public void GetIsoProfile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O() - Composition.Hydrogen;
//Console.WriteLine(neutral);
for (var charge = 22; charge <= 60; charge++)
{
var ion = new Ion(neutral, charge);
Console.WriteLine("{0}\t{1}", charge, ion.GetMostAbundantIsotopeMz());
}
var ion27 = new Ion(neutral, 29);
var isotopes = ion27.GetIsotopes(0.1);
foreach (var isotope in isotopes)
{
Console.WriteLine("{0}\t{1}", ion27.GetIsotopeMz(isotope.Index), isotope.Ratio);
}
}
public void TestBuildingReverseGraph()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string annotation = "_.MARTKQTARK._";
// Configure amino acid set
var methylK = new SearchModification(Modification.Methylation, 'K', SequenceLocation.Everywhere, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
methylK,
//pyroGluQ,
oxM
};
const int numMaxModsPerProtein = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
foreach (var composition in seqGraph.GetSequenceCompositions())
{
Console.WriteLine("{0}\t{1}", composition, composition.Mass);
}
}
public void TestBuildingSequenceGraphLongProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Configure amino acid set
const int numMaxModsPerProtein = 6;
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.ProteinNTerm, false);
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
pyroGluQ,
//dehydro,
//cysteinylC,
//glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
//const string protAnnotation = "A.HAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK.-";
//const string protAnnotation =
// "_.QQ._";
const string protAnnotation =
"_.MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAALRKLMMNHQ._";
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
var seqCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < seqCompositions.Length; modIndex++)
{
var seqComposition = seqCompositions[modIndex];
Console.WriteLine("SequenceComposition: {0}", seqComposition);
var compIndex = 0;
var compositions = seqGraph.GetFragmentCompositions(modIndex, 0).ToList();
foreach (var composition in compositions)
{
if (compIndex < 5 || compIndex >= compositions.Count - 5)
{
Console.WriteLine(" Seq: {0}, Frag: {1}", seqComposition, composition);
}
else if (compIndex == 5)
{
Console.WriteLine(" ...");
}
compIndex++;
}
}
}
public void TestSumIsoProfilesAcrossDifferentCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
//var spec = run.GetSpectrum(46452); // 635.37
var spec = run.GetSummedMs1Spectrum(46437, 46466);
var tolerance = new Tolerance(10);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O();
var theoProfile = neutral.GetIsotopomerEnvelopeRelativeIntensities();
var expProfile = new double[theoProfile.Length];
for (var charge = 22; charge <= 45; charge++)
{
var ion = new Ion(neutral, charge);
var isotopePeaks = spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null)
{
continue;
}
Assert.True(isotopePeaks.Length == theoProfile.Length);
for (var i = 0; i < isotopePeaks.Length; i++)
{
if (isotopePeaks[i] != null)
{
expProfile[i] += isotopePeaks[i].Intensity;
}
}
}
for (var i = 0; i < theoProfile.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", neutral.GetIsotopeMass(i), theoProfile[i], expProfile[i] / expProfile.Max());
}
Console.WriteLine("Corr: " + FitScoreCalculator.GetPearsonCorrelation(theoProfile, expProfile));
}
public IcScores GetScores(ProductSpectrum spec, string seqStr, Composition composition, int charge, int ms2ScanNum)
{
if (spec == null)
{
return(null);
}
var scorer = new CompositeScorer(spec, Tolerance, MinProductCharge, Math.Min(MaxProductCharge, charge), activationMethod: ActivationMethod);
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return(null);
}
var bestScore = double.NegativeInfinity;
Tuple <double, string> bestScoreAndModifications = null;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
if (!protCompositionWithH2O.Equals(composition))
{
continue;
}
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(scorer);
var curScore = curScoreAndModifications.Item1;
if (!(curScore > bestScore))
{
continue;
}
bestScoreAndModifications = curScoreAndModifications;
bestScore = curScore;
}
if (bestScoreAndModifications == null)
{
return(null);
}
var modifications = bestScoreAndModifications.Item2;
var seqObj = Sequence.CreateSequence(seqStr, modifications, AminoAcidSet);
double score;
int nMatchedFragments;
GetCompositeScores(seqObj, charge, ms2ScanNum, out score, out nMatchedFragments);
return(new IcScores(nMatchedFragments, score, modifications));
}
public void TestNumberOfProteoforms()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string annotation = "_.AMCMC._";
const string annotation = "_.MARTKQTARK._";
// Configure amino acid set
var methylK = new SearchModification(Modification.Methylation, 'K', SequenceLocation.Everywhere, false);
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
var methylC = new SearchModification(Modification.Methylation, 'C', SequenceLocation.Everywhere, true);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.PeptideNTerm, false);
var searchModifications = new List <SearchModification>
{
//carbamidomethylC,
//methylC,
methylK,
//pyroGluQ,
oxM,
//acetylN
};
const int numMaxModsPerProtein = 4;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
var protCompositions = seqGraph.GetSequenceCompositions();
var modCombs = seqGraph.GetModificationCombinations();
Console.WriteLine("\n#Protoeoforms by mod combinations: ");
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
Console.Write((modIndex == 0) ? "No modifications" : modCombs[modIndex].ToString());
Console.Write("\t");
Console.WriteLine("{0}", seqGraph.GetNumProteoformSequences(modIndex));
}
Console.WriteLine("\n#Protoeoforms by number of modificaionts: ");
for (var nMod = 0; nMod <= numMaxModsPerProtein; nMod++)
{
Console.Write("#modificaitons = {0}", nMod);
Console.Write("\t");
Console.WriteLine("{0}", seqGraph.GetNumProteoformSequencesByNumMods(nMod));
}
}
public void TestCreatingHistoneGraph()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int numMaxModsPerProtein = 11;
// Histone H4
const string annotation =
"_.MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG._";
// Histone H3.1
// const string annotation =
// "_.MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA._";
var acetylR = new SearchModification(Modification.Acetylation, 'R', SequenceLocation.Everywhere, false);
var acetylK = new SearchModification(Modification.Acetylation, 'K', SequenceLocation.Everywhere, false);
var methylR = new SearchModification(Modification.Methylation, 'R', SequenceLocation.Everywhere, false);
var methylK = new SearchModification(Modification.Methylation, 'K', SequenceLocation.Everywhere, false);
var diMethylR = new SearchModification(Modification.DiMethylation, 'R', SequenceLocation.Everywhere, false);
var diMethylK = new SearchModification(Modification.DiMethylation, 'K', SequenceLocation.Everywhere, false);
var triMethylR = new SearchModification(Modification.TriMethylation, 'R', SequenceLocation.Everywhere, 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 searchModifications = new List <SearchModification>
{
acetylR,
acetylK,
methylR,
methylK,
diMethylR,
diMethylK,
triMethylR,
phosphoS,
phosphoT,
phosphoY
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
var numFragCompositions = graph.GetNumFragmentCompositions();
var numProteoforms = graph.GetNumProteoformCompositions();
var numSeqCompositions = graph.GetNumProteoformCompositions();
Console.WriteLine("NumFragmentCompositions: " + numFragCompositions);
Console.WriteLine("NumProteoforms: " + numProteoforms);
Console.WriteLine("NumSequenceCompositions: " + numSeqCompositions);
}
public void TestGettingSequence()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string annotation = "_.AMCMC._";
const string annotation = "_.MARTKQTARK._";
// Configure amino acid set
var methylK = new SearchModification(Modification.Methylation, 'K', SequenceLocation.Everywhere, false);
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
var methylC = new SearchModification(Modification.Methylation, 'C', SequenceLocation.Everywhere, true);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.PeptideNTerm, false);
var searchModifications = new List <SearchModification>
{
//carbamidomethylC,
//methylC,
methylK,
//pyroGluQ,
oxM,
//acetylN
};
const int numMaxModsPerProtein = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var composition = protCompositions[modIndex];
Console.WriteLine("{0}\t{1}", composition, composition.Mass);
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(new DummyScorer());
if (curScoreAndModifications != null)
{
Console.WriteLine("Score: {0}, Modifications: {1}", curScoreAndModifications.Item1, curScoreAndModifications.Item2);
}
}
}
public IcScores GetIcScores(IInformedScorer informedScorer, IScorer scorer, string seqStr, Composition composition)
{
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return(null);
}
var bestScore = double.NegativeInfinity;
Tuple <double, string> bestScoreAndModifications = null;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
if (!protCompositionWithH2O.Equals(composition))
{
continue;
}
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(scorer);
var curScore = curScoreAndModifications.Item1;
if (!(curScore > bestScore))
{
continue;
}
bestScoreAndModifications = curScoreAndModifications;
bestScore = curScore;
}
if (bestScoreAndModifications == null)
{
return(null);
}
var modifications = bestScoreAndModifications.Item2;
var sequence = Sequence.CreateSequence(seqStr, modifications, this.AminoAcidSet);
var numMatchedFragments = informedScorer.GetNumMatchedFragments(sequence);
var score = informedScorer.GetUserVisibleScore(sequence);
return(new IcScores(numMatchedFragments, score, modifications));
}
public void TestGraphWithModifications()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string annotation = "_.MIALNKTPQTIVFYKPYGVLCQFTDNSAHPRPTLKDYINLPDLYPVGRLDQDSEGLLLLTSNGKLQHRLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADYPTRPAIAKIITEPDFPPRNPPIRYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLVRVQIQVTGRSPQQGKGKSAATWCLTLEGLSPGQWRPLTPWEENFCQQLLTGNPNGPWQKKFGDRR._";
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 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,
nitrosylC,
nethylmaleimideC,
oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
var seqCompositions = seqGraph.GetSequenceCompositions();
var modCombs = seqGraph.GetModificationCombinations();
Console.WriteLine("*** Before cleavage: {0}", seqCompositions.Length);
for (var modIndex = 0; modIndex < seqCompositions.Length; modIndex++)
{
var seqComposition = seqCompositions[modIndex];
Console.WriteLine("SequenceComposition: {0}, ModComb: {1}", seqComposition, modCombs[modIndex]);
}
seqGraph.CleaveNTerm();
seqCompositions = seqGraph.GetSequenceCompositions();
modCombs = seqGraph.GetModificationCombinations();
Console.WriteLine("*** After cleavage: {0}", seqCompositions.Length);
for (var modIndex = 0; modIndex < seqCompositions.Length; modIndex++)
{
var seqComposition = seqCompositions[modIndex];
Console.WriteLine("SequenceComposition: {0}, ModComb: {1}", seqComposition, modCombs[modIndex]);
}
}
public void TestSequenceGraph()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
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 oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var fixCarbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
var searchModifications = new List <SearchModification> {
phosPhoS, phosPhoT, phosPhoY, oxM, fixCarbamidomethylC
};
//var searchModifications = new List<SearchModification> { phosPhoT, fixCarbamidomethylC };
const int numMaxModsPepPeptide = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPepPeptide);
const string annotation = "_.STR._";
var pepSeq = annotation.Substring(2, annotation.Length - 4);
Console.WriteLine(aaSet.GetComposition(pepSeq));
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
Console.WriteLine(graph.GetUnmodifiedSequenceComposition());
Assert.AreEqual(graph.GetUnmodifiedSequenceComposition(), aaSet.GetComposition(pepSeq));
Console.WriteLine("Annotation Compositions:");
var index = -1;
foreach (var composition in graph.GetSequenceCompositions())
{
Console.WriteLine(++index + ": " + composition);
}
//const int seqIndex = 1;
//Console.WriteLine("Fragment Compositions (" + seqIndex +")");
//var scoringGraph = graph.GetScoringGraph(seqIndex);
//foreach (var composition in scoringGraph.GetCompositions())
//{
// Console.WriteLine(composition);
//}
}
public void TestPsm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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);
}
public void TestNTermMods()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string annotation = "_.QARTKQTARK._";
// Configure amino acid set
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.ProteinNTerm, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
acetylN,
pyroGluQ,
//oxM
};
const int numMaxModsPerProtein = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
//aaSet.Display();
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
foreach (var composition in seqGraph.GetSequenceCompositions())
{
Console.WriteLine("{0}\t{1}", composition, composition.Mass);
}
Console.WriteLine("*** Cleave N-term");
seqGraph.CleaveNTerm();
foreach (var composition in seqGraph.GetSequenceCompositions())
{
Console.WriteLine("{0}\t{1}", composition, composition.Mass);
}
}
public void TestSmartIsoWindowSumming()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O();
var ion = new Ion(neutral, 43);
var tolerance = new Tolerance(10);
const int targetMs2ScanNum = 46562;
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
var ms2Spec = run.GetSpectrum(targetMs2ScanNum) as ProductSpectrum;
Assert.True(ms2Spec != null);
var isoWindow = ms2Spec.IsolationWindow;
//var prevScanNum = run.GetPrevScanNum(targetMs2ScanNum, 1);
//var nextScanNum = run.GetNextScanNum(targetMs2ScanNum, 1);
var summedSpec = run.GetSummedMs1Spectrum(targetMs2ScanNum, 2.5);
//var windowSpec = summedSpec.GetPeakListWithin(isoWindow.MinMz, isoWindow.MaxMz);
Console.WriteLine("Corr: " + summedSpec.GetCorrScore(ion, tolerance));
}
private static void TestCountingPeptides()
{
var aaSet = new AminoAcidSet();
var sw = new Stopwatch();
sw.Start();
//const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002166_F86E3B2F.fasta";
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_003456_9B916A8B.fasta";
// const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_004208_295531A4.fasta";
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
indexedDb.Read();
//var numPeptides = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 150).LongCount();
var peptides =
indexedDb.AnnotationsAndOffsets(7, 40, 2, 2, Enzyme.Trypsin);
Parallel.ForEach(peptides, annotationAndOffset =>
//foreach(var annotationAndOffset in peptides)
{
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
}
)
;
// Console.WriteLine("NumPeptides: {0}", numPeptides);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"{0:f4} sec", sec);
}
public void ScorePeptides(string outputFilePath)
{
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Annotation\tCharge\tScanNum");
foreach (var annotation in PeptideEnumerator)
{
// annotation: pre + "." + peptide + "." + post (e.g. R.PEPTIDER.G)
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
foreach (var sequenceComposition in seqGraph.GetSequenceCompositions())
{
var peptideComposition = sequenceComposition + Composition.H2O;
for (var precursorCharge = MinCharge; precursorCharge <= MaxCharge; precursorCharge++)
{
var precursorIon = new Ion(peptideComposition, precursorCharge);
foreach (var scanNum in Run.GetFragmentationSpectraScanNums(precursorIon))
{
writer.WriteLine("{0}\t{1}\t{2}", annotation, precursorCharge, scanNum);
}
}
}
}
}
}
private void FindFeatures()
{
m_FeatureFinderBackgroundWorker.ReportProgress(0, "Finding 3-D Features for Precursor and Fragments");
var seqGraph = SequenceGraph.CreateGraph(m_aminoAcidSet, CurrentPeptide);
// var scoringGraph = seqGraph.GetScoringGraph(0);
// var precursorIon = scoringGraph.GetPrecursorIon(this.CurrentChargeState);
// var monoMz = precursorIon.GetMz();
var sequence = new Sequence(CurrentPeptide, m_aminoAcidSet);
var precursorIon = sequence.GetPrecursorIon(CurrentChargeState);
var monoMz = precursorIon.GetMonoIsotopicMz();
var uimfPointList = UimfUtil.GetXic(monoMz, CurrentTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var watershedPointList = WaterShedMapUtil.BuildWatershedMap(uimfPointList);
var smoother = new SavitzkyGolaySmoother(11, 2);
smoother.Smooth(ref watershedPointList);
FeatureList = FeatureDetection.DoWatershedAlgorithm(watershedPointList).ToList();
IsotopeFeaturesDictionary.Clear();
var precursorTargetList = CurrentChargeState == 2 ? new List <string> {
"-1", "0.5", "1", "1.5", "2", "3"
} : new List <string> {
"-1", "1", "2", "3"
};
foreach (var precursorTarget in precursorTargetList)
{
var targetMz = precursorIon.GetIsotopeMz(double.Parse(precursorTarget));
var isotopeUimfPointList = UimfUtil.GetXic(targetMz, CurrentTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var isotopeWatershedPointList = WaterShedMapUtil.BuildWatershedMap(isotopeUimfPointList);
var isotopeFeatures = FeatureDetection.DoWatershedAlgorithm(isotopeWatershedPointList).ToList();
IsotopeFeaturesDictionary.Add(precursorTarget, isotopeFeatures);
}
LcSlicePlot = new PlotModel();
ImsSlicePlot = new PlotModel();
FragmentFeaturesDictionary.Clear();
// var sequence = new Sequence(this.CurrentPeptide, m_aminoAcidSet);
var ionTypeDictionary = sequence.GetProductIons(m_ionTypeFactory.GetAllKnownIonTypes());
double fragmentCount = ionTypeDictionary.Count;
var index = 0;
foreach (var ionTypeKvp in ionTypeDictionary)
{
var ionTypeTuple = ionTypeKvp.Key;
var ion = ionTypeKvp.Value;
var fragmentMz = ion.GetMonoIsotopicMz();
uimfPointList = UimfUtil.GetXic(fragmentMz, CurrentTolerance, UIMFData.FrameType.MS2, DataReader.ToleranceType.PPM);
watershedPointList = WaterShedMapUtil.BuildWatershedMap(uimfPointList);
smoother.Smooth(ref watershedPointList);
var fragmentFeatureBlobList = FeatureDetection.DoWatershedAlgorithm(watershedPointList).ToList();
FragmentFeaturesDictionary.Add(ionTypeTuple, fragmentFeatureBlobList);
index++;
var progress = (int)((index / fragmentCount) * 100);
m_FeatureFinderBackgroundWorker.ReportProgress(progress);
}
OnPropertyChanged("FeatureList");
OnPropertyChanged("LcSlicePlot");
OnPropertyChanged("ImsSlicePlot");
}
public void TestGeneratingXicsOfAllCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var comparer = new MzComparerWithBinning(27);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O() - Composition.Hydrogen;
var proteinMass = neutral.Mass;
var isoEnv = Averagine.GetIsotopomerEnvelope(proteinMass);
const bool SHOW_ALL_SCANS = false;
var targetColIndex = 0;
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
{
Console.WriteLine("Charge\t" + string.Join("\t", run.GetScanNumbers(1)));
}
else
{
// Just display data for scan 161
Console.WriteLine("Charge\t161");
foreach (var scanNumber in run.GetScanNumbers(1))
{
if (scanNumber == 161)
{
break;
}
targetColIndex++;
}
}
#pragma warning restore 0162
const int minCharge = 2;
const int maxCharge = 60;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var ion = new Ion(neutral, charge);
var mostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex);
//var secondMostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex + 1);
var binNum = comparer.GetBinNumber(mostAbundantIsotopeMz);
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var xic = run.GetFullPrecursorIonExtractedIonChromatogram(mzStart, mzEnd);
Console.Write(charge + "\t");
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
{
Console.WriteLine(string.Join("\t", xic.Select(p => p.Intensity)));
}
else
{
Console.WriteLine(xic[targetColIndex].Intensity);
}
#pragma warning restore 0162
}
}
public void TestCorrMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(10);
var productIonTolerance = new Tolerance(10);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASAKHEDMYTAINELINKLERQLNKVQHKGEAR._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 9;
const int modIndex = 0;
const int ms2ScanNum = 3633;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
//var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var scorer = new CorrMatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(15);
var productIonTolerance = new Tolerance(15);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\protoapps\UserData\Jungkap\Joshua\testData\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 6;
const int modIndex = 0;
const int ms2ScanNum = 4448;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
} // true: target and decoy, false: target only, null: decoy only
public void QuickId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 1;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null)
{
continue;
}
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec.Peaks, minCharge, maxCharge, 2, 1.1, tolerance, corrThreshold);
if (deconvolutedPeaks == null)
{
continue;
}
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin)
{
massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f1} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine(@"Processing, {0} proteins done, {1:f1} sec elapsed",
numProteins,
sw.Elapsed.TotalSeconds);
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
continue;
}
for (var numNTermCleavage = 0; numNTermCleavage <= 1; numNTermCleavage++)
{
if (numNTermCleavage > 0)
{
seqGraph.CleaveNTerm();
}
var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin)
{
continue;
}
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
// prefix
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestScore[ms2ScanNum], bestProtein[ms2ScanNum] ?? "");
}
}
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);
}
}
public void Test43KProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 IcBottomUpScores GetScores(char pre, string sequence, char post, AminoAcid nTerm, AminoAcid cTerm, Composition composition, int charge, int ms2ScanNum)
{
ScoredSpectrum scoredSpectrum;
var index = GetChargetScanNumPairIndex(charge, ms2ScanNum);
if (!_scoredSpectra.TryGetValue(index, out scoredSpectrum))
{
var spec = Run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
return(null);
}
scoredSpectrum = new ScoredSpectrum(spec, _rankScorer, charge, composition.Mass, Tolerance);
_scoredSpectra.Add(index, scoredSpectrum);
}
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, nTerm, sequence, cTerm);
if (seqGraph == null)
{
return(null);
}
Tuple <double, string> scoreAndModifications = null;
var bestScore = double.NegativeInfinity;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
if (!protCompositionWithH2O.Equals(composition))
{
continue;
}
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(scoredSpectrum);
var curScore = curScoreAndModifications.Item1;
if (curScore > bestScore)
{
scoreAndModifications = curScoreAndModifications;
bestScore = curScore;
}
}
if (scoreAndModifications == null)
{
return(null);
}
var ms2Score = scoreAndModifications.Item1;
// TODO: This assumes enzyme is trypsin
const double probN = 0.99999;
const double probC = 0.99999;
const double sumAAProbabilities = 0.1;
var creditN = Math.Log(probN / sumAAProbabilities);
var penaltyN = Math.Log((1.0 - probN) / (1.0 - sumAAProbabilities));
var creditC = Math.Log(probC / sumAAProbabilities);
var penaltyC = Math.Log((1.0 - probC) / (1.0 - sumAAProbabilities));
if (pre == 'K' || pre == 'R' || pre == FastaDatabaseConstants.Delimiter || pre == '-')
{
ms2Score += creditN;
}
else
{
ms2Score += penaltyN;
}
var lastResidue = sequence[sequence.Length - 1];
if (lastResidue == 'K' || lastResidue == 'R' || post == FastaDatabaseConstants.Delimiter || post == '-')
{
ms2Score += creditC;
}
else
{
ms2Score += penaltyC;
}
var modifications = scoreAndModifications.Item2;
return(new IcBottomUpScores(ms2Score, modifications));
}
public void TestTopDownScoringForAllXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Search parameters
const int numNTermCleavages = 1; // 30
const int minLength = 7;
const int maxLength = 1000;
//const int minCharge = 5; // 3
//const int maxCharge = 15; // 67
const int numMaxModsPerProtein = 0; // 6
var precursorTolerance = new Tolerance(10);
const string dbFilePath = @"..\..\..\TestFiles\sprot.Ecoli.2012_07.fasta";
//const string dbFilePath = @"..\..\..\TestFiles\sprot.Ecoli.2012_07.icdecoy.KR.fasta";
//const string dbFilePath = @"..\..\..\TestFiles\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
// const string dbFilePath =
// @"C:\cygwin\home\kims336\Data\TopDown\ID_003558_56D73071.fasta";
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
Console.Write("Reading raw file...");
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
// Configure amino acid set
// var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.ProteinNTerm, false);
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
// var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var targetDb = new FastaDatabase(dbFilePath);
// targetDb.CreateDecoyDatabase(Enzyme.Trypsin);
// System.Environment.Exit(1);
var indexedDb = new IndexedDatabase(targetDb);
var numProteins = 0;
long totalProtCompositions = 0;
//long numXics = 0;
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
sw.Reset();
sw.Start();
Console.WriteLine("Generating XICs...");
foreach (var protAnnotationAndOffset in indexedDb.IntactSequenceAnnotationsAndOffsets(minLength, maxLength))
{
++numProteins;
//if (numProteins > 2000) break;
if (numProteins % 1000 == 0)
{
Console.WriteLine("Processed {0} proteins", numProteins);
}
//Console.WriteLine(protAnnotation);
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotationAndOffset.Annotation);
//Console.WriteLine(seqGraph.GetSequenceCompositions()[0]);
if (seqGraph == null)
{
continue;
}
for (var nTermCleavages = 0; nTermCleavages <= numNTermCleavages; nTermCleavages++)
{
if (nTermCleavages > 0)
{
seqGraph.CleaveNTerm();
}
var protCompositions = seqGraph.GetSequenceCompositions();
foreach (var protComposition in protCompositions)
{
totalProtCompositions++;
// Console.WriteLine(protComposition);
var scorer = new TopDownScorer(protComposition, run, precursorTolerance);
var score = scorer.GetScore();
Console.WriteLine(score);
}
}
}
sw.Stop();
Console.WriteLine("NumProteins: {0}", numProteins);
Console.WriteLine("NumProteinCompositions: {0}", totalProtCompositions);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
private void SearchForMatches(AnnotationAndOffset annotationAndOffset,
ISequenceFilter sequenceFilter, SortedSet <DatabaseSequenceSpectrumMatch>[] matches, int maxNumNTermCleavages, bool isDecoy, CancellationToken?cancellationToken = null)
{
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
//var protein = db.GetProteinName(offset);
var protSequence = annotation.Substring(2, annotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return; // No matches will be found without a sequence graph.
}
for (var numNTermCleavages = 0; numNTermCleavages <= maxNumNTermCleavages; 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;
if (sequenceMass < MinSequenceMass || sequenceMass > MaxSequenceMass)
{
continue;
}
var modCombinations = modCombs[modIndex];
var ms2ScanNums = this.ScanNumbers ?? sequenceFilter.GetMatchingMs2ScanNums(sequenceMass);
Parallel.ForEach(ms2ScanNums, pfeOptions, ms2ScanNum =>
{
if (ms2ScanNum > _ms2ScanNums.Last() || ms2ScanNum < _ms2ScanNums.First())
{
return;
}
var scorer = _ms2ScorerFactory2.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
var isoTargetMz = _isolationWindowTargetMz[ms2ScanNum];
if (!(isoTargetMz > 0))
{
return;
}
var charge = (int)Math.Round(sequenceMass / (isoTargetMz - Constants.Proton));
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];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, numNTermCleavages,
modCombinations, precursorIon, score, isDecoy);
AddMatch(matches, ms2ScanNum, prsm);
});
}
}
}
public void TestTopDownScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string protAnnotation = "A.AHAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK.";
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
//var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
//Console.WriteLine(aaSet.GetAminoAcid('C').GetComposition());
// Create a sequence graph
//var protSeq = protAnnotation.Substring(2, protAnnotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
// TopDownScorer.MaxCharge = 60;
// TopDownScorer.MinCharge = 3;
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
foreach (var protComposition in seqGraph.GetSequenceCompositions())
{
var mostAbundantIsotopeIndex = protComposition.GetMostAbundantIsotopeZeroBasedIndex();
Console.WriteLine("Composition\t{0}", protComposition);
Console.WriteLine("MostAbundantIsotopeIndex\t{0}", mostAbundantIsotopeIndex);
Console.WriteLine(new Ion(protComposition + Composition.H2O, 11).GetIsotopeMz(mostAbundantIsotopeIndex));
Console.WriteLine();
//for (var charge = TopDownScorer.MinCharge; charge <= TopDownScorer.MaxCharge; charge++)
//{
var scorer = new TopDownScorer(protComposition, run, precursorTolerance);
var score = scorer.GetScore();
Console.WriteLine(score);
//var precursorIon = new Ion(protComposition + Composition.H2O, charge);
//var xic = run.GetExtractedIonChromatogram(precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex), precursorTolerance);
//Console.WriteLine(xic[0].ScanNum + " " + xic[1].ScanNum);
//Console.WriteLine("ScanNum\t{0}", string.Join("\t", xic.Select(p => p.ScanNum.ToString())));
//Console.WriteLine("precursorCharge " + charge + "\t" + string.Join("\t", xic.Select(p => p.Intensity.ToString())));
// }
Console.WriteLine("\nCharge\tm/z");
for (var charge = 9; charge <= 18; charge++)
{
var precursorIon = new Ion(protComposition + Composition.H2O, charge);
Console.WriteLine("{0}\t{1}", charge, precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex));
}
}
// sw.Stop();
// Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestMsAlignPlusResults()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string msAlignPlusResultPath = @"C:\workspace\TopDown\E_coli_iscU_60_mock_MSAlign_ResultTable_sam.txt";
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var writer = new StreamWriter(msAlignPlusResultPath + ".txt");
var reader = new StreamReader(msAlignPlusResultPath);
string s;
while ((s = reader.ReadLine()) != null)
{
if (s.StartsWith("Data_file_name\t"))
{
writer.WriteLine(s + "\tScore");
continue;
}
var token = s.Split('\t');
var annotation = token[13];
// Console.WriteLine("***\t" + annotation);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
if (seqGraph == null)
{
writer.WriteLine(s + "\tN/A");
continue;
}
var protCompositions = seqGraph.GetSequenceCompositions();
var scorer = new TopDownScorer(protCompositions[0], run, precursorTolerance);
var score = scorer.GetScore();
writer.WriteLine(s + "\t" + score);
Console.WriteLine(score);
}
writer.Close();
reader.Close();
}
private SortedSet <DatabaseSequenceSpectrumMatch>[] RunSearch(IEnumerable <AnnotationAndOffset> annotationsAndOffsets, ISequenceFilter ms1Filter, bool isDecoy)
{
var sw = new Stopwatch();
var numPeptides = 0;
sw.Reset();
sw.Start();
var matches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1];
// TODO: N-term Met cleavage
foreach (var annotationAndOffset in annotationsAndOffsets)
{
++numPeptides;
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
if (numPeptides % 100000 == 0)
{
Console.Write(@"Processing {0}{1} peptides...", numPeptides,
numPeptides == 1 ? "st" : numPeptides == 2 ? "nd" : numPeptides == 3 ? "rd" : "th");
if (numPeptides != 0)
{
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
sw.Start();
}
}
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
if (seqGraph == null)
{
// Console.WriteLine("Ignoring illegal protein: {0}", annotation);
continue;
}
//var protCompositions = seqGraph.GetSequenceCompositions();
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 <= 2)
{
continue;
}
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = annotation.Substring(2, annotation.Length - 4);
var pre = annotation[0];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, 0, modCombinations,
precursorIon, score, isDecoy);
if (matches[ms2ScanNum] == null)
{
matches[ms2ScanNum] = new SortedSet <DatabaseSequenceSpectrumMatch> {
prsm
};
}
else // already exists
{
var existingMatches = matches[ms2ScanNum];
if (existingMatches.Count < NumMatchesPerSpectrum)
{
existingMatches.Add(prsm);
}
else
{
var minScore = existingMatches.Min.Score;
if (score > minScore)
{
existingMatches.Add(prsm);
existingMatches.Remove(existingMatches.Min);
}
}
}
}
}
}
return(matches);
}
