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;
}
}
}
}
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);
}
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");
}
