public void AddEnvelope(IsotopicEnvelope isotopicEnvelope, int scanIndex, double elutionTime)
{
MinScanIndex = Math.Min(scanIndex, MinScanIndex);
MaxScanIndex = Math.Max(scanIndex, MaxScanIndex);
MinElutionTime = Math.Min(elutionTime, MinElutionTime);
MaxElutionTime = Math.Max(elutionTime, MaxElutionTime);
bool added = false;
foreach (var massGroup in groups)
{
if (Math.Abs(massGroup.Mass - isotopicEnvelope.monoisotopicMass) < 0.5)
{
massGroup.AddEnvelope(scanIndex, elutionTime, isotopicEnvelope);
added = true;
break;
}
}
if (!added)
{
var newMassGroup = new DeconvolutionFeature();
newMassGroup.AddEnvelope(scanIndex, elutionTime, isotopicEnvelope);
groups.Add(newMassGroup);
}
Mass = groups.OrderBy(b => - b.NumPeaks).First().Mass;
TotalNormalizedIntensity += isotopicEnvelope.totalIntensity / isotopicEnvelope.charge;
if (MostIntenseEnvelope == null || MostIntenseEnvelope.totalIntensity < isotopicEnvelope.totalIntensity)
{
MostIntenseEnvelope = isotopicEnvelope;
MostIntenseEnvelopeElutionTime = elutionTime;
}
}
// Mass tolerance must account for different isotope spacing!
public IEnumerable <IsotopicEnvelope> Deconvolute(MzRange theRange, int minAssumedChargeState, int maxAssumedChargeState, double deconvolutionTolerancePpm, double intensityRatioLimit)
{
if (Size == 0)
{
yield break;
}
var isolatedMassesAndCharges = new List <IsotopicEnvelope>();
foreach (var candidateForMostIntensePeak in ExtractIndices(theRange.Minimum, theRange.Maximum))
{
IsotopicEnvelope bestIsotopeEnvelopeForThisPeak = null;
var candidateForMostIntensePeakMz = XArray[candidateForMostIntensePeak];
//Console.WriteLine("candidateForMostIntensePeakMz: " + candidateForMostIntensePeakMz);
var candidateForMostIntensePeakIntensity = YArray[candidateForMostIntensePeak];
for (int chargeState = minAssumedChargeState; chargeState <= maxAssumedChargeState; chargeState++)
{
//Console.WriteLine(" chargeState: " + chargeState);
var testMostIntenseMass = candidateForMostIntensePeakMz.ToMass(chargeState);
var massIndex = Array.BinarySearch(mostIntenseMasses, testMostIntenseMass);
if (massIndex < 0)
{
massIndex = ~massIndex;
}
if (massIndex == mostIntenseMasses.Length)
{
//Console.WriteLine("Breaking because mass is too high: " + testMostIntenseMass);
break;
}
//Console.WriteLine(" massIndex: " + massIndex);
var listOfPeaks = new List <(double, double)> {
(candidateForMostIntensePeakMz, candidateForMostIntensePeakIntensity)
};
var listOfRatios = new List <double> {
allIntensities[massIndex][0] / candidateForMostIntensePeakIntensity
};
// Assuming the test peak is most intense...
// Try to find the rest of the isotopes!
double differenceBetweenTheorAndActual = testMostIntenseMass - mostIntenseMasses[massIndex];
double totalIntensity = candidateForMostIntensePeakIntensity;
for (int indexToLookAt = 1; indexToLookAt < allIntensities[massIndex].Length; indexToLookAt++)
{
//Console.WriteLine(" indexToLookAt: " + indexToLookAt);
double theorMassThatTryingToFind = allMasses[massIndex][indexToLookAt] + differenceBetweenTheorAndActual;
//Console.WriteLine(" theorMassThatTryingToFind: " + theorMassThatTryingToFind);
//Console.WriteLine(" theorMassThatTryingToFind.ToMz(chargeState): " + theorMassThatTryingToFind.ToMz(chargeState));
var closestPeakToTheorMass = GetClosestPeakIndex(theorMassThatTryingToFind.ToMz(chargeState));
var closestPeakmz = XArray[closestPeakToTheorMass.Value];
//Console.WriteLine(" closestPeakmz: " + closestPeakmz);
var closestPeakIntensity = YArray[closestPeakToTheorMass.Value];
if (Math.Abs(closestPeakmz.ToMass(chargeState) - theorMassThatTryingToFind) / theorMassThatTryingToFind * 1e6 <= deconvolutionTolerancePpm &&
Peak2satisfiesRatio(allIntensities[massIndex][0], allIntensities[massIndex][indexToLookAt], candidateForMostIntensePeakIntensity, closestPeakIntensity, intensityRatioLimit) &&
!listOfPeaks.Contains((closestPeakmz, closestPeakIntensity)))
{
//Found a match to an isotope peak for this charge state!
//Console.WriteLine(" * Found a match to an isotope peak for this charge state!");
//Console.WriteLine(" * chargeState: " + chargeState);
//Console.WriteLine(" * closestPeakmz: " + closestPeakmz);
listOfPeaks.Add((closestPeakmz, closestPeakIntensity));
totalIntensity += closestPeakIntensity;
listOfRatios.Add(allIntensities[massIndex][indexToLookAt] / closestPeakIntensity);
}
/// <summary>
/// Shortreed's idea for top-down ms1 deconvolution (Jan. 6, 2020)
/// Potential utility for non-isotopically resolved envelopes
/// deconvolute the whole spectrum by treating every peak as charge 1, 2, 3, etc and recording the masses
/// do a histogram to find which masses have multiple charge states: those with high overlap are the real species
/// Could possibly avoid doing the whole spectrum by just targeting areas of interest
/// </summary>
//public IEnumerable<IsotopicEnvelope> TopDownDeconvolution(int minAssumedChargeState, int maxAssumedChargeState)
//{
// //cycle through all charge states
//}
// Mass tolerance must account for different isotope spacing!
public IEnumerable <IsotopicEnvelope> Deconvolute(MzRange theRange, int minAssumedChargeState, int maxAssumedChargeState, double deconvolutionTolerancePpm, double intensityRatioLimit)
{
//if no peaks, stop
if (Size == 0)
{
yield break;
}
var isolatedMassesAndCharges = new List <IsotopicEnvelope>();
(int start, int end)indexes = ExtractIndices(theRange.Minimum, theRange.Maximum);
//find the most intense peak in the range
double maxIntensity = 0;
for (int index = indexes.start; index < indexes.end; index++)
{
if (YArray[index] > maxIntensity)
{
maxIntensity = YArray[index];
}
}
//go through each peak in the selected range and assume it is the most intense peak of its isotopic envelope (if it's not, it will hopefully get a low score)
//cycle through possible charge states and select the one that has the best score (fit) with the averagine model
for (int candidateForMostIntensePeakIndex = indexes.start; candidateForMostIntensePeakIndex < indexes.end; candidateForMostIntensePeakIndex++)
{
double candidateForMostIntensePeakIntensity = YArray[candidateForMostIntensePeakIndex];
if (candidateForMostIntensePeakIntensity * 100 >= maxIntensity) //ignore peptides that are over 100 times less intense than the most intense peak in the range (heuristic from Top-Down yeast)
{
IsotopicEnvelope bestIsotopeEnvelopeForThisPeak = null;
double candidateForMostIntensePeakMz = XArray[candidateForMostIntensePeakIndex];
//Find what charge states this peak might be based on the spacing of nearby peaks (assumes isotopic resolution)
HashSet <int> allPossibleChargeStates = new HashSet <int>();
for (int i = candidateForMostIntensePeakIndex + 1; i < XArray.Length; i++) //look at peaks of higher m/z
{
double deltaMass = XArray[i] - candidateForMostIntensePeakMz;
if (deltaMass < 1.1) //if we're past a Th spacing, we're no longer looking at the closest isotope
{
//get the lower bound charge state
int charge = (int)Math.Floor(1 / deltaMass); //e.g. deltaMass = 0.4 Th, charge is now 2 (but might be 3)
if (charge >= minAssumedChargeState && charge <= maxAssumedChargeState)
{
allPossibleChargeStates.Add(charge);
}
//get the upper bound charge state
charge++;
if (charge >= minAssumedChargeState && charge <= maxAssumedChargeState)
{
allPossibleChargeStates.Add(charge);
}
}
else
{
break;
}
}
//investigate the putative charge states
foreach (int chargeState in allPossibleChargeStates)
{
//get the mass of this peak assuming it's the charge we're looking at
double testMostIntenseMass = candidateForMostIntensePeakMz.ToMass(chargeState);
//get the index of the theoretical isotopic envelope for an averagine model that's close in mass
int massIndex = Array.BinarySearch(mostIntenseMasses, testMostIntenseMass);
if (massIndex < 0)
{
massIndex = ~massIndex;
}
if (massIndex == mostIntenseMasses.Length)
{
break;
}
if (massIndex != 0 && mostIntenseMasses[massIndex] - testMostIntenseMass > testMostIntenseMass - mostIntenseMasses[massIndex - 1])
{
massIndex--;
}
//create a list for each isotopic peak from this envelope. This is used to fine tune the monoisotopic mass and is populated in "FindIsotopicEnvelope"
List <double> monoisotopicMassPredictions = new List <double>();
//Look for other isotopes using the assumed charge state
IsotopicEnvelope putativeIsotopicEnvelope = FindIsotopicEnvelope(massIndex, candidateForMostIntensePeakMz, candidateForMostIntensePeakIntensity,
testMostIntenseMass, chargeState, deconvolutionTolerancePpm, intensityRatioLimit, monoisotopicMassPredictions);
if (putativeIsotopicEnvelope.Peaks.Count >= 2) //if there are at least two isotopes
{
//look for other charge states, using them for scoring and monoisotopic mass estimates
//need to use this method before comparing scores because it changes the score of the test envelope
int numOtherChargeStatesObserved = ObserveAdjacentChargeStates(putativeIsotopicEnvelope, candidateForMostIntensePeakMz, massIndex, deconvolutionTolerancePpm, intensityRatioLimit, minAssumedChargeState, maxAssumedChargeState, monoisotopicMassPredictions);
//is this the best charge state for this peak?
if ((bestIsotopeEnvelopeForThisPeak == null || putativeIsotopicEnvelope.Score > bestIsotopeEnvelopeForThisPeak.Score) && //and the score is better for this charge state than others
(putativeIsotopicEnvelope.Charge / 5 <= numOtherChargeStatesObserved)) //and if we suspect there to be multiple charge states and there are (higher the charge, more states expected, z=5, need 2 charge states, z=10, need 3 charge states, etc
{
putativeIsotopicEnvelope.SetMedianMonoisotopicMass(monoisotopicMassPredictions); //take the median mass from all of the isotopes (this is fine tuning!)
bestIsotopeEnvelopeForThisPeak = putativeIsotopicEnvelope;
}
}
}
if (bestIsotopeEnvelopeForThisPeak != null) //add this envelope (it might be wrong, but hopefully it has a low score and gets outscored later by the right thing)
{
isolatedMassesAndCharges.Add(bestIsotopeEnvelopeForThisPeak);
}
}
}
HashSet <double> seen = new HashSet <double>();
foreach (var ok in isolatedMassesAndCharges.OrderByDescending(b => b.Score))
{
if (seen.Overlaps(ok.Peaks.Select(b => b.mz)))
{
continue;
}
foreach (var ah in ok.Peaks.Select(b => b.mz))
{
seen.Add(ah);
}
yield return(ok);
}
}
