public IEnumerable <int> GetMatchingMs2ScanNums(double sequenceMass)
{
var sequenceMassBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(sequenceMass);
IList <int> ms2ScanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(sequenceMassBinNum, out ms2ScanNums))
{
return(ms2ScanNums);
}
ms2ScanNums = new List <int>();
var averagineEnvelope = Averagine.GetIsotopomerEnvelope(sequenceMass);
var mostAbundantIsotopeIndex = averagineEnvelope.MostAbundantIsotopeIndex;
for (var precursorCharge = _minCharge; precursorCharge <= _maxCharge; precursorCharge++)
{
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, precursorCharge, mostAbundantIsotopeIndex);
var binNumber = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(mostAbundantIsotopeMz);
IList <ChargeAndScanNum> chargeAndScanNumList;
if (!_mostAbundantIsotopeMzIndexToChargeAndScanNums.TryGetValue(binNumber, out chargeAndScanNumList))
{
continue;
}
foreach (var chargeAndScanNum in chargeAndScanNumList)
{
if (chargeAndScanNum.Charge == precursorCharge)
{
ms2ScanNums.Add(chargeAndScanNum.ScanNum);
}
}
}
_sequenceMassBinToScanNumsMap.Add(sequenceMassBinNum, ms2ScanNums);
return(ms2ScanNums);
}
public void TestPsm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const char pre = 'R';
const string sequence = "LENWPPASLADDL";
const char post = 'A';
const string annotation = "R.LENWPPASLADDL._";
const int charge = 2;
const int ms2ScanNum = 25534;
var aaSet = new AminoAcidSet();
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 2, 10, 0, 1.1);
ms2Scorer.DeconvoluteAllProductSpectra();
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
graph.SetSink(0);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedBottomUpScorer(run, aaSet, 1, 15, new Tolerance(10));
var refinedScore = informedScorer.GetScores(pre, sequence, post, composition, charge, ms2ScanNum);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
internal DeisotopedPeak(double monoIsotopicMass, int charge, double score)
{
MonoIsotopicMass = monoIsotopicMass;
MonoIsotopicMassIndex = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(MonoIsotopicMass);
Charge = charge;
Score = score;
}
public FeatureBasedTagSearchEngine(
LcMsRun run,
Ms1FtParser featureParser,
ProductScorerBasedOnDeconvolutedSpectra ms2Scorer,
SequenceTagParser tagParser,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
{
_run = run;
_ms2Scorer = ms2Scorer;
_featureParser = featureParser;
_ms1FtFilter = new Ms1FtFilter(run, tolerance, featureParser.Ms1FtFileName);
_tagParser = tagParser;
_fastaDb = fastaDb;
_searchableDb = new SearchableDatabase(fastaDb);
_tolerance = tolerance;
_aaSet = aaSet;
_maxSequenceMass = maxSequenceMass;
_minProductIonCharge = minProductIonCharge;
_maxProductIonCharge = maxProductIonCharge;
}
public IEnumerable <int> GetMatchingMs2ScanNums(double sequenceMass)
{
var sequenceMassBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(sequenceMass);
IList <int> ms2ScanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(sequenceMassBinNum, out ms2ScanNums))
{
return(ms2ScanNums);
}
return(new int[0]);
}
private readonly Dictionary <int, IList <int> > _sequenceMassBinToScanNumsMap; // mass -> scan numbers
private void PrecomputePossibleSequenceMasses()
{
var ms2ScanNums = _run.GetScanNumbers(2);
foreach (var ms2ScanNum in ms2ScanNums)
{
var possibleSequenceMasses = GetPossibleSequenceMasses(ms2ScanNum);
var binNumHash = new HashSet <int>();
foreach (var sequenceMass in possibleSequenceMasses)
{
var dMass = sequenceMass * _ppmTolerance * 1e-6;
var minMass = sequenceMass - dMass;
var maxMass = sequenceMass + dMass;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (!binNumHash.Add(binNum))
{
continue;
}
IList <int> scanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(binNum, out scanNums))
{
scanNums.Add(ms2ScanNum);
}
else
{
scanNums = new List <int> {
ms2ScanNum
};
_sequenceMassBinToScanNumsMap.Add(binNum, scanNums);
}
}
}
}
}
private void PrecomputeMostAbundantMzToMatches()
{
var ms2ScanNums = _run.GetScanNumbers(2);
_mostAbundantIsotopeMzIndexToChargeAndScanNums = new Dictionary <int, IList <ChargeAndScanNum> >();
foreach (var ms2ScanNum in ms2ScanNums)
{
var possibleSequenceMatches = GetPossibleSequenceMatches(ms2ScanNum);
foreach (var match in possibleSequenceMatches)
{
var mostAbundantIsotopeMz = match.MostAbundantIsotopeMz;
var charge = match.Charge;
var deltaMz = mostAbundantIsotopeMz * _ppmTolerance * 1e-6;
var minMz = mostAbundantIsotopeMz - deltaMz;
var maxMz = mostAbundantIsotopeMz + deltaMz;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minMz);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxMz);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
IList <ChargeAndScanNum> chargeAndScanNums;
if (_mostAbundantIsotopeMzIndexToChargeAndScanNums.TryGetValue(binNum,
out chargeAndScanNums))
{
chargeAndScanNums.Add(new ChargeAndScanNum(charge, ms2ScanNum));
}
else
{
chargeAndScanNums = new List <ChargeAndScanNum> {
new ChargeAndScanNum(charge, ms2ScanNum)
};
_mostAbundantIsotopeMzIndexToChargeAndScanNums.Add(binNum, chargeAndScanNums);
}
}
}
}
}
public bool RunSearch(double corrThreshold)
{
var sw = new Stopwatch();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
sw.Start();
_run = InMemoryLcMsRun.GetLcMsRun(SpecFilePath, 1.4826, 1.4826);
_bottomUpScorer = new InformedBottomUpScorer(_run, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Determining precursor masses...");
sw.Start();
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(_run, PrecursorIonTolerance, MinPrecursorIonCharge, MaxPrecursorIonCharge,
400, 5000, corrThreshold, 0, 0);
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Deconvoluting MS2 spectra...");
sw.Start();
_ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(
_run,
MinProductIonCharge, MaxProductIonCharge,
new Tolerance(10),
0
);
_ms2ScorerFactory.DeconvoluteAllProductSpectra();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
// string dirName = OutputDir ?? Path.GetDirectoryName(SpecFilePath);
var baseName = Path.GetFileNameWithoutExtension(SpecFilePath);
var targetOutputFilePath = Path.Combine(OutputDir, baseName + TargetFileExtension);
var decoyOutputFilePath = Path.Combine(OutputDir, baseName + DecoyFileExtension);
var tdaOutputFilePath = Path.Combine(OutputDir, baseName + TdaFileExtension);
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
var targetMatches = RunSearch(GetAnnotationsAndOffsets(targetDb), ms1Filter, false);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Target database search elapsed time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing target results...");
sw.Start();
WriteResultsToFile(targetMatches, targetOutputFilePath, targetDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
Console.Write(@"Reading the decoy database...");
sw.Start();
var decoyDb = targetDb.Decoy(Enzyme);
decoyDb.Read();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
var decoyMatches = RunSearch(GetAnnotationsAndOffsets(decoyDb), ms1Filter, true);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Decoy database search elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing decoy results...");
sw.Start();
WriteResultsToFile(decoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
Console.WriteLine(@"Done");
return true;
}
public void TestMs2Caching()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
//const int minPrecursorIonCharge = 3; // 3
//const int maxPrecursorIonCharge = 30;// 67
//const int minProductIonCharge = 1;
//const int maxProductIonCharge = 10;
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var runCache = new ProductScorerBasedOnDeconvolutedSpectra(run);
runCache.DeconvoluteAllProductSpectra();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void Test43KProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Configure amino acid set
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false);
var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C',
SequenceLocation.ProteinNTerm, false);
var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false);
var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false);
var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false);
var nitrosylC = new SearchModification(Modification.Nitrosyl, 'C', SequenceLocation.Everywhere, false);
var nethylmaleimideC = new SearchModification(Modification.Nethylmaleimide, 'C', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
glutathioneC,
oxM,
dethiomethylM,
acetylN,
//phosphoS,
//phosphoT,
//phosphoY,
deamidatedN,
// deamidatedQ,
glutathioneC,
pyroCarbamidomethylC,
nitrosylC,
nethylmaleimideC
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
// var aaSet = new AminoAcidSet();
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(aaSet, AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null) return;
var ms1Filter = new SimpleMs1Filter();
var ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(run);
foreach(var ms2ScanNum in Ms2ScanNums) ms2ScorerFactory.GetScorer(ms2ScanNum);
for (var numNTermCleavages = 0; numNTermCleavages <= 0; numNTermCleavages++)
{
if (numNTermCleavages > 0) seqGraph.CleaveNTerm();
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
var modCombinations = modCombs[modIndex];
foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass))
{
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null) continue;
var charge =
(int)
Math.Round(sequenceMass /
(spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var scorer = ms2ScorerFactory.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
if (score <= 3) continue;
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = protSequence.Substring(numNTermCleavages);
var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1];
var post = annotation[annotation.Length - 1];
Console.WriteLine("{0}.{1}.{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", pre, sequence, post, ms2ScanNum, modCombinations,
precursorIon.GetMostAbundantIsotopeMz(), precursorIon.Charge, precursorIon.Composition.Mass, score);
}
}
}
}
public void TestPrSm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownYufeng\raw\yufeng_column_test2.raw";
//const string annotation =
// "_.MKTKLSVLSAAMLAATLTMMPAVSQAAIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVG" +
// "LHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTV" +
// "TSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVG" +
// "IGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGS" +
// "AAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEA" +
// "NQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDL" +
// "KSLKELLKDQEGAVALKIVRGKSMLYLVLR._";
//var aaSet = new AminoAcidSet();
//const int charge = 60;
//const int ms2ScanNum = 46661;
const string specFilePath = @"D:\Research\Data\Jon\AH_SF_mouseliver_3-1_Intact_2_6Feb14_Bane_PL011402.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const int ms2ScanNum = 19011;
const int charge = 7;
const string annotation = "_.SKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVGSC._";
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, true);
var modVal = Modification.RegisterAndGetModification("AddVal", new Composition(5, 9, 1, 1, 0));
var searchMods = AminoAcid.StandardAminoAcidCharacters.Select(residue => new SearchModification(modVal, residue, SequenceLocation.Everywhere, false)).ToList();
searchMods.Add(acetylN);
const int numMaxModsPerProtein = 1;
var aaSet = new AminoAcidSet(searchMods, numMaxModsPerProtein);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
Console.WriteLine("NumProteoforms: " + graph.GetNumProteoformCompositions());
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 15);
ms2Scorer.GetScorer(ms2ScanNum);
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
Assert.NotNull(scorer, "Scorer is null!");
for (var i = 0; i < graph.GetNumProteoformCompositions(); i++)
{
graph.SetSink(i);
Console.WriteLine("ModComb: " + graph.GetModificationCombinations()[i]);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 30, new Tolerance(10));
var refinedScore = informedScorer.GetScores(AminoAcid.ProteinNTerm, SimpleStringProcessing.GetStringBetweenDots(annotation), AminoAcid.ProteinCTerm, composition, charge, ms2ScanNum);
Console.WriteLine("Modifications: {0}", refinedScore.Modifications);
Console.WriteLine("Composition: {0}", composition);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
}
