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 CreateSequenceMassToMs2ScansMap(LcMsRun run, Tolerance tolerance, double minMass, double maxMass)
{
// Make a bin to scan numbers map without considering tolerance
var massBinToScanNumsMapNoTolerance = new Dictionary<int, List<int>>();
var minBinNum = GetBinNumber(minMass);
var maxBinNum = GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
IList<IntRange> scanRanges;
if (!_map.TryGetValue(binNum, out scanRanges)) continue;
var sequenceMass = GetMass(binNum);
var ms2ScanNums = new List<int>();
foreach (var scanRange in scanRanges)
{
for (var scanNum = scanRange.Min; scanNum <= scanRange.Max; scanNum++)
{
if (scanNum < run.MinLcScan || scanNum > run.MaxLcScan) continue;
if (run.GetMsLevel(scanNum) == 2)
{
var productSpec = run.GetSpectrum(scanNum) as ProductSpectrum;
if (productSpec == null) continue;
var isolationWindow = productSpec.IsolationWindow;
var isolationWindowTargetMz = isolationWindow.IsolationWindowTargetMz;
var charge = (int)Math.Round(sequenceMass / isolationWindowTargetMz);
var mz = Ion.GetIsotopeMz(sequenceMass, charge,
Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);
if (productSpec.IsolationWindow.Contains(mz)) ms2ScanNums.Add(scanNum);
}
}
}
ms2ScanNums.Sort();
massBinToScanNumsMapNoTolerance.Add(binNum, ms2ScanNums);
}
// Account for mass tolerance
_sequenceMassBinToScanNumsMap = new Dictionary<int, IEnumerable<int>>();
var sumScanNums = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var sequenceMass = GetMass(binNum);
var deltaMass = tolerance.GetToleranceAsDa(sequenceMass, 1);
var curMinBinNum = GetBinNumber(sequenceMass - deltaMass);
var curMaxBinNum = GetBinNumber(sequenceMass + deltaMass);
var ms2ScanNums = new HashSet<int>();
for (var curBinNum = curMinBinNum; curBinNum <= curMaxBinNum; curBinNum++)
{
if (curBinNum < minBinNum || curBinNum > maxBinNum) continue;
List<int> existingMs2ScanNums;
if (!massBinToScanNumsMapNoTolerance.TryGetValue(curBinNum, out existingMs2ScanNums)) continue;
foreach (var ms2ScanNum in existingMs2ScanNums)
{
ms2ScanNums.Add(ms2ScanNum);
}
}
_sequenceMassBinToScanNumsMap[binNum] = ms2ScanNums.ToArray();
sumScanNums += ms2ScanNums.Count;
}
Console.WriteLine("#MS/MS matches per sequence: {0}", sumScanNums / (float)(maxBinNum-minBinNum+1));
_map = null;
}
public bool RunSearch(double corrThreshold = 0.7, CancellationToken? cancellationToken = null, IProgress<ProgressData> progress = null)
{
// Get the Normalized spec file/folder path
SpecFilePath = MassSpecDataReaderFactory.NormalizeDatasetPath(SpecFilePath);
var prog = new Progress<ProgressData>();
var progData = new ProgressData(progress);
if (progress != null)
{
prog = new Progress<ProgressData>(p =>
{
progData.Status = p.Status;
progData.StatusInternal = p.StatusInternal;
progData.Report(p.Percent);
});
}
var sw = new Stopwatch();
var swAll = new Stopwatch();
swAll.Start();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
progData.Status = "Reading spectra file";
progData.StepRange(10.0);
sw.Start();
_run = PbfLcMsRun.GetLcMsRun(SpecFilePath, 0, 0, prog);
_ms2ScanNums = _run.GetScanNumbers(2).ToArray();
_isolationWindowTargetMz = new double[_run.MaxLcScan + 1];
foreach (var ms2Scan in _ms2ScanNums)
{
var ms2Spec = _run.GetSpectrum(ms2Scan) as ProductSpectrum;
if (ms2Spec == null) continue;
_isolationWindowTargetMz[ms2Scan] = ms2Spec.IsolationWindow.IsolationWindowTargetMz;
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(20.0);
ISequenceFilter ms1Filter;
if (this.ScanNumbers != null && this.ScanNumbers.Any())
{
ms1Filter = new SelectedMsMsFilter(this.ScanNumbers);
}
else if (string.IsNullOrWhiteSpace(FeatureFilePath))
{
// Checks whether SpecFileName.ms1ft exists
var ms1FtFilePath = MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, LcMsFeatureFinderLauncher.FileExtension);
if (!File.Exists(ms1FtFilePath))
{
Console.WriteLine(@"Running ProMex...");
sw.Start();
var param = new LcMsFeatureFinderInputParameter
{
InputPath = SpecFilePath,
MinSearchMass = MinSequenceMass,
MaxSearchMass = MaxSequenceMass,
MinSearchCharge = MinPrecursorIonCharge,
MaxSearchCharge = MaxPrecursorIonCharge,
CsvOutput = false,
ScoreReport = false,
LikelihoodScoreThreshold = -10
};
var featureFinder = new LcMsFeatureFinderLauncher(param);
featureFinder.Run();
}
sw.Reset();
sw.Start();
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, ms1FtFilePath, -10);
}
else
{
sw.Reset();
sw.Start();
var extension = Path.GetExtension(FeatureFilePath);
if (extension.ToLower().Equals(".csv"))
{
Console.Write(@"Reading ICR2LS/Decon2LS results...");
ms1Filter = new IsosFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else if (extension.ToLower().Equals(".ms1ft"))
{
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, FeatureFilePath, -10);
}
else if (extension.ToLower().Equals(".msalign"))
{
Console.Write(@"Reading MS-Align+ results...");
ms1Filter = new MsDeconvFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else ms1Filter = null; //new Ms1FeatureMatrix(_run);
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// pre-generate deconvoluted spectra for scoring
_massBinComparer = new FilteredProteinMassBinning(AminoAcidSet, MaxSequenceMass+1000);
_ms2ScorerFactory2 = new CompositeScorerFactory(_run, _massBinComparer, AminoAcidSet,
MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Reset();
Console.WriteLine(@"Generating deconvoluted spectra for MS/MS spectra...");
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
Parallel.ForEach(_ms2ScanNums, pfeOptions, ms2ScanNum =>
{
_ms2ScorerFactory2.DeconvonluteProductSpectrum(ms2ScanNum);
});
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(10.0);
progData.Status = "Reading Fasta File";
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
targetDb.Read();
// Generate sequence tags for all MS/MS spectra
if (TagBasedSearch)
{
progData.StepRange(25.0);
progData.Status = "Generating Sequence Tags";
sw.Reset();
Console.WriteLine(@"Generating sequence tags for MS/MS spectra...");
sw.Start();
var seqTagGen = GetSequenceTagGenerator();
_tagMs2ScanNum = seqTagGen.GetMs2ScanNumsContainingTags().ToArray();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
_tagSearchEngine = new ScanBasedTagSearchEngine(_run, seqTagGen, new LcMsPeakMatrix(_run, ms1Filter), targetDb, ProductIonTolerance, AminoAcidSet,
_ms2ScorerFactory2,
ScanBasedTagSearchEngine.DefaultMinMatchedTagLength,
MaxSequenceMass, MinProductIonCharge, MaxProductIonCharge);
}
var specFileName = MassSpecDataReaderFactory.RemoveExtension(Path.GetFileName(SpecFilePath));
var targetOutputFilePath = Path.Combine(OutputDir, specFileName + TargetFileNameEnding);
var decoyOutputFilePath = Path.Combine(OutputDir, specFileName + DecoyFileNameEnding);
var tdaOutputFilePath = Path.Combine(OutputDir, specFileName + TdaFileNameEnding);
progData.StepRange(60.0);
progData.Status = "Running Target search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
var targetMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
progData.MaxPercentage = 42.5;
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the target database");
sw.Start();
RunTagBasedSearch(targetMatches, targetDb, null, prog);
Console.WriteLine(@"Target database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 60.0;
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
RunSearch(targetMatches, targetDb, ms1Filter, null, prog);
Console.WriteLine(@"Target database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for target-spectrum matches");
sw.Start();
var bestTargetMatches = RunGeneratingFunction(targetMatches);
WriteResultsToFile(bestTargetMatches, targetOutputFilePath, targetDb);
sw.Stop();
Console.WriteLine(@"Target-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(95.0); // total to 95%
progData.Status = "Running Decoy search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
sw.Start();
var decoyDb = targetDb.Decoy(null, true);
Console.Write(@"Reading the decoy database...");
decoyDb.Read();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.MaxPercentage = 77.5;
var decoyMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the decoy database");
sw.Start();
RunTagBasedSearch(decoyMatches, decoyDb, null, prog);
Console.WriteLine(@"Decoy database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 95.0;
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
RunSearch(decoyMatches, decoyDb, ms1Filter, null, prog);
Console.WriteLine(@"Decoy database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for decoy-spectrum matches");
sw.Start();
var bestDecoyMatches = RunGeneratingFunction(decoyMatches);
WriteResultsToFile(bestDecoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
Console.WriteLine(@"Decoy-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(100.0);
progData.Status = "Writing combined results file";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
// Add "Qvalue" and "PepQValue"
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
progData.Report(100.0);
Console.WriteLine(@"Done.");
swAll.Stop();
Console.WriteLine(@"Total elapsed time for search: {0:f1} sec ({1:f2} min)", swAll.Elapsed.TotalSeconds, swAll.Elapsed.TotalMinutes);
return true;
}
private List<ProductSpectrum> GetMatchedSpectrums(LcMsRun run, IList<int> ms2List ,Tuple<int,double, double, double, double,double> feature, int fileIndex)
{
var spectrumList = new List<ProductSpectrum>();
var mass = feature.Item2;
var minElution = feature.Item3;
var maxElution = feature.Item4;
var featureId = feature.Item1 - 1;
var det = new Tuple<int, double, int>(-1, -1.0, -1);
for (var i = 0; i < ms2List.Count; i++)
{
var scanElutionTime = run.GetElutionTime(ms2List[i]);
if (scanElutionTime < minElution || scanElutionTime > maxElution) continue;
var spectrum = run.GetSpectrum(ms2List[i]) as ProductSpectrum;
var window = spectrum.IsolationWindow;
var minMz = window.MinMz - .5;
var maxMz = window.MaxMz + .5;
var mzTable = GetFeatureMassTable(mass);
for (var j = 0; j < mzTable.Length; j++)
{
var mz = mzTable[j];
if (mz < minMz || mz > maxMz) continue;
spectrumList.Add(spectrum);
if(!(det.Item1 > -1)) det = new Tuple<int, double, int>(ms2List[i],mz,j+2);
break;
}
_identifiedFeatures[featureId][fileIndex] = det;
}
return spectrumList;
}
private List<XYData> LoadSpectra(LcMsRun ipbReader, int scan)
{
var spec = ipbReader.GetSpectrum(scan);
if (spec.Peaks == null)
return new List<XYData>();
//var data = new List<XYData>(spec.Peaks.Length);
//for (var i = 0; i < spec.Peaks.Length; i++)
//{
// data.Add(new XYData(spec.Peaks[i].Mz, spec.Peaks[i].Intensity));
//}
//return data;
return spec.Peaks.Select(peak => new XYData(peak.Mz, peak.Intensity)).ToList();
}
private ScanSummary GetScanSummary(int scan, LcMsRun ipbReader)
{
var spec = ipbReader.GetSpectrum(scan, true);
var summary = new ScanSummary
{
MsLevel = spec.MsLevel,
Time = spec.ElutionTime,
Scan = spec.ScanNum,
//TotalIonCurrent = Convert.ToInt64(header.TotalIonCurrent), // Only used in PNNLOmics.Algorithms.Chromatograms.XicCreator.CreateXic(...)
TotalIonCurrent = spec.Peaks.Select(peak => (long)peak.Intensity).Sum(), // Only used in PNNLOmics.Algorithms.Chromatograms.XicCreator.CreateXic(...)
PrecursorMz = 0,
CollisionType = CollisionType.Other,
};
if (spec is ProductSpectrum)
{
var pspec = spec as ProductSpectrum;
if (pspec.IsolationWindow.MonoisotopicMass != null)
{
summary.PrecursorMz = pspec.IsolationWindow.MonoisotopicMass.Value;
}
switch (pspec.ActivationMethod)
{
case ActivationMethod.CID:
summary.CollisionType = CollisionType.Cid;
break;
case ActivationMethod.HCD:
summary.CollisionType = CollisionType.Hcd;
break;
case ActivationMethod.ETD:
summary.CollisionType = CollisionType.Etd;
break;
case ActivationMethod.ECD:
summary.CollisionType = CollisionType.Ecd;
break;
case ActivationMethod.PQD:
//summary.CollisionType = CollisionType.Hid; // HID? what is HID?
break;
}
}
return summary;
}
