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);
}
}
