calculate mass from.</param>
/// <param name="charge">Charge state.</param>
/// <returns>Mass-to-charge ratio of precursor ion for the sequence.</returns>
public static double GetPrecursorMz(Sequence sequence, int charge)
{
if (sequence.Count == 0)
{
return(0.0);
}
var composition = sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var ion = new Ion(composition + Composition.H2O, charge);
return(Math.Round(ion.GetMostAbundantIsotopeMz(), 2));
}
public void TestMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(15);
var productIonTolerance = new Tolerance(15);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\protoapps\UserData\Jungkap\Joshua\testData\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 6;
const int modIndex = 0;
const int ms2ScanNum = 4448;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestCorrMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(10);
var productIonTolerance = new Tolerance(10);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASAKHEDMYTAINELINKLERQLNKVQHKGEAR._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 9;
const int modIndex = 0;
const int ms2ScanNum = 3633;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
//var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var scorer = new CorrMatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void GeneratePrmInfo(string resultFilePath, string outputFilePath)
{
Console.Write("Processing {0}", Path.GetFileName(resultFilePath));
Console.Out.Flush();
var rawFilePath =
@"D:\Research\Data\EDRN\DDA\raw\" + Path.GetFileNameWithoutExtension(resultFilePath) + ".raw";
var reader = new XCaliburReader(rawFilePath);
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath);
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
const string spikedInPeptideFile = @"D:\Research\Data\EDRN\SpikedPeptides.txt";
var spikedInPeptides = File.ReadAllLines(spikedInPeptideFile);
var spikedInPepSet = new HashSet <string>();
foreach (var p in spikedInPeptides)
{
spikedInPepSet.Add(p);
}
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Frac7_NTT2.tsv";
//const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Heavy\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\NTT1_NoMod\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
const double qValueThreshold = 0.01;
var pepSet = new HashSet <string>();
MsGfPlusHeaderInformation headerInfo = null;
//var prefix = new HashSet<string>();
//var suffix = new HashSet<string>();
var numPeptides = 0;
var prevScanNum = -1;
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Peptide\tCharge\tMonoMz\tMostAbundantMz\tMs2ScanNum\tRtMs2\tRtApex\tRtStart\tRtEnd\tSpecEValue\tPepQValue");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
headerInfo = new MsGfPlusHeaderInformation(line);
continue;
}
var match = new MsGfMatch(line, headerInfo);
if (match.ScanNum == prevScanNum)
{
continue;
}
prevScanNum = match.ScanNum;
if (!match.IsValid || match.Protein.StartsWith(FastaDatabase.DecoyProteinPrefix))
{
continue;
}
if (match.PepQValue > qValueThreshold)
{
continue;
}
var peptide = match.Peptide.Replace("C+57.021", "C").Replace("K+8.014", "K").Replace("R+10.008", "R");
if (pepSet.Contains(peptide))
{
continue;
}
pepSet.Add(peptide);
if (spikedInPepSet.Contains(peptide))
{
var ion = new Ion(match.Formula, match.Charge);
var mostAbundantIonMz = ion.GetMostAbundantIsotopeMz();
var xic = run.GetPrecursorExtractedIonChromatogram(mostAbundantIonMz, tolerance, match.ScanNum);
if (xic.Count == 0)
{
continue;
}
var minScan = xic.Min().ScanNum;
var maxScan = xic.Max().ScanNum;
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}",
peptide,
match.Charge,
ion.GetMonoIsotopicMz(),
mostAbundantIonMz,
match.ScanNum,
reader.RtFromScanNum(match.ScanNum),
reader.RtFromScanNum(xic.GetApexScanNum()), // Rt apex
reader.RtFromScanNum(minScan), // Rt start
reader.RtFromScanNum(maxScan), // Rt end
match.SpecEValue,
match.PepQValue);
++numPeptides;
}
//else
//{
// foreach (var spikedInPeptide in spikedInPeptides)
// {
// if (spikedInPeptide.StartsWith(peptide)) prefix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// else if (spikedInPeptide.EndsWith(peptide)) suffix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// }
//}
}
}
//Console.WriteLine("*********Prefix");
//foreach(var p in prefix) Console.WriteLine(p);
//Console.WriteLine("*********Suffix");
//foreach (var p in suffix) Console.WriteLine(p);
Console.WriteLine("\t{0}", numPeptides);
}
public void TestMs1Filtering()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string resultFilePath =
// @"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.tsv";
@"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.decoy.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
//const int minPrecursorCharge = 3;
//const int maxPrecursorCharge = 30;
//const int tolerancePpm = 15;
var tolerance = new Tolerance(15);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 0.7, 40);
////var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//ISequenceFilter ms1Filter = ms1BasedFilter;
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var qValues = tsvReader.GetData("QValue");
var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Annotation");
//var hist = new int[11];
Console.WriteLine("ScanNum\tScore\tPrecursor\tNext\tSum\tNextIsotope\tLessCharge\tMoreCharge\tMax\tNumXicPeaks");
for (var i = 0; i < compositions.Count; i++)
{
if (qValues != null)
{
var qValue = Convert.ToDouble(qValues[i]);
if (qValue > 0.01)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var composition = Composition.Parse(compositions[i]);
var charge = Convert.ToInt32(charges[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
var score = Convert.ToDouble(scores[i]);
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var preIsotopeCorr = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var nextIsotopeCorr = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var xicMostAbundant = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var apexScanNum = xicMostAbundant.GetApexScanNum();
if (apexScanNum < run.MinLcScan)
{
apexScanNum = scanNum;
}
//var sumSpec = run.GetSummedMs1Spectrum(apexScanNum);
// var apexIsotopeCorr = sumSpec.GetCorrScore(precursorIon, tolerance, 0.1);
// var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
var xicNextIsotope = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz() + Constants.C13MinusC12 / charge, tolerance, scanNum);
var plusOneIsotopeCorr = xicMostAbundant.GetCorrelation(xicNextIsotope);
var precursorIonChargeMinusOne = new Ion(composition, charge - 1);
var xicChargeMinusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargeMinusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargeMinusOneCorr = xicMostAbundant.GetCorrelation(xicChargeMinusOne);
var precursorIonChargePlusOne = new Ion(composition, charge + 1);
var xicChargePlusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargePlusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargePlusOneCorr = xicMostAbundant.GetCorrelation(xicChargePlusOne);
//var max = new[] {preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr}.Max();
//Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}",
// scanNum, score, preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr, max, xicMostAbundant.Count);
}
//Console.WriteLine("Histogram");
//for (var i = 0; i < hist.Length; i++)
//{
// Console.WriteLine("{0:f1}\t{1}", i / 10.0, hist[i]);
//}
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
//var ms1BasedFilter = new Ms1BasedFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm);
//
//var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//var ms1BasedFilter = new ProductScorerBasedOnDeconvolutedSpectra(run,
// minPrecursorCharge, maxPrecursorCharge,
// 0, 0,
// 600.0, 1800.0, new Tolerance(tolerancePpm), null);
//ms1BasedFilter.CachePrecursorMatchesBinCentric();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.5, 0.5, 0.5, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon_4PTMs.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("Score");
var qvalues = tsvReader.GetData("QValue");
var sequences = tsvReader.GetData("Sequence");
var sequenceCount = new Dictionary <string, int>();
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01)
{
continue;
}
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
var sequence = sequences[i];
if (sequenceCount.TryGetValue(sequence, out var count))
{
sequenceCount[sequence] = count + 1;
}
else
{
sequenceCount[sequence] = 1;
}
}
//var sequences = tsvReader.GetData("Annotation");
var seqSet = new HashSet <string>();
var allSeqSet = new HashSet <string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01)
{
continue;
}
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
//var xic = run.GetFullPrecursorIonExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance);
////xic.Display();
//var apexScanNum = xic.GetNearestApexScanNum(run.GetPrecursorScanNum(scanNum), false);
//var apexSpec = run.GetSpectrum(apexScanNum);
//var corr3 = apexSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax, sequenceCount[sequences[i]]);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.7, 0.7, 0.7, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
//const string prot =
// "ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLLA";
//var protMass = (new AminoAcidSet().GetComposition(prot) + Composition.H2O).Mass;
//Console.WriteLine("************ScanNums: " + string.Join("\t", ms1Filter.GetMatchingMs2ScanNums(protMass)));
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\MSAlign\NoMod.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var scanNums = tsvReader.GetData("Scan(s)");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("E-value");
var sequences = tsvReader.GetData("Peptide");
//const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_N30_C30.tsv";
//var tsvReader = new TsvFileParser(resultFilePath);
//var scanNums = tsvReader.GetData("ScanNum");
//var charges = tsvReader.GetData("Charge");
//var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Sequence");
var aaSet = new AminoAcidSet();
var seqSet = new HashSet <string>();
var allSeqSet = new HashSet <string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < scores.Count; i++)
{
var score = Convert.ToDouble(scores[i]);
if (score > 1E-4)
{
continue;
}
//if (score < 10) continue;
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var sequence = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (sequence == null || sequence.Contains("("))
{
continue;
}
//var sequence = sequences[i];
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void Test43KProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Configure amino acid set
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false);
var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C',
SequenceLocation.ProteinNTerm, false);
var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false);
var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false);
var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false);
var nitrosylC = new SearchModification(Modification.Nitrosyl, 'C', SequenceLocation.Everywhere, false);
var nethylmaleimideC = new SearchModification(Modification.Nethylmaleimide, 'C', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
glutathioneC,
oxM,
dethiomethylM,
acetylN,
//phosphoS,
//phosphoT,
//phosphoY,
deamidatedN,
// deamidatedQ,
glutathioneC,
pyroCarbamidomethylC,
nitrosylC,
nethylmaleimideC
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
// var aaSet = new AminoAcidSet();
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(aaSet, AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
var ms1Filter = new SimpleMs1Filter();
var ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(run);
foreach (var ms2ScanNum in Ms2ScanNums)
{
ms2ScorerFactory.GetScorer(ms2ScanNum);
}
for (var numNTermCleavages = 0; numNTermCleavages <= 0; numNTermCleavages++)
{
if (numNTermCleavages > 0)
{
seqGraph.CleaveNTerm();
}
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
var modCombinations = modCombs[modIndex];
foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass))
{
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
continue;
}
var charge =
(int)
Math.Round(sequenceMass /
(spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var scorer = ms2ScorerFactory.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
if (score <= 3)
{
continue;
}
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = protSequence.Substring(numNTermCleavages);
var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1];
var post = annotation[annotation.Length - 1];
Console.WriteLine("{0}.{1}.{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", pre, sequence, post, ms2ScanNum, modCombinations,
precursorIon.GetMostAbundantIsotopeMz(), precursorIon.Charge, precursorIon.Composition.Mass, score);
}
}
}
}
/// <summary>
/// Gets scan numbers of the fragmentation spectra whose isolation window contains the precursor ion specified
/// </summary>
/// <param name="precursorIon"></param>
/// <returns>scan numbers of fragmentation spectra</returns>
public int[] GetFragmentationSpectraScanNums(Ion precursorIon)
{
var mostAbundantIsotopeMz = precursorIon.GetMostAbundantIsotopeMz();
return(GetFragmentationSpectraScanNums(mostAbundantIsotopeMz));
}
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);
}