public SpectrumMatch Filter(SpectrumMatch specMatch)
{
var charge = specMatch.PrecursorCharge;
var peaks = specMatch.Spectrum.Peaks;
var indexes = new List<int>();
for (int i = 0; i < _offsets.Charge; i++)
{
var ion = _precursorIonTypes[i].GetIon(specMatch.PeptideComposition);
var mz = ion.GetMonoIsotopicMz();
var offsets = _offsets.GetChargeOffsets(i + 1);
foreach (var offset in offsets)
{
var offsetMz = mz + offset;
var peakIndex = specMatch.Spectrum.FindPeakIndex(offsetMz, _tolerance);
if (peakIndex > 0) indexes.Add(peakIndex);
}
}
indexes = indexes.Distinct().ToList();
var filteredPeaks = peaks.Where((t, i) => !indexes.Contains(i)).ToList();
var spectrum = new Spectrum(filteredPeaks, specMatch.Spectrum.ScanNum);
var filteredSpecMatch = new SpectrumMatch(specMatch.Sequence, spectrum, specMatch.ScanNum, charge, specMatch.Decoy);
return filteredSpecMatch;
}
public SpectrumMatch Filter(SpectrumMatch specMatch)
{
var charge = specMatch.PrecursorCharge;
var peaks = specMatch.Spectrum.Peaks;
var indexes = new List <int>();
for (int i = 0; i < _offsets.Charge; i++)
{
var ion = _precursorIonTypes[i].GetIon(specMatch.PeptideComposition);
var mz = ion.GetMonoIsotopicMz();
var offsets = _offsets.GetChargeOffsets(i + 1);
foreach (var offset in offsets)
{
var offsetMz = mz + offset;
var peakIndex = specMatch.Spectrum.FindPeakIndex(offsetMz, _tolerance);
if (peakIndex > 0)
{
indexes.Add(peakIndex);
}
}
}
indexes = indexes.Distinct().ToList();
var filteredPeaks = peaks.Where((t, i) => !indexes.Contains(i)).ToList();
var spectrum = new Spectrum(filteredPeaks, specMatch.Spectrum.ScanNum);
var filteredSpecMatch = new SpectrumMatch(specMatch.Sequence, spectrum, specMatch.ScanNum, charge, specMatch.Decoy);
return(filteredSpecMatch);
}
public void AddMatch(SpectrumMatch match)
{
var charge = match.PrecursorCharge;
if (!_offsets.ContainsKey(charge)) throw new Exception("Invalid charge.");
for (int i = charge; i > 0; i--)
{
_offsets[i].AddMatches(new List<SpectrumMatch>{match});
}
}
public void AddMatch(SpectrumMatch match)
{
Total++;
var ion = _precursorIonTypes[Charge - 1].GetIon(match.PeptideComposition);
var monoIsotopicMz = ion.GetMonoIsotopicMz();
var min = GetMinMz(monoIsotopicMz);
var max = GetMaxMz(monoIsotopicMz);
var peaks = match.Spectrum.Peaks;
var offsetMzCollection = (from peak in peaks
where peak.Mz >= min && peak.Mz <= max
select peak.Mz - monoIsotopicMz).ToList();
AddOffsets(offsetMzCollection);
}
public SpectrumMatch(SpectrumMatch match, bool decoy)
{
Peptide = match.Peptide;
_spectrum = match._spectrum;
_lcms = match._lcms;
ScanNum = match.ScanNum;
PrecursorCharge = match.PrecursorCharge;
Decoy = decoy;
Sequence = new Sequence(match.Sequence);
if (decoy)
{
CreateDecoy();
}
}
/// <summary>
/// Filter out all peaks in a spectrum that are not explained by certain ion types.
/// </summary>
/// <param name="sequence">Sequence to calculate ions from.</param>
/// <param name="spectrum">Spectrum to filter.</param>
/// <param name="ionTypes">Ion types to find peaks for.</param>
/// <param name="tolerance"></param>
/// <returns>Filtered Peptide Spectrum Match</returns>
public static Spectrum FilterIonPeaks(Sequence sequence, Spectrum spectrum, IonType[] ionTypes, Tolerance tolerance)
{
var filteredPeaks = new List<Peak>();
var specMatch = new SpectrumMatch(sequence, spectrum);
foreach (var ionType in ionTypes)
{
var ions = specMatch.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var peak = spectrum.FindPeak(ion.GetMonoIsotopicMz(), tolerance);
if (peak != null) filteredPeaks.Add(peak);
}
}
filteredPeaks.Sort();
return new Spectrum(filteredPeaks, spectrum.ScanNum) {MsLevel = 2};
}
public double GetScore(Sequence sequence, int charge, int scan, LcMsRun lcmsRun)
{
var mass = sequence.Composition.Mass + Composition.H2O.Mass;
var spectrum = lcmsRun.GetSpectrum(scan);
var ionTypes = _rankScore.GetIonTypes(charge, mass);
var filteredSpectrum = SpectrumFilter.FilterIonPeaks(sequence, spectrum, ionTypes, _tolerance);
var match = new SpectrumMatch(sequence, filteredSpectrum, charge);
var score = 0.0;
var rankedPeaks = new RankedPeaks(filteredSpectrum);
foreach (var ionType in ionTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = rankedPeaks.RankIon(ion, _tolerance);
score += _rankScore.GetScore(ionType, rank, charge, mass);
}
}
return score;
}
public void AddMatch(SpectrumMatch match)
{
foreach (var ionType in _ionTypes)
{
var charge = ionType.Charge;
var sequence = match.Sequence;
var pepSeq = ionType.IsPrefixIon
? sequence.GetRange(0, sequence.Count - 1)
: sequence.GetRange(1, sequence.Count - 1);
var ions = match.GetCleavageIons(ionType);
var nextIonIndex = 1;
while (nextIonIndex < ions.Count)
{
// look for peaks for current ion and next ion
_totalPairs++;
var currIonIndex = nextIonIndex - 1;
var currMz = ions[currIonIndex].GetMonoIsotopicMz();
var currPeak = match.Spectrum.FindPeak(currMz, _tolerance);
var nextMz = ions[nextIonIndex].GetMonoIsotopicMz();
var nextPeak = match.Spectrum.FindPeak(nextMz, _tolerance);
if (currPeak == null && nextPeak == null)
_ionPairFrequency[ionType].AddDatum(IonPairFound.Neither);
else if (nextPeak == null)
_ionPairFrequency[ionType].AddDatum(IonPairFound.First);
else if (currPeak == null)
_ionPairFrequency[ionType].AddDatum(IonPairFound.Second);
else
{
// found both peaks, compute mass error
_ionPairFrequency[ionType].AddDatum(IonPairFound.Both);
var aaIndex = (ionType.IsPrefixIon ? nextIonIndex : currIonIndex);
var aaMz = pepSeq[aaIndex].Mass/charge;
var massError = Math.Abs(nextPeak.Mz - currPeak.Mz) - aaMz;
_massError[ionType].AddDatum(massError);
}
nextIonIndex++;
}
}
}
/// <summary>
/// Add single Peptide-Spectrum match to RankTable.
/// </summary>
/// <param name="match"></param>
public void AddMatch(SpectrumMatch match)
{
var ranks = new RankedPeaks(match.Spectrum);
for (int i = 0; i < ranks.Peaks.Length; i++)
{
var index = i;
if (index >= MaxRanks) index = MaxRanks - 1;
_rankTotals[index]++;
_rankTotals[MaxRanks]++;
}
foreach (var ionType in IonTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = ranks.RankIon(ion, _tolerance);
var rankIndex = GetRankIndex(rank);
_rankTable[ionType][rankIndex]++;
}
}
}
/// <summary>
/// Filter out all peaks in a spectrum that are not explained by certain ion types.
/// </summary>
/// <param name="sequence">Sequence to calculate ions from.</param>
/// <param name="spectrum">Spectrum to filter.</param>
/// <param name="ionTypes">Ion types to find peaks for.</param>
/// <param name="tolerance"></param>
/// <returns>Filtered Peptide Spectrum Match</returns>
public static Spectrum FilterIonPeaks(Sequence sequence, Spectrum spectrum, IonType[] ionTypes, Tolerance tolerance)
{
var filteredPeaks = new List <Peak>();
var specMatch = new SpectrumMatch(sequence, spectrum);
foreach (var ionType in ionTypes)
{
var ions = specMatch.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var peak = spectrum.FindPeak(ion.GetMonoIsotopicMz(), tolerance);
if (peak != null)
{
filteredPeaks.Add(peak);
}
}
}
filteredPeaks.Sort();
return(new Spectrum(filteredPeaks, spectrum.ScanNum)
{
MsLevel = 2
});
}
/// <summary>
/// Add Peptide-Spectrum match to ion Probability table.
/// </summary>
/// <param name="match"></param>
public void AddMatch(SpectrumMatch match)
{
var spectrum = match.Spectrum;
var prefixes = match.Prefixes;
var suffixes = match.Suffixes;
for (int i = 0; i < prefixes.Count; i++)
{
var ionTypeFound = new Dictionary<IonType, bool>();
foreach (var ionType in _ionTypes)
{
var it = ionType;
if (_combineCharges)
it = ReducedChargeIonType(ionType);
if (!ionTypeFound.ContainsKey(it))
ionTypeFound.Add(it, false);
var cleavagePoints = ionType.BaseIonType.IsPrefix ? prefixes : suffixes;
var ion = ionType.GetIon(cleavagePoints[i]);
if (spectrum.ContainsIon(ion, _tolerance, _relativeIntensityThreshold))
{
ionTypeFound[it] = true;
}
}
foreach (var key in ionTypeFound.Keys)
{
int found = 0;
const int total = 1;
if (ionTypeFound[key]) found = 1;
AddIonProbability(new Probability<IonType>(key, found, total));
}
}
}
public SpectrumMatch(SpectrumMatch match, bool decoy)
{
Peptide = match.Peptide;
_spectrum = match._spectrum;
_lcms = match._lcms;
ScanNum = match.ScanNum;
PrecursorCharge = match.PrecursorCharge;
Decoy = decoy;
Sequence = new Sequence(match.Sequence);
if (decoy) CreateDecoy();
}
private void ComputeMatch(SpectrumMatch match, int charge, int massIndex)
{
var isDecoy = match.Decoy;
var massErrors = _massErrors[charge][massIndex];
var rankTable = (isDecoy ? _drankTables[charge][massIndex] : _rankTables[charge][massIndex]);
var ionFrequencies = _ionProbabilities[charge][massIndex];
var acMatch = match;
if (Config.AcquisitionMethod == AcquisitionMethod.Dia)
{
// filter out all peaks except ion peaks
var ionPeakSpectrum = SpectrumFilter.FilterIonPeaks(match.Sequence, match.Spectrum,
Config.IonTypes, Config.Tolerance);
acMatch = new SpectrumMatch(acMatch.Sequence, ionPeakSpectrum, acMatch.ScanNum, acMatch.PrecursorCharge, acMatch.Decoy);
}
else
{
_precursorOffsets[charge][massIndex].AddMatch(match);
// filter precursor peaks
var precursorFilter = new PrecursorFilter(_precursorOffsets[charge][massIndex],
Config.MassErrorTolerance);
acMatch = precursorFilter.Filter(acMatch);
}
rankTable.AddMatch(acMatch);
if (isDecoy) return;
massErrors.AddMatch(match);
var filteredSpectrum = SpectrumFilter.GetFilteredSpectrum(match.Spectrum, Config.WindowWidth,
Config.RetentionCount);
var filteredMatch = new SpectrumMatch(match.Sequence, filteredSpectrum, match.PrecursorCharge);
ionFrequencies.AddMatch(filteredMatch);
}
private void Compute()
{
if (_computed) return;
Initialize();
var total = _dataSet.Count;
for (int i = 0; i < total; i++)
{
var target = _dataSet.Dequeue();
var charge = target.PrecursorCharge;
if (!_charges.Contains(charge)) continue;
var decoy = new SpectrumMatch(target, true);
var mass = target.PrecursorComposition.Mass;
var index = _massSorter[charge].GetBinIndex(mass);
ComputeMatch(target, charge, index);
ComputeMatch(decoy, charge, index);
}
_computed = true;
}
public IList<SpectrumMatch> Read()
{
var specMatches = new List<SpectrumMatch>();
var file = File.ReadLines(_fileName);
var mgfState = MgfState.Label;
var sequence = "";
int scanNum = 0, charge = 0;
var peaks = new List<Peak>();
var peptideSet = new HashSet<string>();
foreach (var line in file)
{
switch (mgfState)
{
case MgfState.Label:
if (line == "BEGIN IONS") mgfState = MgfState.Parameter;
else throw new FormatException("Invalid MGF file.");
break;
case MgfState.Parameter:
var parameter = line.Split('=');
if (parameter.Length < 2) throw new FormatException("Invalid line in MGF file: " + line);
if (parameter[0] == "SEQ") sequence = parameter[1];
else if (parameter[0] == "SCANS") scanNum = Convert.ToInt32(parameter[1]);
else if (parameter[0] == "CHARGE")
{
var chargeStr = parameter[1].Substring(0, parameter[1].Length - 1);
charge = Convert.ToInt32(chargeStr);
mgfState = MgfState.Peak;
if (sequence == "" || scanNum == 0 || charge == 0)
throw new FormatException("Incomplete spectrum entry.");
}
break;
case MgfState.Peak:
if (line == "END IONS")
{
if (peaks.Count == 0) throw new FormatException("Empty peak list.");
mgfState = MgfState.Label;
if (peptideSet.Contains(sequence))
{
sequence = "";
scanNum = 0;
charge = 0;
peaks.Clear();
continue;
}
peptideSet.Add(sequence);
var spectrum = new ProductSpectrum(peaks, scanNum) { MsLevel = 2 };
var sequenceReader = new MgfSequenceReader();
var seq = sequenceReader.GetSequence(sequence);
var specMatch = new SpectrumMatch(seq, spectrum, scanNum, charge, _decoy);
sequence = "";
scanNum = 0;
charge = 0;
specMatches.Add(specMatch);
peaks.Clear();
}
else
{
var parts = line.Split('\t');
if (parts.Length < 2) throw new FormatException("Invalid line in MGF file: " + line);
var mz = Convert.ToDouble(parts[0]);
var intensity = Convert.ToDouble(parts[1]);
peaks.Add(new Peak(mz, intensity));
}
break;
}
}
return specMatches;
}
