public void CreateTargetList()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string databaseFilePath = @"D:\Research\Data\IPRG2014\database\SpikedInPeptides.fasta";
if (!File.Exists(databaseFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, databaseFilePath);
}
var database = new FastaDatabase(databaseFilePath);
database.Read();
var indexedDatabase = new IndexedDatabase(database);
var numTargets = 0;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
Console.WriteLine("Peptide\tFormula\tProtein");
foreach (var annotationAndOffset in indexedDatabase.AnnotationsAndOffsets(6, 30, 1, 1, Enzyme.Trypsin))
{
var annotation = annotationAndOffset.Annotation;
var peptide = annotation.Substring(2, annotation.Length - 4);
var offset = annotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}", peptide, (aaSet.GetComposition(peptide) + Composition.H2O).ToPlainString(), database.GetProteinName(offset));
numTargets++;
}
Console.WriteLine("NumTargets: {0}", numTargets);
}
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 TestNominalMassErrors()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const int minLength = 300;
const int maxLength = 400;
var sw = new System.Diagnostics.Stopwatch();
var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\ID_003962_71E1A1D4.fasta"));
var db = new FastaDatabase(fastaFile.FullName);
db.Read();
var indexedDb = new IndexedDatabase(db);
var numSequences = 0L;
sw.Start();
var hist = new long[11];
var aaSet = new AminoAcidSet();
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsetsNoEnzyme(minLength, maxLength))
{
++numSequences;
var annotation = peptideAnnotationAndOffset.Annotation;
var sequenceStr = annotation.Substring(2, annotation.Length - 4);
var sequenceComp = aaSet.GetComposition(sequenceStr);
var mass = sequenceComp.Mass;
var nominalMass = sequenceComp.NominalMass;
var error = (int)Math.Round(mass * Constants.RescalingConstant) - nominalMass;
var errorBin = error + hist.Length / 2;
if (errorBin < 0)
{
errorBin = 0;
}
if (errorBin >= hist.Length)
{
errorBin = hist.Length - 1;
}
hist[errorBin]++;
}
Console.WriteLine("NumSequences: {0}", numSequences);
for (var i = 0; i < hist.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", i - hist.Length / 2, hist[i], hist[i] / (double)numSequences);
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestNominalMassErrors()
{
const int minLength = 300;
const int maxLength = 400;
var sw = new System.Diagnostics.Stopwatch();
// const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
const string dbFile = @"C:\cygwin\home\kims336\Data\TopDownJia\database\ID_003962_71E1A1D4.fasta";
//const string dbFile = @"C:\cygwin\home\kims336\Data\TopDownJia\database\TargetProteins.fasta";
var db = new FastaDatabase(dbFile);
db.Read();
var indexedDb = new IndexedDatabase(db);
var numSequences = 0L;
sw.Start();
var hist = new long[11];
var aaSet = new AminoAcidSet();
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsetsNoEnzyme(minLength, maxLength))
{
++numSequences;
var annotation = peptideAnnotationAndOffset.Annotation;
var sequenceStr = annotation.Substring(2, annotation.Length - 4);
var sequenceComp = aaSet.GetComposition(sequenceStr);
var mass = sequenceComp.Mass;
var nominalMass = sequenceComp.NominalMass;
var error = (int)Math.Round(mass * Constants.RescalingConstant) - nominalMass;
var errorBin = error + hist.Length / 2;
if (errorBin < 0)
{
errorBin = 0;
}
if (errorBin >= hist.Length)
{
errorBin = hist.Length - 1;
}
hist[errorBin]++;
}
Console.WriteLine("NumSequences: {0}", numSequences);
for (var i = 0; i < hist.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", i - hist.Length / 2, hist[i], hist[i] / (double)numSequences);
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void ComputeSpikedInPeptideMzHist()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pepListFile = @"C:\cygwin\home\kims336\Data\DIA\SpikedPeptides.txt";
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var charges = new[] { 2 };
var hist = new int[4];
var sum = 0;
Console.WriteLine("Peptide\tCharge\tMz");
foreach (var line in File.ReadLines(pepListFile))
{
if (line.Length == 0)
{
continue;
}
var peptide = line;
var composition = aaSet.GetComposition(peptide) + Composition.H2O;
foreach (var charge in charges)
{
var precursorIon = new Ion(composition, charge);
var precursorIonMz = precursorIon.GetMonoIsotopicMz();
if (precursorIonMz < 400 || precursorIonMz >= 900)
{
continue;
}
var histIndex = (int)((precursorIonMz - 400) / 125);
hist[histIndex]++;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", peptide, charge, precursorIonMz, histIndex);
sum++;
}
}
Console.WriteLine("\nRange\tNum\tRatio");
for (var i = 0; i < hist.Length; i++)
{
Console.WriteLine("{0}-{1}\t{2}\t{3}", 400 + i * 125, 525 + i * 125, hist[i], hist[i] / (float)sum);
}
}
public static Dictionary <string, MatchedTagSet> GetProteinToMatchedTagsMap(
IEnumerable <SequenceTag.SequenceTag> tags,
SearchableDatabase searchableDb,
AminoAcidSet aaSet,
Tolerance tolerance,
Tolerance relaxedTolerance)
{
var fastaDb = searchableDb.FastaDatabase;
var proteinsToTags = new Dictionary <string, MatchedTagSet>();
foreach (var tag in tags)
{
var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray();
if (matchedIndices.Length > MaxNumProteinMatchesPerTag)
{
continue;
}
foreach (var index in matchedIndices)
{
var proteinName = fastaDb.GetProteinName(index);
var startIndex = fastaDb.GetZeroBasedPositionInProtein(index);
var mass = aaSet.GetComposition(tag.Sequence).Mass;
var matchedTag = new MatchedTag(tag, startIndex)
{
Mass = mass
};
MatchedTagSet existingMatchedTagSet;
if (proteinsToTags.TryGetValue(proteinName, out existingMatchedTagSet))
{
existingMatchedTagSet.Add(matchedTag);
}
else
{
var proteinSequence = fastaDb.GetProteinSequence(proteinName);
if (proteinSequence == null)
{
proteinSequence = proteinName;
}
var matchedTagSet = new MatchedTagSet(proteinSequence, aaSet, tolerance, relaxedTolerance);
matchedTagSet.Add(matchedTag);
proteinsToTags.Add(proteinName, matchedTagSet);
}
}
}
return(proteinsToTags);
}
public void TestIsoProfile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string sequence = "MWYMISAQDVENSLEKRLAARPAHLARLQELADEGRLLVAGPHPAIDSENPGDAGFSGSLVVADFDSLATAQAWADADPYFAAGVYQSVVVKPFKRVLP";
var aaSet = new AminoAcidSet();
var comp = aaSet.GetComposition(sequence) + Composition.H2O;
var ion = new Ion(comp, 9);
foreach (var i in ion.GetIsotopes(0.1))
{
Console.WriteLine(ion.GetIsotopeMz(i.Index) + "\t" + i.Ratio);
}
}
private static MSMSSpectrum ReadSpectrum(string s)
{
var precursorMz = 0.0;
var charge = 0;
Sequence annotation = null;
var peaks = new List <MSMSSpectrumPeak>();
var token = s.Split('\n');
foreach (var t in token)
{
if (t.Length == 0)
{
continue;
}
if (char.IsDigit(t[0]))
{
var p = t.Split(new [] { "\t", " " }, StringSplitOptions.None);
peaks.Add(new MSMSSpectrumPeak(double.Parse(p[0]), double.Parse(p[1])));
}
else if (t.StartsWith("CHARGE"))
{
var chargeStr = t.Substring(t.IndexOf('=') + 1).Trim();
if (chargeStr.StartsWith("+"))
{
chargeStr = chargeStr.Substring(1);
}
if (chargeStr.EndsWith("+"))
{
chargeStr = chargeStr.Substring(0, chargeStr.Length - 1);
}
charge = int.Parse(chargeStr);
}
else if (t.StartsWith("SEQ"))
{
var annotationStr = t.Substring(t.LastIndexOf('=') + 1);
var precursorComposition = AminoAcidSet.GetComposition(annotationStr);
var peptideComposition = precursorComposition + Composition.H2O;
annotation = new Sequence(annotationStr, AminoAcidSet);
}
else if (t.StartsWith("PEPMASS"))
{
var p = t.Substring(t.IndexOf('=') + 1).Split(new[] { "\\s+" }, StringSplitOptions.None);
precursorMz = double.Parse(p[0]);
}
}
return(new MSMSSpectrum(charge, precursorMz, annotation, peaks));
}
public void TestXicGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
// Test
var tolerance = new Tolerance(30);
const string peptide = "AIANGQVDGFPTQEECR";
const int targetScanNum = 37633;
const int charge = 2;
//const string peptide = "IVDTNGAGDAFAGGFMAGLTK";
//const int targetScanNum = 67513;
//const int charge = 3;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
Console.WriteLine("Theoretical isotopomer profile:");
foreach (var p in precursorIon.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}", precursorIon.GetIsotopeMz(p.Index), p.Ratio);
}
var xicArr = new Dictionary <int, Xic>();
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
for (var i = -1; i < 3; i++)
{
xicArr[i] = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetIsotopeMz(i), tolerance, targetScanNum);
}
for (var i = -1; i < 3; i++)
{
Console.WriteLine("\nIndex: {0}", i);
Console.WriteLine("m/z: {0}", precursorIon.GetIsotopeMz(i));
Console.WriteLine("#XicPeaks: {0}", xicArr[i].Count);
Console.WriteLine("Intensity: {0}", xicArr[i].GetSumIntensities() / xicArr[basePeakIndex].GetSumIntensities());
Console.WriteLine("Correlation: {0}", xicArr[i].GetCorrelation(xicArr[basePeakIndex]));
}
}
public void ValidateIcResultsWithModifications()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1_Rescored.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var parser = new TsvFileParser(resultFilePath);
var sequences = parser.GetData("Sequence");
var modifications = parser.GetData("Modifications");
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var scanNums = parser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var aaSet = new AminoAcidSet();
for (var i = 0; i < parser.NumData; i++)
{
var sequenceComp = aaSet.GetComposition(sequences[i]) + Composition.H2O;
var modComposition = Composition.Zero;
var modsStr = modifications[i].Substring(1, modifications[i].Length - 2);
var mods = modsStr.Split(',');
foreach (var modStr in mods)
{
if (modStr.Length == 0)
{
continue;
}
var modName = modStr.Split()[0];
var mod = Modification.Get(modName);
modComposition += mod.Composition;
}
var compFromSeqAndMods = sequenceComp + modComposition;
Assert.True(compFromSeqAndMods.Equals(compositions[i]));
}
}
public void TestPeptide()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
//const string sequence = "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
const string sequence = "IRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
//const string sequence = "MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG";
//const string sequence = "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK";
//const string sequence =
// "METTKPSFQDVLEFVRLFRRKNKLQREIQDVEKKIRDNQKRVLLLDNLSDYIKPGMSVEAIQGIIASMKGDYEDRVDDYIIKNAELSKERRDISKKLKAMGEMKNGEAK";
var aaSet = new AminoAcidSet();
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
Console.WriteLine(composition);
Console.WriteLine(composition.Mass);
Console.WriteLine(composition.NominalMass);
// 2nd isotope
Console.WriteLine(composition.GetIsotopeMass(0));
Console.WriteLine(composition.GetIsotopeMass(1));
Console.WriteLine(composition.GetIsotopeMass(2));
//Assert.AreEqual(composition.ToPlainString(), "C34H51N7O14");
Console.WriteLine("Isotopomer Envelope:");
foreach (var e in composition.GetIsotopomerEnvelopeRelativeIntensities())
{
Console.WriteLine(e);
}
Console.WriteLine();
Console.WriteLine("Isotope ions:");
var ion = new Ion(composition + Composition.H2O, 13);
foreach (var p in ion.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}", ion.GetIsotopeMz(p.Index), p.Ratio);
}
Console.WriteLine();
}
public void TestRescoring()
{
//const string specFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string specFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
//const string sequence = "SGWYELSKSSNDQFKFVLKAGNGEVILTSELYTGKSGAMNGIESVQTNSPIEARYAKEVAKNDKPYFNLKAANHQIIGTSQMYSSTA";
//const int scanNum = 4084;
const string sequence = "SKTKHPLPEQWQKNQEAAKATQVAFDLDEKFQYSIRKAALDAGVSPSDQIRTILGLSVSRRPTRPRLTVSLNADDYVQLAEKYDLNADAQLEIKRRVLEDLVRFVAED";
const int scanNum = 5448;
const int charge = 11;
// 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);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
glutathioneC,
oxM,
acetylN,
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 15, new Tolerance(10));
var scores = informedScorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm, composition, charge, scanNum);
Console.WriteLine("Total Score = " + scores.Score);
Console.WriteLine("#Fragments = " + scores.NumMatchedFrags);
}
public void TestTimeToComputeIsotopomerProfiles()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string dbFilePath = @"C:\cygwin\home\kims336\Data\IMS_Sarc\HumanPeptides.txt";
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
int numPeptides = 0;
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var isoCalc = IsotopicDistributionCalculator.Instance;
foreach (var annotation in File.ReadLines(dbFilePath))
{
++numPeptides;
var peptide = annotation.Substring(2, annotation.Length - 4);
var composition = aaSet.GetComposition(peptide);
var molFormula = composition.ToPlainString();
isoCalc.GetIsotopePattern(molFormula);
composition.GetIsotopomerEnvelopeRelativeIntensities();
}
Console.WriteLine("NumPeptides: " + numPeptides);
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestRescoring(int scanNum, int charge, string sequence, double expectedScore)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
// 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);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
glutathioneC,
oxM,
acetylN,
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName, 0, 0);
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 15, new Tolerance(10));
var scores = informedScorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm, composition, charge, scanNum);
Console.WriteLine("Total Score = " + scores.Score);
Console.WriteLine("#Fragments = " + scores.NumMatchedFrags);
Assert.AreEqual(expectedScore, scores.Score, 0.0001);
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.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);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.7, 0.7, 0.7, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
//const string prot =
// "ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLLA";
//var protMass = (new AminoAcidSet().GetComposition(prot) + Composition.H2O).Mass;
//Console.WriteLine("************ScanNums: " + string.Join("\t", ms1Filter.GetMatchingMs2ScanNums(protMass)));
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\MSAlign\NoMod.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var scanNums = tsvReader.GetData("Scan(s)");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("E-value");
var sequences = tsvReader.GetData("Peptide");
//const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_N30_C30.tsv";
//var tsvReader = new TsvFileParser(resultFilePath);
//var scanNums = tsvReader.GetData("ScanNum");
//var charges = tsvReader.GetData("Charge");
//var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Sequence");
var aaSet = new AminoAcidSet();
var seqSet = new HashSet <string>();
var allSeqSet = new HashSet <string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < scores.Count; i++)
{
var score = Convert.ToDouble(scores[i]);
if (score > 1E-4)
{
continue;
}
//if (score < 10) continue;
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var sequence = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (sequence == null || sequence.Contains("("))
{
continue;
}
//var sequence = sequences[i];
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
//const double isotopeRatioTolerance = 2;
//const double correlationThreshold = 0.3;
const double fdrThreshold = 0.01;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\oldResult\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
var numTargets = 0;
var numValidTargets = 0;
var numDecoys = 0;
var numValidDecoys = 0;
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
if (isDecoy)
{
numDecoys++;
}
else
{
numTargets++;
}
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
var isValid = true;
foreach (var isotope in precursorIon.GetIsotopes(relativeIntensityThreshold))
{
if (isotope.Index == basePeakIndex)
{
continue;
}
var isotopeMz = precursorIon.GetIsotopeMz(isotope.Index);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
if (xic.Count == 0)
{
isValid = false;
break;
}
//if (xic.Count > 0)
//{
// var isotopeRatio = xic.GetSumIntensities() / baseIntensity / isotope.Item2;
// var correlation = xic.GetCorrelation(baseXic);
// if (isotopeRatio > 0.8 && isotopeRatio < 1.2
// && correlation > 0.8)
// {
// isValid = true;
// }
//}
// Check if isotope ratio is within tolerance
//if (isotopeRatio > isotopeRatioTolerance || isotopeRatio < 1 / isotopeRatioTolerance)
//{
// isValid = false;
// //Console.WriteLine("Off ratio\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, isotopeRatio);
// break;
//}
// Check if correlation is high
//if (correlation < correlationThreshold)
//{
// isValid = false;
// //Console.WriteLine("Low correlation\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, correlation);
// break;
//}
}
if (isValid && !isDecoy)
{
numValidTargets++;
}
else if (isValid)
{
numValidDecoys++;
}
//Console.WriteLine("{0}\t{1}\t{2}", peptide, scanNum, charge);
}
Console.WriteLine("#Targets: {0}", numTargets);
Console.WriteLine("#ValidTargets: {0}\t{1}", numValidTargets, numValidTargets / (double)numTargets);
Console.WriteLine("#Decoys: {0}", numDecoys);
Console.WriteLine("#ValidDecoys: {0}\t{1}", numValidDecoys, numValidDecoys / (double)numDecoys);
sw.Stop();
Console.WriteLine(@"TimeForPrecursorValidation {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void AnalyizeFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
//const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
const double fdrThreshold = 0.01;
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
Console.WriteLine("IsDecoy\tPeptide\tScanNum\tCharge\tSpecEValue\tQValue\tPrecursorMz" +
"\tTheo0\tTheo1\tTheo2\tTheo3" +
"\tObs0\tCorr0\tObs1\tCorr1\tObs2\tCorr2\tObs3\tCorr3\tObs-1\tCorr-1\tObs0.5\tCorr0.5");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var specEValue = Convert.ToDouble(token[12]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
Console.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", (isDecoy ? 1 : 0), peptide, scanNum, charge, specEValue, qValue, precursorIon.GetMonoIsotopicMz());
var isotopeIndices = new double[] { 0, 1, 2, 3, -1, 0.5 };
var theoIsotopes = precursorIon.GetIsotopes(0.01);
var numIsotopes = 0;
foreach (var theoIsotope in theoIsotopes)
{
Console.Write("\t" + theoIsotope.Ratio);
if (++numIsotopes == 4)
{
break;
}
}
foreach (var isotopeIndex in isotopeIndices)
{
var isotopeMz = precursorIon.GetIsotopeMz(isotopeIndex);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
var relativeIntensity = xic.GetSumIntensities() / baseIntensity;
var correlation = xic.GetCorrelation(baseXic);
Console.Write("\t{0}\t{1}", relativeIntensity, correlation);
}
Console.WriteLine();
}
}
