Spectral decon

mzLib/Chemistry/IsotopicDistribution.cs

@@ -56,7 +56,22 @@ private IsotopicDistribution(int count)
             intensities = new double[count];
         }
 
-        // Clone() produces shallow copies, but because double is a primitive type, this is acceptable
+        public double MostAbundantMass
+        {
+            get
+            {
+                double maxIntensity = intensities.Max();
+                for (int i = 0; i < masses.Length; i++)
+                {
+                    if (Math.Abs(intensities[i] - maxIntensity) < 0.0001)
+                    {
+                        return (masses[i]);
+                    }
+                }
+                return Double.NaN;
+            }
+        }
+        public double MonoIsotopicMass => masses[0];
         public double[] Masses => (double[]) masses.Clone();
         public double[] Intensities => (double[]) intensities.Clone();
 

mzLib/MassSpectrometry/Deconvolution/Algorithms/ClassicDeconvolutionAlgorithm.cs

@@ -26,7 +26,12 @@ public ClassicDeconvolutionAlgorithm(DeconvolutionParameters deconParameters) :
         /// <returns></returns>
         public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrumToDeconvolute)
         {
-            var deconParams = DeconvolutionParameters as ClassicDeconvolutionParameters ?? throw new MzLibException("Deconvolution params and algorithm do not match");
+            var deconParams = DeconvolutionParameters as ClassicDeconvolutionParameters;
+            if (deconParams == null)
+            {
+                throw new MzLibException("Deconvolution params and algorithm do not match");
+            }
+
             spectrum = spectrumToDeconvolute;
             //if no peaks, stop
             if (spectrum.Size == 0)
@@ -174,7 +179,9 @@ public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrumToD
             }
         }
 
-        private IsotopicEnvelope FindIsotopicEnvelope(int massIndex, double candidateForMostIntensePeakMz, double candidateForMostIntensePeakIntensity, double testMostIntenseMass, int chargeState, double deconvolutionTolerancePpm, double intensityRatioLimit, List<double> monoisotopicMassPredictions)
+        private IsotopicEnvelope FindIsotopicEnvelope(int massIndex, double candidateForMostIntensePeakMz, double candidateForMostIntensePeakIntensity,
+            double testMostIntenseMass, int chargeState, double deconvolutionTolerancePpm, double intensityRatioLimit,
+            List<double> monoisotopicMassPredictions)
         {
             double[] theoreticalMasses = allMasses[massIndex];
             double[] theoreticalIntensities = allIntensities[massIndex];
@@ -215,7 +222,9 @@ private IsotopicEnvelope FindIsotopicEnvelope(int massIndex, double candidateFor
             return new IsotopicEnvelope(listOfObservedPeaks, monoisotopicMass, chargeState, totalIntensity, Statistics.StandardDeviation(listOfRatios), massIndex);
         }
 
-        private int ObserveAdjacentChargeStates(IsotopicEnvelope originalEnvelope, double mostIntensePeakMz, int massIndex, double deconvolutionTolerancePpm, double intensityRatioLimit, double minChargeToLookFor, double maxChargeToLookFor, List<double> monoisotopicMassPredictions)
+        private int ObserveAdjacentChargeStates(IsotopicEnvelope originalEnvelope, double mostIntensePeakMz, int massIndex,
+            double deconvolutionTolerancePpm, double intensityRatioLimit, double minChargeToLookFor, double maxChargeToLookFor,
+            List<double> monoisotopicMassPredictions)
         {
             //look for the higher and lower charge states using the proposed mass
             int numAdjacentChargeStatesObserved = 0;
@@ -250,7 +259,8 @@ private int ObserveAdjacentChargeStates(IsotopicEnvelope originalEnvelope, doubl
             return numAdjacentChargeStatesObserved;
         }
 
-        private bool FindChargeStateOfMass(IsotopicEnvelope originalEnvelope, int zToInvestigate, double mostAbundantNeutralIsotopeToInvestigate, int massIndex, double deconvolutionTolerancePpm, double intensityRatioLimit, List<double> monoisotopicMassPredictions)
+        private bool FindChargeStateOfMass(IsotopicEnvelope originalEnvelope, int zToInvestigate, double mostAbundantNeutralIsotopeToInvestigate, int massIndex,
+            double deconvolutionTolerancePpm, double intensityRatioLimit, List<double> monoisotopicMassPredictions)
         {
             //we know the mass and the charge that we're looking for, just see if the expected m/z and its isotopes are there or not
             double mostAbundantIsotopeMzForThisZTheoretical = mostAbundantNeutralIsotopeToInvestigate.ToMz(zToInvestigate);

mzLib/MassSpectrometry/Deconvolution/Algorithms/SpectralDeconvolutionAlgorithm.cs

@@ -0,0 +1,281 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Chemistry;
+using Easy.Common.Extensions;
+using MassSpectrometry.Deconvolution;
+using MassSpectrometry.Deconvolution.Scoring;
+using Proteomics;
+using Proteomics.ProteolyticDigestion;
+using MzLibUtil;
+
+namespace MassSpectrometry.Deconvolution.Algorithms
+{
+    public class SpectralDeconvolutionAlgorithm : DeconvolutionAlgorithm
+    {
+        // TODO: Make a charge state envelope class, complete with "MostAbundantChargeState"
+        public Dictionary<PeptideWithSetModifications, List<IsotopicEnvelope>> EnvelopeDictionary { get; private set; }
+
+        // Consider defining this as a jagged array to increase performance
+        public List<MinimalSpectrum>[,] IndexedLibrarySpectra { get; private set; }
+        // SpectrumIndexToPwsmMap maps the location of each spectrum within IndexedLibrarySpectra to its respective PeptideWithSetMods and charge
+        public Dictionary<(int, int, int), PeptideWithSetModifications> SpectrumIndexToPwsmMap { get; private set; }
+        public int MaxThreads; // This should be in the Parameters abstract 
+        public SpectralDeconvolutionParameters SpectralParams { get; }
+        public PpmTolerance PpmTolerance { get; }
+        public Scorer Scorer { get; }
+
+        public SpectralDeconvolutionAlgorithm(DeconvolutionParameters parameters) : base(parameters)
+        {
+            var deconvolutionParameters = DeconvolutionParameters as SpectralDeconvolutionParameters;
+            if (deconvolutionParameters == null)
+            {
+                throw new MzLibException(
+                    "Improper Deconvolution Parameters were pass to the SpectralDeconvolutionAlgorithm");
+            }
+            else
+            {
+                SpectralParams = deconvolutionParameters;
+            }
+
+            PpmTolerance = new PpmTolerance(parameters.DeconvolutionTolerancePpm);
+
+            FindLibraryEnvelopes();
+            IndexEnvelopes();
+            Scorer = new Scorer(Scorer.ScoringMethods.SpectralContrastAngle, PpmTolerance);
+
+        }
+
+        public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum)
+        {
+
+            if (spectrum == null || spectrum.Size == 0)
+            {
+                yield break;
+            }
+
+            // For each charge state (key) store the indices corresponding to every potential isotopic envelope (value)
+            Dictionary<int, List<MinimalSpectrum>> potentialEnvelopes = FindPotentialEnvelopes(spectrum);
+
+            // iterate through charge states (potentially not necessary/performant. Could flatten)
+            foreach (var keyValuePair in potentialEnvelopes)
+            {
+                int chargeBinIndex = keyValuePair.Key - SpectralParams.MinAssumedChargeState;
+                // iterate through potential envelopes
+                foreach (var experimentalSpectrum in keyValuePair.Value)
+                {
+                    double mostAbundantMz =  experimentalSpectrum.MostAbundantMz;
+                    int massBinIndex = (int)Math.Floor((mostAbundantMz - SpectralParams.ScanRange.Minimum) *
+                                                   SpectralParams.BinsPerDalton);
+                    if (!IndexedLibrarySpectra[massBinIndex, chargeBinIndex].IsNotNullOrEmpty()) continue; // continue if there are no corresponding library spectra
+
+                    int? bestMatchListPosition = null;
+                    int currentListPosition = 0;
+                    double bestFoundScore = Scorer.PoorScore;
+                    // Score against matching theoretical envelopes
+                    foreach (MinimalSpectrum theoreticalSpectrum in IndexedLibrarySpectra[massBinIndex, chargeBinIndex])
+                    {
+                        // TODO: Rename to FindBestScore
+                        if (Scorer.TestForScoreImprovement(
+                                Scorer.Score(experimentalSpectrum,theoreticalSpectrum),
+                                bestFoundScore,
+                                out double betterScore)
+                            )
+                        {
+                            bestMatchListPosition = currentListPosition;
+                            bestFoundScore = betterScore;
+                        }
+                        currentListPosition++;
+                    }
+
+                    if (bestMatchListPosition.HasValue && 
+                        SpectrumIndexToPwsmMap.TryGetValue((massBinIndex, chargeBinIndex, (int)bestMatchListPosition), out var pwsmMatch))
+                    {
+                        yield return new IsotopicEnvelope(experimentalSpectrum, pwsmMatch, bestFoundScore);
+                    }
+                    else
+                    {
+                        //TODO: Add some averagine bullshit here
+                    }
+
+                }
+            }
+        }
+
+        /// <summary>
+        /// Populates the EnvelopeDictionary by digesting each protein in the parameters into PeptideWithSetMods,
+        /// then calculating an isotopic envelope for each charge state from min to max assumed charge state
+        /// </summary>
+        private void FindLibraryEnvelopes()
+        {
+            EnvelopeDictionary = new();
+
+
+            //TODO: Parallelize this section of the code
+            foreach (Protein protein in SpectralParams.Proteins)
+            {
+                // I'm not sure if calling protein.Digest within the foreach statement would call the method anew for every loop
+                IEnumerable<PeptideWithSetModifications> uniquePeptides = protein.Digest(
+                    SpectralParams.DigestionParams, SpectralParams.FixedModifications,
+                    SpectralParams.VariableModifications, SpectralParams.SilacLabels,
+                    topDownTruncationSearch: SpectralParams.FindTopDownTruncationProducts);
+
+                foreach (PeptideWithSetModifications pwsm in uniquePeptides)
+                {
+                    EnvelopeDictionary.Add(pwsm, new List<IsotopicEnvelope>());
+                    IsotopicDistribution pwsmDistribution = IsotopicDistribution.GetDistribution(pwsm.FullChemicalFormula,
+                        fineResolution: SpectralParams.FineResolutionForIsotopicDistribution,
+                        minProbability: SpectralParams.MinProbabilityForIsotopicDistribution);
+
+                    // iterates through all possible charge states, from largest to smallest.
+                    // Any isotopic envelope whose most abundant peak would fall within the scan range is written to the envelope dictionary
+                    // Once the mass to charge ratio of the most abundant peak is greater than the scan range maximum, the loop breaks
+                    for (int charge = SpectralParams.MaxAssumedChargeState;
+                         charge >= SpectralParams.MinAssumedChargeState;
+                         charge--)
+                    {
+                        double theoreticalMz = pwsm.MostAbundantMass.ToMz(charge);
+                        if (SpectralParams.ScanRange.Contains(theoreticalMz))
+                        {
+                            EnvelopeDictionary[pwsm].Add(new 
+                                IsotopicEnvelope(pwsmDistribution, charge, SpectralParams.AmbiguityThresholdForIsotopicDistribution));
+                        }
+                        else if (SpectralParams.ScanRange.CompareTo(theoreticalMz) < 0)
+                        {
+                            break;
+                        }
+                    }
+                }
+
+            }
+        }
+
+        /// <summary>
+        /// For each envelope in Envelope Dictionary, indexes it according to mass and charge,
+        /// resulting in a 2D array of lists of minimal spectra
+        /// </summary>
+        private void IndexEnvelopes()
+        {
+
+            int numberOfBinsForIndexing = (int) (SpectralParams.ScanRange.Width * SpectralParams.BinsPerDalton).Ceiling(0);
+            IndexedLibrarySpectra = new List<MinimalSpectrum>[numberOfBinsForIndexing,
+                SpectralParams.MaxAssumedChargeState + 1 - SpectralParams.MinAssumedChargeState];
+            SpectrumIndexToPwsmMap = new();
+
+            foreach (var keyValuePair in EnvelopeDictionary)
+            {
+                foreach (IsotopicEnvelope envelope in keyValuePair.Value)
+                {
+                    int massBinIndex = (int)Math.Floor((envelope.MostAbundantObservedIsotopicMz - SpectralParams.ScanRange.Minimum) * 
+                                                     SpectralParams.BinsPerDalton);
+                    int chargeBinIndex = envelope.Charge - SpectralParams.MinAssumedChargeState;
+                    if (IndexedLibrarySpectra[massBinIndex, chargeBinIndex] == null)
+                    {
+                        IndexedLibrarySpectra[massBinIndex, chargeBinIndex] = new();
+                    }
+                    MinimalSpectrum envelopeMinimalSpectrum = new MinimalSpectrum(envelope.MzArray, envelope.IntensityArray, envelope.Charge);
+                    IndexedLibrarySpectra[massBinIndex, chargeBinIndex].Add(envelopeMinimalSpectrum);
+                    SpectrumIndexToPwsmMap.Add(
+                        (massBinIndex, chargeBinIndex, IndexedLibrarySpectra[massBinIndex, chargeBinIndex].Count - 1), // tuple consisting of bin index (mass, charge) and list position of MinimalSpectrum object
+                        keyValuePair.Key // tuple consisting of PeptideWithSetMods and charge state
+                        );
+
+                    // In situations where the most abundant isotope frequency is close to the second most abundant isotope's frequency
+                    // ( ratio >= IsotopicEnvelope.AmbiguityRatioMinimum), 
+                    // The Spectrum is stored in the index of the second most abundant isotope as well
+                    if(envelope.SecondMostAbundantObservedIsotopicMz > 0 )
+                    {
+                        // Ceiling or floor????
+                        int secondBinIndex = (int)Math.Floor( 
+                            ((double)envelope.SecondMostAbundantObservedIsotopicMz - SpectralParams.ScanRange.Minimum ) * SpectralParams.BinsPerDalton);
+                        if (secondBinIndex != massBinIndex)
+                        {
+                            if (IndexedLibrarySpectra[secondBinIndex, chargeBinIndex] == null) IndexedLibrarySpectra[secondBinIndex, chargeBinIndex] = new();
+                            IndexedLibrarySpectra[secondBinIndex, chargeBinIndex].Add(envelopeMinimalSpectrum);
+                            SpectrumIndexToPwsmMap.Add(
+                                (secondBinIndex, chargeBinIndex, IndexedLibrarySpectra[secondBinIndex, chargeBinIndex].Count - 1),
+                                keyValuePair.Key
+                            );
+                        }
+                    }
+                }
+            }
+        }
+
+        /// <summary>
+        /// Iterates through all peaks in a spectrum to find all potential isotopic envelopes.
+        /// It does this by examining the spacing of peaks in the m/z domain
+        /// e.g. for charge of 2, a peak at 200 m/z would result in a search for a peak at 200.5 and 201 m/z
+        ///      if either is found, the process continues until SpectralParams.MaxConsecutiveMissedIsotopicPeaks number of consecutive
+        ///      isotope peaks are missed
+        /// Anything consistent with an isotopic envelope in a given charge state is stored in the dictionary
+        /// </summary>
+        /// <param name="spectrum"></param>
+        /// <returns></returns>
+        private Dictionary<int, List<MinimalSpectrum>> FindPotentialEnvelopes(MzSpectrum spectrum)
+        {
+
+            // For each charge state (key) store the indices corresponding to every potential isotopic envelope (value)
+            Dictionary<int, List<MinimalSpectrum>> potentialEnvelopes = new();
+
+            for (int charge = SpectralParams.MinAssumedChargeState; charge <= SpectralParams.MaxAssumedChargeState; charge++)
+            {
+                List<int> indicesOfKnownPeaks = new();
+
+                // Spectrum Search Loop
+                for (int i = 0; i < spectrum.Size; i++)
+                {
+                    if (indicesOfKnownPeaks.Contains(i))
+                    {
+                        continue;
+                    }
+                    List<int> envelopeIndices = new();
+                    envelopeIndices.Add(i);
+
+                    // Envelope Search Loop
+                    for (int j = i + 1; j < spectrum.Size; j++)
+                    {
+                        if (PpmTolerance.Within(spectrum.XArray[j],
+                                spectrum.XArray[envelopeIndices.Last()] + Constants.C13MinusC12 / charge))
+                        {
+                            envelopeIndices.Add(j);
+                        }
+                        else if (spectrum.XArray[j] > PpmTolerance.GetMaximumValue(spectrum.XArray[envelopeIndices.Last()] +
+                                     (1 + SpectralParams.MaxConsecutiveMissedIsotopicPeaks) * Constants.C13MinusC12 / charge))
+                        {
+                            // exit the Envelope loop if we missed more consecutive isotopic peaks than were allowed
+                            break;
+                        }
+                    }
+
+                    // Convert to MinimalSpectrum here? Write helper function to do so?
+                    if (envelopeIndices.Count > 1)
+                    {
+                        if (!potentialEnvelopes.ContainsKey(charge)) potentialEnvelopes.Add(charge, new());
+                        potentialEnvelopes[charge].Add(GetMinimalSpectrumFromIndices(spectrum, envelopeIndices, charge));
+                        indicesOfKnownPeaks.AddRange(envelopeIndices);
+                    }
+                }
+            }
+
+            return potentialEnvelopes;
+        }
+
+
+        private static MinimalSpectrum GetMinimalSpectrumFromIndices(MzSpectrum spectrum, List<int> indices, int charge = 0)
+        {
+            double[] mzArray = new double[indices.Count];
+            double[] intensityArray = new double[indices.Count];
+            for (int i = 0; i < indices.Count; i++)
+            {
+                mzArray[i] = spectrum.XArray[indices[i]];
+                intensityArray[i] = spectrum.YArray[indices[i]];
+            }
+
+            return new MinimalSpectrum(mzArray, intensityArray, charge);
+        }
+
+    }
+}