Example #1
0
        private FlankingMassMatch GetBestMatchInTheGraph(ShiftedSequenceGraph seqGraph, ProductSpectrum spec, double?featureMass)
        {
            FlankingMassMatch match = null;
            var bestScore           = double.NegativeInfinity;
            var protCompositions    = seqGraph.GetSequenceCompositions();

            for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
            {
                seqGraph.SetSink(modIndex);
                var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
                var sequenceMass           = protCompositionWithH2O.Mass;
                if (featureMass != null && !_tolerance.IsWithin(sequenceMass, (double)featureMass))
                {
                    continue;
                }

                var charge =
                    (int)
                    Math.Round(sequenceMass /
                               (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));

                var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, charge,
                                                             Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);

                if (!spec.IsolationWindow.Contains(mostAbundantIsotopeMz))
                {
                    continue;
                }

                //var feature = new TargetFeature(sequenceMass, charge, spec.ScanNum);

                if (_featureFinder != null)
                {
                    var ms1Corr = _featureFinder.GetMs1EvidenceScore(spec.ScanNum, sequenceMass, charge);
                    if (ms1Corr < Ms1CorrThreshold)
                    {
                        continue;
                    }
                }

                var curScoreAndModifications = seqGraph.GetScoreAndModifications(_ms2Scorer);
                var curScore = curScoreAndModifications.Item1;
//                var curScore = seqGraph.GetFragmentScore(_ms2Scorer);
                if (curScore > bestScore)
                {
                    match = new FlankingMassMatch(curScore,
                                                  sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, curScoreAndModifications.Item2);
                    //match = new FlankingMassMatch(curScore,
                    //    sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, new ModificationInstance[0]);
                    bestScore = curScore;
                }
            }

            return(match);
        }
Example #2
0
        private FlankingMassMatch GetBestMatchInTheGraph(ShiftedSequenceGraph seqGraph, ProductSpectrum spec, double? featureMass)
        {
            FlankingMassMatch match = null;
            var bestScore = double.NegativeInfinity;
            var protCompositions = seqGraph.GetSequenceCompositions();
            for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
            {
                seqGraph.SetSink(modIndex);
                var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
                var sequenceMass = protCompositionWithH2O.Mass;
                if (featureMass != null && !_tolerance.IsWithin(sequenceMass, (double)featureMass)) continue;

                var charge =
                    (int)
                        Math.Round(sequenceMass /
                                   (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));

                var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, charge,
                    Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);

                if (!spec.IsolationWindow.Contains(mostAbundantIsotopeMz)) continue;

                //var feature = new TargetFeature(sequenceMass, charge, spec.ScanNum);
                
                if (_featureFinder != null)
                {
                    var ms1Corr = _featureFinder.GetMs1EvidenceScore(spec.ScanNum, sequenceMass, charge);
                    if (ms1Corr < Ms1CorrThreshold) continue;
                }

                var curScoreAndModifications = seqGraph.GetScoreAndModifications(_ms2Scorer);
                var curScore = curScoreAndModifications.Item1;
//                var curScore = seqGraph.GetFragmentScore(_ms2Scorer);
                if (curScore > bestScore)
                {
                    match = new FlankingMassMatch(curScore,
                        sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, curScoreAndModifications.Item2);
                    //match = new FlankingMassMatch(curScore,
                    //    sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, new ModificationInstance[0]);
                    bestScore = curScore;
                }
            }

            return match;
        }