internal DeconvScorer(ProductSpectrum deconvolutedSpectrum, Tolerance productTolerance)
{
if (deconvolutedSpectrum.ActivationMethod != ActivationMethod.ETD)
{
_prefixOffsetMass = BaseIonType.B.OffsetComposition.Mass;
_suffixOffsetMass = BaseIonType.Y.OffsetComposition.Mass;
}
else
{
_prefixOffsetMass = BaseIonType.C.OffsetComposition.Mass;
_suffixOffsetMass = BaseIonType.Z.OffsetComposition.Mass;
}
_ionMassBins = new HashSet <int>();
foreach (var p in deconvolutedSpectrum.Peaks)
{
var mass = p.Mz;
var deltaMass = productTolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = GetBinNumber(minMass);
var maxBinNum = GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
_ionMassBins.Add(binNum);
}
}
}
public CompositeScorerBasedOnDeconvolutedSpectrum(DeconvolutedSpectrum deconvolutedSpectrum, ProductSpectrum spec, Tolerance productTolerance, IMassBinning comparer)
: base(deconvolutedSpectrum, productTolerance)
{
ReferencePeakIntensity = GetRefIntensity(spec.Peaks);
_comparer = comparer;
_massBinToPeakMap = new Dictionary <int, DeconvolutedPeak>();
foreach (var p in deconvolutedSpectrum.Peaks)
{
var mass = p.Mz;
var deltaMass = productTolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var binNum = comparer.GetBinNumber(mass);
if (binNum < 0)
{
binNum = comparer.GetBinNumber(minMass);
if (binNum < 0)
{
binNum = comparer.GetBinNumber(maxMass);
}
}
// filter out
if (binNum < 0)
{
continue;
}
UpdateDeconvPeak(binNum, p as DeconvolutedPeak);
// going up
for (var nextBinNum = binNum + 1; nextBinNum < comparer.NumberOfBins; nextBinNum++)
{
var nextBinMass = comparer.GetMassStart(nextBinNum);
if (minMass < nextBinMass && nextBinMass < maxMass)
{
UpdateDeconvPeak(nextBinNum, p as DeconvolutedPeak); //_ionMassChkBins[nextBinNum] = true;
}
else
{
break;
}
}
// going down
for (var prevBinNum = binNum - 1; prevBinNum < comparer.NumberOfBins; prevBinNum--)
{
var prevBinMass = comparer.GetMassEnd(prevBinNum);
if (minMass < prevBinMass && prevBinMass < maxMass)
{
UpdateDeconvPeak(prevBinNum, p as DeconvolutedPeak); //_ionMassChkBins[prevBinNum] = true;
}
else
{
break;
}
}
}
}
} // true: target and decoy, false: target only, null: decoy only
public void QuickId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 1;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null)
{
continue;
}
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec.Peaks, minCharge, maxCharge, 2, 1.1, tolerance, corrThreshold);
if (deconvolutedPeaks == null)
{
continue;
}
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin)
{
massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f1} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine(@"Processing, {0} proteins done, {1:f1} sec elapsed",
numProteins,
sw.Elapsed.TotalSeconds);
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
continue;
}
for (var numNTermCleavage = 0; numNTermCleavage <= 1; numNTermCleavage++)
{
if (numNTermCleavage > 0)
{
seqGraph.CleaveNTerm();
}
var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin)
{
continue;
}
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
// prefix
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestScore[ms2ScanNum], bestProtein[ms2ScanNum] ?? "");
}
}
