// Feature, precursorScore, totalScore
public Tuple<Feature, double, double> GetBestFeatureAndScore(int precursorCharge)
{
var precursorIon = new Ion(_sequenceComposition + Composition.H2O, precursorCharge);
var imsScorer = _imsScorerFactory.GetImsScorer(_imsData, precursorIon);
var precursorFeatureSet = _imsData.GetPrecursorFeatures(precursorIon.GetMz());
var bestPrecursorScore = double.NegativeInfinity;
var bestScore = double.NegativeInfinity;
Feature bestFeature = null;
foreach (var precursorFeature in precursorFeatureSet)
{
var precursorScore = imsScorer.GetPrecursorScore(precursorFeature);
if (precursorScore < PrecursorScoreThreshold) continue;
var productScore = GetProductIonScore(imsScorer, precursorFeature);
var curFeatureScore = precursorScore + productScore;
if (curFeatureScore > bestScore)
{
bestPrecursorScore = precursorScore;
bestScore = curFeatureScore;
bestFeature = precursorFeature;
}
}
return new Tuple<Feature, double, double>(bestFeature, bestPrecursorScore, bestScore);
}
public void TestGetAllIsotopePeaks()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 IsValidForMs1Scan(Ion precursorIon, int scanNum)
{
if (scanNum < Run.MinLcScan || scanNum > Run.MaxLcScan) return false;
if (Run.GetMsLevel(scanNum) != 1) return true;
var spec = Run.GetSpectrum(scanNum);
return spec != null && spec.ContainsIon(precursorIon, MzTolerance, RelativeIsotopeIntensityThreshold);
}
public override double GetFragmentScore(Composition prefixFragmentComposition, Composition suffixFragmentComposition)
{
var score = 0.0;
foreach (var baseIonType in BaseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? prefixFragmentComposition + baseIonType.OffsetComposition
: suffixFragmentComposition + baseIonType.OffsetComposition;
if (fragmentComposition.Mass < Ms2Spectrum.Peaks[0].Mz) continue;
var chargeRange = GetMinMaxChargeRange(fragmentComposition);
var containsIon = false;
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
if (Ms2Spectrum.ContainsIon(ion, Tolerance, RelativeIsotopeIntensityThreshold))
{
containsIon = true;
break;
}
}
if (containsIon) score += 1.0;
}
return score;
}
public GroupParameter(Composition cutComposition, char nTermAA, char cTermAA, Ion precursorIon)
{
MassIndex = GetMassIndex(precursorIon.Composition);
Charge = Math.Max(MinCharge, Math.Min(precursorIon.Charge, MaxCharge));
LocationIndex = GetLocationIndex(precursorIon.Composition, cutComposition);
FlankingResidueIndex = GetFlankingResidueIndex(nTermAA, cTermAA);
}
public double GetFragmentScore(Composition prefixFragmentComposition, Composition suffixFragmentComposition)
{
var score = 0.0;
foreach (var baseIonType in _baseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? prefixFragmentComposition + baseIonType.OffsetComposition
: suffixFragmentComposition + baseIonType.OffsetComposition;
fragmentComposition.ComputeApproximateIsotopomerEnvelop();
var isotopomerEnvelope = fragmentComposition.GetIsotopomerEnvelop();
//var bestFitScore = 1.0;
var bestCosineScore = 0.0;
var bestObsIntensity = -1.0;
for (var charge = _minCharge; charge <= _maxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var cosineScore = _ms2Spec.GetConsineScore(ion, _tolerance, RelativeIntensityThreshold);
if (cosineScore > bestCosineScore) bestCosineScore = cosineScore;
//var observedPeaks = _ms2Spec.GetAllIsotopePeaks(ion, _tolerance, RelativeIntensityThreshold);
//if (observedPeaks == null) continue;
//var theoIntensities = new float[observedPeaks.Length];
//var observedIntensities = new float[observedPeaks.Length];
//var maxObservedIntensity = float.NegativeInfinity;
//for (var i = 0; i < observedPeaks.Length; i++)
//{
// theoIntensities[i] = isotopomerEnvelope[i];
// if (observedPeaks[i] != null)
// {
// var observedIntensity = (float)observedPeaks[i].Intensity;
// observedIntensities[i] = observedIntensity;
// if (observedIntensity > maxObservedIntensity) maxObservedIntensity = observedIntensity;
// }
// else
// {
// observedIntensities[i] = 0;
// }
//}
//for (var i = 0; i < observedPeaks.Length; i++)
//{
// observedIntensities[i] /= maxObservedIntensity;
//}
//var fitScore = FitScoreCalculator.GetFitOfNormalizedVectors(isotopomerEnvelope, observedIntensities);
//if (fitScore < bestFitScore)
//{
// bestFitScore = fitScore;
// bestObsIntensity = maxObservedIntensity;
//}
}
//score += GetScore(baseIonType, bestFitScore, bestObsIntensity);
score += GetScore(baseIonType, bestCosineScore, bestObsIntensity);
}
return score;
}
public void AddMostAbundantIsotopePeakIntensity()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string resultFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143_IcTda.tsv";
var parser = new TsvFileParser(resultFilePath);
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var scanNums = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var precursorIntensities = new double[parser.NumData];
var tolerance = new Tolerance(10);
for (var i = 0; i < parser.NumData; i++)
{
var scanNum = scanNums[i];
var composition = compositions[i];
var charge = charges[i];
var precursorIon = new Ion(composition, charge);
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var isotopePeaks = precursorSpec.GetAllIsotopePeaks(precursorIon, tolerance, 0.1);
if (isotopePeaks != null)
{
var maxIntensity = 0.0;
for (var j = 0; j < isotopePeaks.Length; j++)
{
if (isotopePeaks[j] != null && isotopePeaks[j].Intensity > maxIntensity)
maxIntensity = isotopePeaks[j].Intensity;
}
precursorIntensities[i] = maxIntensity;
}
}
// Writing
const string newResultFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143_IcTdaWithIntensities.tsv";
using (var writer = new StreamWriter(newResultFilePath))
{
writer.WriteLine(string.Join("\t", parser.GetHeaders())+"\t"+"PrecursorIntensity");
for (var i = 0; i < parser.NumData; i++)
{
writer.WriteLine(parser.GetRows()[i]+"\t"+precursorIntensities[i]);
}
}
Console.WriteLine("Done");
}
public const double RelativeIsotopeIntensityThreshold = 0.8; // 0.5
public bool IsValid(Ion precursorIon, int scanNum)
{
if (Run.GetMsLevel(scanNum) != 2) return false;
var precursorScanNum = Run.GetPrecursorScanNum(scanNum);
var nextMs1ScanNum = Run.GetNextScanNum(scanNum);
var isValid =
IsValidForMs1Scan(precursorIon, precursorScanNum)
|| IsValidForMs1Scan(precursorIon, nextMs1ScanNum);
return isValid;
}
public const double RelativeIsotopeIntensityThreshold = 0.8; // 0.5
public bool IsValid(Ion precursorIon, int scanNum)
{
if (Run.GetMsLevel(scanNum) != 2) return false;
var precursorScanNum = Run.GetPrecursorScanNum(scanNum);
var nextMs1ScanNum = Run.GetNextScanNum(scanNum);
var isValid =
IsValidForMs1Scan(precursorIon, precursorScanNum)
|| IsValidForMs1Scan(precursorIon, nextMs1ScanNum);
//Console.WriteLine("{0}\t{1}\t{2}\t{3}", precursorIon.GetMonoIsotopicMz(), precursorIon.precursorCharge, scanNum, isValid);
return isValid;
}
public void OutputStatistics(ProductSpectrum spectrum, Sequence sequence)
{
var baseIonTypes = spectrum.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCid : BaseIonTypesEtd;
var cleavages = sequence.GetInternalCleavages().ToArray();
var tolerance = new Tolerance(10);
var maxIntensity = spectrum.Peaks.Max(p => p.Intensity);
foreach (var c in cleavages)
{
foreach (var baseIonType in baseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = spectrum.GetAllIsotopePeaks(ion, tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null) continue;
var mostAbundantIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
// representative peak intensity
var ionPeakIntensity = observedPeaks[mostAbundantIsotopeIndex].Intensity;
// calc. correlation
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
var corrCoeff = FitScoreCalculator.GetPearsonCorrelation(isotopomerEnvelope, observedIntensities);
// mz error
var mostAbundantIsotopeMz = ion.GetIsotopeMz(mostAbundantIsotopeIndex);
var errorPpm = ((observedPeaks[mostAbundantIsotopeIndex].Mz - mostAbundantIsotopeMz)/
mostAbundantIsotopeMz)*1e6;
}
}
}
}
public void TestFitScoreCalculationCid()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestLcMsRun.TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestLcMsRun.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestLcMsRun.TestTopDownRawFilePathCid, 5743, 5743);
var spec = run.GetSpectrum(5743);
Assert.True(spec != null);
const string protein = "MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG";
var protComp = new AminoAcidSet().GetComposition(protein) + Composition.H2O;
Assert.True(protComp != null);
Assert.True(protComp.C == 1035);
Assert.True(protComp.H == 1683);
Assert.True(protComp.N == 289);
Assert.True(protComp.O == 318);
Assert.True(protComp.P == 0);
Assert.True(protComp.S == 7);
Assert.True(Math.Abs(protComp.Mass - 23473.245267145) < 0.0000001);
Assert.True(protComp.NominalMass == 23461);
var ion = new Ion(protComp, 20);
// ion.Composition.ComputeApproximateIsotopomerEnvelop();
var isotopomerEnvelop = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine(@"MonoMz: {0}, MonoMass: {1}", ion.GetMonoIsotopicMz(), ion.Composition.Mass);
var matchedPeaks = spec.GetAllIsotopePeaks(ion, new Tolerance(15), 0.1);
for (var i = 0; i < matchedPeaks.Length; i++)
{
Console.WriteLine(@"{0} {1} {2} {3}", i, ion.GetIsotopeMz(i), isotopomerEnvelop[i], matchedPeaks[i] == null ? 0 : matchedPeaks[i].Intensity);
}
var fitScore = spec.GetFitScore(ion, new Tolerance(15), 0.1);
var cosine = spec.GetConsineScore(ion, new Tolerance(15), 0.1);
var corr = spec.GetCorrScore(ion, new Tolerance(15), 0.1);
Console.WriteLine(@"FitScore: {0}", fitScore);
Console.WriteLine(@"Cosine: {0}", cosine);
Console.WriteLine(@"Corr: {0}", corr);
Assert.True(Math.Abs(fitScore - 0.181194589537041) < 0.0001);
Assert.True(Math.Abs(cosine - 0.917609346566222) < 0.0001);
Assert.True(Math.Abs(corr - 0.808326778009839) < 0.0001);
}
/// <summary>
/// Find intensity rank of ion in spectrum.
/// </summary>
/// <param name="ion">Ion to search for.</param>
/// <param name="tolerance"></param>
/// <returns>Intensity rank of ion. 1-based.</returns>
public int RankIon(Ion ion, Tolerance tolerance)
{
var peak = _spectrum.FindPeak(ion.GetMonoIsotopicMz(), tolerance);
int position;
if (peak != null)
{
var searchPeak = new Peak(peak.Mz, peak.Intensity);
position = Array.BinarySearch(Peaks, searchPeak, new IntensityComparer());
position++;
}
else
{
position = -1;
}
return position;
}
protected IEnumerable<DeconvolutedPeak> FindMatchedPeaks(Composition.Composition fragmentComposition,
double corrThreshold, double distThreshold)
{
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
//var matchedPeak = new MatchedFragmentPeak();
//var deconvPeak = new DeconvolutedPeak()
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz) yield break;
var prevObservedCharge = 0;
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1) yield break;
continue;
}
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1) yield break;
continue;
}
var matchedPeak = new DeconvolutedPeak(fragmentIonMass, observedPeaks[mostAbundantIsotopeIndex].Intensity, charge, distCorr.Item2, distCorr.Item1, observedPeaks);
prevObservedCharge = charge;
yield return matchedPeak;
}
}
internal ScoringGraph(AminoAcid[] aminoAcidSequence, Composition sequenceComposition, ScoringGraphNode rootNode,
int minPrecursorCharge, int maxPrecursorCharge)
{
_aminoAcidSequence = aminoAcidSequence;
_sequenceComposition = sequenceComposition;
_rootNode = rootNode;
_minPrecursorCharge = minPrecursorCharge;
_maxPrecursorCharge = maxPrecursorCharge;
_precursorIon = new Dictionary<int, Ion>();
for (var precursorCharge = _minPrecursorCharge; precursorCharge <= _maxPrecursorCharge; precursorCharge++)
{
_precursorIon[precursorCharge] = new Ion(_sequenceComposition, precursorCharge);
}
// store all nodes in an array
var nodes = new HashSet<ScoringGraphNode>();
var curNodes = new HashSet<ScoringGraphNode> { _rootNode };
while (curNodes.Any())
{
var newNodes = new HashSet<ScoringGraphNode>();
foreach (var node in curNodes)
{
if (nodes.Add(node)) // if node is new
{
foreach (var nextNode in node.GetNextNodes())
{
newNodes.Add(nextNode);
}
}
}
curNodes = newNodes;
}
_nodes = nodes.ToArray();
}
public void ScorePeptides(string outputFilePath)
{
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Annotation\tCharge\tScanNum");
foreach (var annotation in PeptideEnumerator)
{
// annotation: pre + "." + peptide + "." + post (e.g. R.PEPTIDER.G)
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
foreach (var sequenceComposition in seqGraph.GetSequenceCompositions())
{
var peptideComposition = sequenceComposition + Composition.H2O;
for (var precursorCharge = MinCharge; precursorCharge <= MaxCharge; precursorCharge++)
{
var precursorIon = new Ion(peptideComposition, precursorCharge);
foreach (var scanNum in Run.GetFragmentationSpectraScanNums(precursorIon))
{
writer.WriteLine("{0}\t{1}\t{2}", annotation, precursorCharge, scanNum);
}
}
}
}
}
}
public static Tuple<double, double> GetDistCorr(Ion ion, Peak[] observedPeaks)
{
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var envelope = isotopomerEnvelope;
var observedIntensities = new double[envelope.Length];
for (var i = 0; i < isotopomerEnvelope.Length; i++)
{
if (observedPeaks[i] != null) observedIntensities[i] = observedPeaks[i].Intensity;
}
return FitScoreCalculator.GetDistanceAndCorrelation(envelope, observedIntensities);
//var bcDist = FitScoreCalculator.GetBhattacharyyaDistance(envelope, observedIntensities);
//var corr = FitScoreCalculator.GetPearsonCorrelation(envelope, observedIntensities);
//return new Tuple<double, double>(bcDist, corr);
}
/*
protected Peak[] FindMostAbundantPeak(Composition.Composition fragmentComposition,
double corrThreshold, double distThreshold,
out int observedCharge, out double envelopeCorr, out double envelopeDist)
{
//Peak[] intenseObservedPeaks = null;
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
observedCharge = 0;
envelopeCorr = 0d;
envelopeDist = 1.0d;
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz) return null;
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null) continue;
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold) continue;
//var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
//if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
//{
//intenseObservedPeaks = observedPeaks;
observedCharge = charge;
envelopeDist = distCorr.Item1;
envelopeCorr = distCorr.Item2;
return observedPeaks;
//}
}
return null;
}
*/
protected Peak[] FindMostIntensePeak(Composition.Composition fragmentComposition, double corrThreshold, double distThreshold, out int observedCharge, out double envelopeCorr, out double envelopeDist)
{
Peak[] intenseObservedPeaks = null;
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
observedCharge = 0;
envelopeCorr = 0d;
envelopeDist = 1.0d;
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz) return null;
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null) continue;
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold) continue;
var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
{
intenseObservedPeaks = observedPeaks;
observedCharge = charge;
envelopeDist = distCorr.Item1;
envelopeCorr = distCorr.Item2;
}
}
return intenseObservedPeaks;
}
private SortedSet<DatabaseSequenceSpectrumMatch>[] RunSearch(IEnumerable<AnnotationAndOffset> annotationsAndOffsets, ISequenceFilter ms1Filter, bool isDecoy)
{
var sw = new Stopwatch();
var numPeptides = 0;
sw.Reset();
sw.Start();
var matches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
// TODO: N-term Met cleavage
foreach (var annotationAndOffset in annotationsAndOffsets)
{
++numPeptides;
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
if (numPeptides % 100000 == 0)
{
Console.Write(@"Processing {0}{1} peptides...", numPeptides,
numPeptides == 1 ? "st" : numPeptides == 2 ? "nd" : numPeptides == 3 ? "rd" : "th");
if (numPeptides != 0)
{
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
sw.Start();
}
}
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
if (seqGraph == null)
{
// Console.WriteLine("Ignoring illegal protein: {0}", annotation);
continue;
}
//var protCompositions = seqGraph.GetSequenceCompositions();
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 <= 2) continue;
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = annotation.Substring(2, annotation.Length - 4);
var pre = annotation[0];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, 0, modCombinations,
precursorIon, score, isDecoy);
if (matches[ms2ScanNum] == null)
{
matches[ms2ScanNum] = new SortedSet<DatabaseSequenceSpectrumMatch> { prsm };
}
else // already exists
{
var existingMatches = matches[ms2ScanNum];
if (existingMatches.Count < NumMatchesPerSpectrum) existingMatches.Add(prsm);
else
{
var minScore = existingMatches.Min.Score;
if (score > minScore)
{
existingMatches.Add(prsm);
existingMatches.Remove(existingMatches.Min);
}
}
}
}
}
}
return matches;
}
public Tuple<int, int, int, int, string, string> GetLongestSequence(ProductSpectrum spectrum, Sequence sequence)
{
_spectrum = spectrum;
_sequence = sequence;
_baseIonTypes = _spectrum.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCid : BaseIonTypesEtd;
var cleavages = _sequence.GetInternalCleavages().ToArray();
var prefixValueArr = new int[cleavages.Length];
var suffixValueArr = new int[cleavages.Length];
var prefixPeakArr = new Peak[cleavages.Length];
var suffixPeakArr = new Peak[cleavages.Length];
//var peakList = new double[_spectrum.Peaks.Length];
int cleavageIndex = 0;
/*
for (int i = 0; i < peakList.Length; i++)
{
peakList[i] = _spectrum.Peaks[i].Intensity;
}*/
//var rankings = ArrayUtil.GetRankings(peakList);
foreach (var c in cleavages)
{
foreach (var baseIonType in _baseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
for (var charge = _minCharge; charge <= _maxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
if (_spectrum.GetCorrScore(ion, _tolerance, RelativeIsotopeIntensityThreshold) < .7) continue;
if (baseIonType.IsPrefix) prefixValueArr[cleavageIndex] = 1;
else suffixValueArr[cleavageIndex] = 1;
}
}
cleavageIndex++;
}
var prefixSequenceArr = new int[_sequence.Count];
var suffixSequenceArr = new int[_sequence.Count];
prefixSequenceArr[0] = prefixValueArr[0];
suffixSequenceArr[suffixSequenceArr.Length - 1] = suffixValueArr[suffixValueArr.Length - 1];
for (int i = 1; i < prefixValueArr.Length; i++)
{
if (prefixValueArr[i] == 1 && prefixValueArr[i - 1] == 1)
{
if (_sequence[i] is ModifiedAminoAcid) continue;
prefixSequenceArr[i] = 1;
}
}
for (int i = suffixValueArr.Length - 2; i >= 0; i--)
{
if (suffixValueArr[i] == 1 && suffixValueArr[i + 1] == 1)
{
if (_sequence[i + 1] is ModifiedAminoAcid) continue;
suffixSequenceArr[i + 1] = 1;
}
}
var prefixSubString = FindLongestSubstring(prefixSequenceArr);
var prefixStartIndex = -1;
var prefixEndIndex = -1;
//var prefixSequencePeaks = new List<Peak>();
//var prefixPval = -1.0;
var prefixSequence = "";
if (prefixSubString != "")
{
var prefixIndex = string.Concat(prefixSequenceArr);
prefixStartIndex = prefixIndex.IndexOf(prefixSubString) + 1;
prefixEndIndex = (prefixStartIndex == 1) ? 1 : prefixStartIndex + prefixSubString.Length - 1;
//prefixSequencePeaks = GetPrefixSequencePeaks(prefixPeakArr, prefixStartIndex, prefixEndIndex);
//var prefixRankSum = GetSequenceRankSum(prefixSequencePeaks, rankings, peakList);
//prefixPval = FitScoreCalculator.GetRankSumPvalue(peakList.Length, prefixSequencePeaks.Count, prefixRankSum);
prefixSequence = GetStringSubSequence(_sequence, prefixStartIndex, prefixEndIndex);
}
var suffixSubString = FindLongestSubstring(suffixSequenceArr);
var suffixStartIndex = -1;
var suffixEndIndex = -1;
//var suffixSequencePeaks = new List<Peak>();
//var suffixPval = -1.0;
var suffixSequence = "";
if (suffixSubString != "")
{
var suffixIndex = string.Concat(suffixSequenceArr);
suffixStartIndex = suffixIndex.IndexOf(suffixSubString) + 1;
suffixEndIndex = (suffixStartIndex == 1) ? 1 : suffixStartIndex + suffixSubString.Length - 1;
//suffixSequencePeaks = GetSuffixSequencePeaks(suffixPeakArr, suffixStartIndex, suffixEndIndex);
//var suffixRankSum = GetSequenceRankSum(suffixSequencePeaks, rankings, peakList);
//suffixPval = FitScoreCalculator.GetRankSumPvalue(peakList.Length, suffixSequencePeaks.Count, suffixRankSum);
suffixSequence = GetStringSubSequence(_sequence, suffixStartIndex, suffixEndIndex);
}
return new Tuple<int, int, int, int, string, string>(prefixStartIndex, prefixEndIndex, suffixStartIndex, suffixEndIndex, prefixSequence, suffixSequence);
}
public Peak[] GetAllIsotopePeaks(Spectrum spec, Ion ion, Tolerance tolerance, double relativeIntensityThreshold, out int[] peakIndexList)
{
var mostAbundantIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
peakIndexList = new int[isotopomerEnvelope.Length];
var mostAbundantIsotopeMz = ion.GetIsotopeMz(mostAbundantIsotopeIndex);
var mostAbundantIsotopeMatchedPeakIndex = spec.FindPeakIndex(mostAbundantIsotopeMz, tolerance);
if (mostAbundantIsotopeMatchedPeakIndex < 0) return null;
var observedPeaks = new Peak[isotopomerEnvelope.Length];
observedPeaks[mostAbundantIsotopeIndex] = spec.Peaks[mostAbundantIsotopeMatchedPeakIndex];
peakIndexList[mostAbundantIsotopeIndex] = mostAbundantIsotopeMatchedPeakIndex;
// go down
var peakIndex = mostAbundantIsotopeMatchedPeakIndex - 1;
for (var isotopeIndex = mostAbundantIsotopeIndex - 1; isotopeIndex >= 0; isotopeIndex--)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold) break;
var isotopeMz = ion.GetIsotopeMz(isotopeIndex);
var tolTh = tolerance.GetToleranceAsTh(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i >= 0; i--)
{
var peakMz = spec.Peaks[i].Mz;
if (peakMz < minMz)
{
peakIndex = i;
break;
}
if (peakMz <= maxMz) // find match, move to prev isotope
{
var peak = spec.Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Intensity)
{
observedPeaks[isotopeIndex] = peak;
peakIndexList[isotopeIndex] = i;
}
}
}
}
// go up
peakIndex = mostAbundantIsotopeMatchedPeakIndex + 1;
for (var isotopeIndex = mostAbundantIsotopeIndex + 1; isotopeIndex < isotopomerEnvelope.Length; isotopeIndex++)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold) break;
var isotopeMz = ion.GetIsotopeMz(isotopeIndex);
var tolTh = tolerance.GetToleranceAsTh(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i < spec.Peaks.Length; i++)
{
var peakMz = spec.Peaks[i].Mz;
if (peakMz > maxMz)
{
peakIndex = i;
break;
}
if (peakMz >= minMz) // find match, move to prev isotope
{
var peak = spec.Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Intensity)
{
observedPeaks[isotopeIndex] = peak;
peakIndexList[isotopeIndex] = i;
}
}
}
}
return observedPeaks;
}
public void TestMs1Filtering()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && 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]);
//}
}
private void GetMatchStatistics(ProductSpectrum ms2Spec, Sequence sequence, int parentIonCharge, StreamWriter writer)
{
if (ms2Spec == null) return;
if (sequence == null) return;
var BaseIonTypesCID = new[] { BaseIonType.B, BaseIonType.Y };
var BaseIonTypesETD = new[] { BaseIonType.C, BaseIonType.Z };
var tolerance = new Tolerance(12);
var MinProductCharge = 1;
var MaxProductCharge = Math.Min(parentIonCharge+2, 20);
var baseIonTypes = ms2Spec.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCID : BaseIonTypesETD;
var refIntensity = CompositeScorer.GetRefIntensity(ms2Spec.Peaks);
var activationMethodFlag = ms2Spec.ActivationMethod == ActivationMethod.ETD ? 2 : 1;
var cleavages = sequence.GetInternalCleavages();
var nComplementaryFrags = 0;
var prefixStat = new FragmentStat();
var suffixStat = new FragmentStat();
var minMz = ms2Spec.Peaks.First().Mz;
var maxMz = ms2Spec.Peaks.Last().Mz;
var cleavageIndex = 0;
var preFixIonCheck = new bool[sequence.Count + 1];
var sufFixIonCheck = new bool[sequence.Count + 1];
foreach (var c in cleavages)
{
var prefixHit = false;
var suffixHit = false;
foreach (var baseIonType in baseIonTypes)
{
var stat = baseIonType.IsPrefix ? prefixStat : suffixStat;
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
if (fragmentComposition.Mass < ms2Spec.Peaks[0].Mz) continue;
var curFragMass = fragmentComposition.Mass;
/*var curObsIonCharge = 0;
var curObsIonDist = 1.0d;
var curObsIonCorr = 0d;
var curObsIonIntensity = 0d;
var curObsIonMassError = 0d;*/
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMostAbuMass = fragmentComposition.Mass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var maxCharge = (int)Math.Floor(fragmentIonMostAbuMass / (minMz - Constants.Proton));
var minCharge = (int)Math.Ceiling(fragmentIonMostAbuMass / (maxMz - Constants.Proton));
if (maxCharge < 1 || maxCharge > MaxProductCharge) maxCharge = MaxProductCharge;
if (minCharge < 1 || minCharge < MinProductCharge) minCharge = MinProductCharge;
//var ionMatch = false;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var isotopePeaks = ms2Spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null) continue;
var distCorr = CompositeScorer.GetDistCorr(ion, isotopePeaks);
if (distCorr.Item2 < 0.7 && distCorr.Item1 > 0.03) continue;
var mostAbuPeak = isotopePeaks[mostAbundantIsotopeIndex];
var intScore = mostAbuPeak.Intensity / refIntensity;
/*
if (ionMatch == false || curObsIonIntensity < intScore)
{
curObsIonCharge = charge;
curObsIonCorr = distCorr.Item2;
curObsIonDist = distCorr.Item1;
curObsIonIntensity = intScore;
var mostAbuPeakMz = Ion.GetIsotopeMz(curFragMass, charge, mostAbundantIsotopeIndex);
curObsIonMassError = (Math.Abs(mostAbuPeak.Mz - mostAbuPeakMz) / mostAbuPeakMz) * 1e6;
//var curObsIonMass = Ion.GetMonoIsotopicMass(mostAbuPeak.Mz, charge, mostAbundantIsotopeIndex);
//curObsIonMassError = (Math.Abs(curFragMass - curObsIonMass) / curFragMass) * 1e6;
}
ionMatch = true;
*/
var mostAbuPeakMz = Ion.GetIsotopeMz(curFragMass, charge, mostAbundantIsotopeIndex);
var curObsIonMassError = (Math.Abs(mostAbuPeak.Mz - mostAbuPeakMz) / mostAbuPeakMz) * 1e6;
stat.Count++;
stat.Intensity += Math.Min(intScore, 1.0);
stat.Corr += distCorr.Item2;
stat.Dist += distCorr.Item1;
stat.MassError += curObsIonMassError;
if (baseIonType.IsPrefix) prefixHit = true;
else suffixHit = true;
}
//if (!ionMatch) continue;
}
if (prefixHit) preFixIonCheck[cleavageIndex] = true;
if (suffixHit) sufFixIonCheck[cleavageIndex] = true;
if (prefixHit && suffixHit)
{
nComplementaryFrags++;
}
cleavageIndex++;
}
var preContCount = 0;
var sufContCount = 0;
for (var i = 0; i < preFixIonCheck.Length - 1; i++)
{
if (preFixIonCheck[i] && preFixIonCheck[i + 1]) preContCount++;
if (sufFixIonCheck[i] && sufFixIonCheck[i + 1]) sufContCount++;
}
writer.Write(activationMethodFlag);
writer.Write("\t");
writer.Write(sequence.Composition.Mass);
writer.Write("\t");
writer.Write(sequence.Count);
writer.Write("\t");
writer.Write(nComplementaryFrags);
writer.Write("\t");
writer.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", prefixStat.Count, preContCount, prefixStat.Intensity, prefixStat.Corr, prefixStat.Dist, prefixStat.MassError);
writer.Write("\t");
writer.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", suffixStat.Count, sufContCount, suffixStat.Intensity, suffixStat.Corr, suffixStat.Dist, suffixStat.MassError);
writer.Write("\n");
}
public ImsScorer GetImsScorer(ImsDataCached imsData, Ion precursorIon)
{
return new ImsScorer(imsData, precursorIon, _subScoreFactory);
}
private double[][][] GetXicArray()
{
var scanNumberIndex = new Dictionary<int, int>();
var i = 0;
foreach (var scanNumber in _run.GetScanNumbers(1))
{
// Console.WriteLine(scanNumber + " " + i);
scanNumberIndex[scanNumber] = i++;
}
var xicArray = new double[MaxCharge - MinCharge + 1][][];
// Console.WriteLine("***");
for (var charge = MinCharge; charge <= MaxCharge; charge++)
{
var xicArrayForThisCharge = new double[_isotopeEnvelope.Length][];
for (var j = 0; j < xicArrayForThisCharge.Length; j++)
xicArrayForThisCharge[j] = new double[scanNumberIndex.Count];
var precursorIon = new Ion(_proteinCompositionPlusWater, charge);
// Console.Write("precursorCharge " + charge);
for (var k = 0; k < xicArrayForThisCharge.Length; k++)
{
var mz = precursorIon.GetIsotopeMz(k + _minIsotopeIndex);
var xic = _run.GetPrecursorExtractedIonChromatogram(mz, _tolerance);
//Console.WriteLine("Mz" + mz);
foreach (var xicPeak in xic)
{
// Console.WriteLine(xicPeak.MostAbundantIsotopeMz);
xicArrayForThisCharge[k][scanNumberIndex[xicPeak.ScanNum]] = xicPeak.Intensity;
// if (k == _maxIntensityIsotopeIndex-_minIsotopeIndex)
// Console.WriteLine(charge + "\t" + xicPeak.MostAbundantIsotopeMz + "\t" + xicPeak.Intensity + "\t" + scanNumberIndex[xicPeak.MostAbundantIsotopeMz]);
//if(k == 0 && charge == 13) Console.WriteLine(xicPeak.MostAbundantIsotopeMz + " " + xicPeak.Intensity);
}
// Console.WriteLine();
}
// System.Environment.Exit(1);
//
xicArray[charge - MinCharge] = xicArrayForThisCharge;
}
return xicArray;
}
private void FindMatchedPeaks()
{
var cleavages = _sequence.GetInternalCleavages();
_prefixIonPeakIndex = new List<int>(); // list of cleavage indices
_suffixIonPeakIndex = new List<int>();
_nTheoreticalIonPeaks = 0;
_nObservedIonPeaks = 0;
int index = 0; // cleavage index
foreach (var c in cleavages)
{
foreach (var baseIonType in _baseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
for (var charge = _minCharge; charge <= _maxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
int baseIsotopePeakIndex;
int nIsotopes;
int nMatchedIsotopes;
if (FindIon(ion, _tolerance, RelativeIsotopeIntensityThreshold, out baseIsotopePeakIndex, out nIsotopes, out nMatchedIsotopes))
{
if (baseIonType.IsPrefix) _prefixIonPeakIndex.Add(baseIsotopePeakIndex);
else _suffixIonPeakIndex.Add(baseIsotopePeakIndex);
_nObservedIonPeaks++;
}
//_nObservedIonPeaks += nMatchedIsotopes;
//_nTheoreticalIonPeaks += nIsotopes;
_nTheoreticalIonPeaks++;
}
}
index++;
}
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && 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);
}
/// <summary>
/// Gets MS/MS spectra whose isolation windows contain the most abundant peak of the precursorIon
/// </summary>
/// <param name="precursorIon"></param>
/// <returns></returns>
public IEnumerable<ProductSpectrum> GetMatchingMs2Spectra(Ion precursorIon)
{
throw new System.NotImplementedException();
}
private void GetNodeStatistics(bool isDecoy, ProductSpectrum ms2Spec, Sequence sequence, StreamWriter writer) //, StreamWriter mzErrorWriter)
{
if (ms2Spec == null) return;
if (sequence == null) return;
//var refIntensity = ms2Spec.Peaks.Max(p => p.Intensity) * 0.01;
//refIntensity = Math.Min(ms2Spec.Peaks.Select(p => p.Intensity).Median(), refIntensity);
var BaseIonTypesCID = new[] { BaseIonType.B, BaseIonType.Y };
var BaseIonTypesETD = new[] { BaseIonType.C, BaseIonType.Z };
var tolerance = new Tolerance(15);
var minCharge = 1;
var maxCharge = 20;
var baseIonTypes = ms2Spec.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCID : BaseIonTypesETD;
var refIntensity = ms2Spec.Peaks.Max(p => p.Intensity);
var activationMethodFlag = ms2Spec.ActivationMethod == ActivationMethod.ETD ? 1 : 2;
var cleavages = sequence.GetInternalCleavages();
var prevPrefixFragMass = 0d;
var prevPrefixObsIonMass = 0d;
var prevPrefixObsIonCharge = 0;
var prevPrefixObsIonIntensity = 0d;
var prevSuffixFragMass = 0d;
var prevSuffixObsIonMass = 0d;
var prevSuffixObsIonCharge = 0;
var prevSuffixObsIonIntensity = 0d;
var nComplementaryFrags = 0;
var cleavageIndex = 0;
foreach (var c in cleavages)
{
var bothObs = true;
foreach (var baseIonType in baseIonTypes)
{
var peakType = baseIonType.IsPrefix ? 1 : 2; // unexplained
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
var curFragMass = fragmentComposition.Mass;
var curObsIonMass = 0d;
var curObsIonCharge = 0;
var curObsIonDist = 1.0d;
var curObsIonCorr = 0d;
var curObsIonIntensity = 0d;
var ionMatch = false;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var isotopePeaks = ms2Spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null) continue;
var distCorr = AbstractFragmentScorer.GetDistCorr(ion, isotopePeaks);
if (distCorr.Item2 < 0.7 && distCorr.Item1 > 0.07) continue;
var mostAbundantIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var mostAbuPeak = isotopePeaks[mostAbundantIsotopeIndex];
var summedIntensity = isotopePeaks.Where(p => p != null).Sum(p => p.Intensity);
var intScore = summedIntensity/refIntensity;
//var intScore = mostAbuPeak.Intensity / medIntensity;
//var intScore = summedIntensity / refIntensity;
if (ionMatch == false || curObsIonIntensity < intScore)
{
curObsIonMass = Ion.GetMonoIsotopicMass(mostAbuPeak.Mz, charge, mostAbundantIsotopeIndex);
curObsIonCharge = charge;
curObsIonCorr = distCorr.Item2;
curObsIonDist = distCorr.Item1;
curObsIonIntensity = intScore;
}
ionMatch = true;
}
if (!ionMatch)
{
bothObs = false;
continue;
}
writer.Write(activationMethodFlag);
writer.Write("\t");
writer.Write(peakType);
writer.Write("\t");
writer.Write("{0:0.000}", curFragMass);
writer.Write("\t");
writer.Write("{0}", curObsIonCharge);
writer.Write("\t");
writer.Write("{0:0.000}", curObsIonDist);
writer.Write("\t");
writer.Write("{0:0.000}", curObsIonCorr);
writer.Write("\t");
writer.Write("{0:0.000}", curObsIonIntensity);
writer.Write("\t");
writer.Write("{0:0.000}", (Math.Abs(curFragMass - curObsIonMass)/curFragMass)*1e6);
writer.Write("\n");
// mz error output
/*
if (baseIonType.IsPrefix && prevPrefixFragMass > 0 & prevPrefixObsIonMass > 0)
{
var aaMass = Math.Abs(prevPrefixFragMass - curFragMass);
var massError = Math.Abs(Math.Abs(prevPrefixObsIonMass - curObsIonMass) - aaMass);
var massErrorPpm = (massError / curObsIonMass) * 1e6;
mzErrorWriter.WriteLine("{0}\t{1:0.000}\t{2}", activationMethodFlag, massErrorPpm, Math.Abs(prevPrefixObsIonCharge - curObsIonCharge));
}
else if (prevSuffixFragMass > 0 & prevSuffixObsIonMass > 0)
{
var aaMass = Math.Abs(prevSuffixFragMass - curFragMass);
var massError = Math.Abs(Math.Abs(prevSuffixObsIonMass - curObsIonMass) - aaMass);
var massErrorPpm = (massError / curObsIonMass) * 1e6;
mzErrorWriter.WriteLine("{0}\t{1:0.000}\t{2}", activationMethodFlag, massErrorPpm, Math.Abs(prevSuffixObsIonCharge - curObsIonCharge));
}
*/
if (baseIonType.IsPrefix)
{
prevPrefixFragMass = curFragMass;
prevPrefixObsIonMass = curObsIonMass;
prevPrefixObsIonCharge = curObsIonCharge;
prevPrefixObsIonIntensity = curObsIonIntensity;
//Array.Copy(curObsIonMass, prevPrefixObsIonMass, curObsIonMass.Length);
}
else
{
prevSuffixFragMass = curFragMass;
prevSuffixObsIonMass = curObsIonMass;
prevSuffixObsIonCharge = curObsIonCharge;
prevSuffixObsIonIntensity = curObsIonIntensity;
//Array.Copy(curObsIonMass, prevSuffixObsIonMass, curObsIonMass.Length);
}
}
if (bothObs)
{
//pairWriter.Write("{0}\t{1}\t", prevPrefixObsIonIntensity, prevSuffixObsIonIntensity);
nComplementaryFrags++;
}
cleavageIndex++;
}
Console.WriteLine("{0}\t{1}", nComplementaryFrags, sequence.Count);
//if (!isDecoy) Console.WriteLine("{0}", totalExplainedAbundanceRatio);
}
public void TestTopDownScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string protAnnotation = "A.AHAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK.";
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var searchModifications = new List<SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
//var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
//Console.WriteLine(aaSet.GetAminoAcid('C').GetComposition());
// Create a sequence graph
//var protSeq = protAnnotation.Substring(2, protAnnotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
// TopDownScorer.MaxCharge = 60;
// TopDownScorer.MinCharge = 3;
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
foreach (var protComposition in seqGraph.GetSequenceCompositions())
{
var mostAbundantIsotopeIndex = protComposition.GetMostAbundantIsotopeZeroBasedIndex();
Console.WriteLine("Composition\t{0}", protComposition);
Console.WriteLine("MostAbundantIsotopeIndex\t{0}", mostAbundantIsotopeIndex);
Console.WriteLine(new Ion(protComposition + Composition.H2O, 11).GetIsotopeMz(mostAbundantIsotopeIndex));
Console.WriteLine();
//for (var charge = TopDownScorer.MinCharge; charge <= TopDownScorer.MaxCharge; charge++)
//{
var scorer = new TopDownScorer(protComposition, run, precursorTolerance, null);
var score = scorer.GetScore();
Console.WriteLine(score);
//var precursorIon = new Ion(protComposition + Composition.H2O, charge);
//var xic = run.GetExtractedIonChromatogram(precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex), precursorTolerance);
//Console.WriteLine(xic[0].ScanNum + " " + xic[1].ScanNum);
//Console.WriteLine("ScanNum\t{0}", string.Join("\t", xic.Select(p => p.ScanNum.ToString())));
//Console.WriteLine("precursorCharge " + charge + "\t" + string.Join("\t", xic.Select(p => p.Intensity.ToString())));
// }
Console.WriteLine("\nCharge\tm/z");
for (var charge = 9; charge <= 18; charge++)
{
var precursorIon = new Ion(protComposition + Composition.H2O, charge);
Console.WriteLine("{0}\t{1}", charge, precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex));
}
}
// sw.Stop();
// Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
var sequence = sequences[i];
int count;
if (sequenceCount.TryGetValue(sequence, out 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 spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && 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);
}