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 TestForVlad()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\Research\Data\Vlad\raw\Alz_RA_C1_HCD_11012013_SW_03Nov2013.raw";
const string dbFilePath = @"D:\Research\Data\Vlad\database\ID_004221_1C042A1F.fasta";
//const string dbFilePath = @"D:\Research\Data\Vlad\database\HBA_MOUSE.fasta";
const string outputDir = @"D:\Research\Data\Vlad\Ic\POPSICLETest_M1";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// 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 thrToAla = new SearchModification(Modification.ThrToAla, 'T', 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 serToAsn = new SearchModification(Modification.SerToAsn, 'S', 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);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
// glutathioneC,
oxM,
// dethiomethylM,
acetylN,
phosphoS,
phosphoT,
phosphoY
// thrToAla,
// serToAsn,
// deamidatedN,
// deamidatedQ,
// pyroCarbamidomethylC
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int searchMode = 1; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = false; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
public void TestBuildingSequenceGraphLongProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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);
foreach (var composition in seqGraph.GetFragmentCompositions(modIndex, 0))
{
//if (composition.GetMass() > seqComposition.GetMass())
{
Console.WriteLine("***Seq: {0}, Frag: {1}", seqComposition, composition);
}
}
}
}
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 TestTopDownScoringForAllXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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, null);
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);
}
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 TestMsAlignPlusResults()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 "))
{
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, null);
var score = scorer.GetScore();
writer.WriteLine(s+"\t"+score);
Console.WriteLine(score);
}
writer.Close();
reader.Close();
}
public void TestTopDownScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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, null);
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 TestForSbepData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//// Salmonella
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\SBEP_STM_001_02272012_Aragon.raw";
const string dbFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002166_F86E3B2F.fasta";
const string outputDir = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\Results\Mod_M2";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
if (!Directory.Exists(outputDir))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, outputDir);
}
// 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);
const int searchMode = 2; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
public void TestDdaPlus()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// QC_Shew QE
const string specFilePath = @"H:\Research\DDAPlus\raw\20140701_yeast_DDA_01.raw";
const string dbFilePath = @"H:\Research\DDAPlus\database\Yeast_SGD_withContam.fasta";
const string outputDir = @"H:\Research\DDAPlus\Test";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerPeptide = 2;
var searchModifications = new List<SearchModification>
{
//carbamidomethylC,
acetylN,
oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerPeptide);
const int ntt = 2; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestBottomUpSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, ntt);
}
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 void TestForAaronData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownAaron\raw\MTB_intact_1.raw";
const string dbFilePath = @"C:\cygwin\home\kims336\Data\TopDownAaron\database\ID_003121_998584F8.fasta";
const string outputDir = @"C:\cygwin\home\kims336\Data\TopDownAaron\Ic\Mode1_07";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// 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 tevFp2C = new SearchModification(Modification.TevFp2, 'S', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
//glutathioneC,
//nitrosylC,
//nethylmaleimideC,
oxM,
acetylN,
tevFp2C
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int searchMode = 1; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
public void TestCreatingAminoAcidSet()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Configure amino acid set
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.PeptideNTerm, 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);
//var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
aaSet.Display();
}
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 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 TestIcRescoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SpecFiles\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
//const string icResultPath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_Map07_Re.icdresult";
//const string outputPath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_Map07_Re_Rescored.icdresult";
const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1.raw";
const string icResultPath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1.ictresult";
const string outputPath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1_Rescored.ictresult";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(icResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, icResultPath);
}
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 tolerance = new Tolerance(10.0);
var rescorer = new IcRescorer(specFilePath, icResultPath, outputPath, aaSet, tolerance, 0.7);
Console.WriteLine("Done");
}
public void TestForJiaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// QC_Shew
//const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
//const string dbFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002216_235ACCEA.fasta";
//const string dbFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\database\Test.fasta";
// Jia's data
const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1.raw";
const string dbFilePath = @"C:\cygwin\home\kims336\Data\TopDownJia\database\ID_003962_71E1A1D4.fasta";
const string outputDir = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\D1_1_Mode1";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// Configure amino acid set
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);
//var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
glutathioneC,
nitrosylC,
nethylmaleimideC,
oxM,
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int searchMode = 1; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
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 TestForQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// QC_Shew
const string specFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string dbFilePath = @"D:\MSPathFinder\Fasta\ID_002216_235ACCEA.fasta";
const string outputDir = @"D:\MassSpecFiles\training\test";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int searchMode = 2; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
public void ProcessMhcData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\carone_C1309_All.tsv";
const string outputFilePath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\IPA_Summary.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\ImmunoPeptidomics\Benchmarking\raw", "*.raw");
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List<SearchModification>
{
oxM
};
var aaSet = new AminoAcidSet(searchModifications, 2);
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(5), new Tolerance(3));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestCompositeScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string rawFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SpecFiles\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string rawFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
const int minCharge = 1;
const int maxCharge = 20;
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
var aminoAcidSet = new AminoAcidSet();
//var scorer = new MatchedPeakPostScorer(tolerance, minCharge, maxCharge);
var scorer = new InformedTopDownScorer(run, aminoAcidSet, minCharge, maxCharge, tolerance);
var fileExt = new string[] {"IcTarget", "IcDecoy"};
foreach (var ext in fileExt)
{
var resultFileName = string.Format(@"D:\MassSpecFiles\training\Rescoring\QC_Shew_Intact_26Sep14_Bane_C2Column3_{0}.tsv", ext);
var parser = new TsvFileParser(resultFileName);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var protSequences = parser.GetData("Sequence").ToArray();
var modStrs = parser.GetData("Modifications").ToArray();
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var protMass = parser.GetData("Mass").Select(s => Convert.ToDouble(s)).ToArray();
var outputFileName = string.Format(@"D:\MassSpecFiles\training\Rescoring\QC_Shew_Intact_26Sep14_Bane_C2Column3_{0}_Rescored.tsv", ext);
using (var writer = new StreamWriter(outputFileName))
{
writer.WriteLine(string.Join("\t", parser.GetHeaders().ToArray(), 0, 15) + "\tScore\tEValue");
var lines = new string[parser.NumData];
//for (var i = 0; i < parser.NumData; i++)
Parallel.For(0, parser.NumData, i =>
{
var scan = scans[i];
var charge = charges[i];
var protSequence = protSequences[i];
var modStr = modStrs[i];
var sequence = Sequence.CreateSequence(protSequence, modStr, aminoAcidSet);
Assert.True(sequence.Composition.Equals(compositions[i] - Composition.H2O));
var ms2Spec = run.GetSpectrum(scan) as ProductSpectrum;
Assert.True(ms2Spec != null);
var scores = scorer.GetScores(sequence, charge, scan);
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(ms2Spec, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
var deconvScorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, ms2Spec, tolerance,
comparer);
var graph = graphFactory.CreateScoringGraph(deconvScorer, protMass[i]);
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
var specEvalue = gf.GetSpectralEValue(scores.Score);
var rowStr = parser.GetRows()[i];
var items = rowStr.Split('\t').ToArray();
var newRowStr = string.Join("\t", items, 0, 15);
//writer.WriteLine("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
lock (lines)
{
lines[i] = string.Format("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
}
//Console.WriteLine("{0}\t{1}\t{2}", items[0], scores.Score, specEvalue);
});
foreach (var line in lines) writer.WriteLine(line);
}
Console.WriteLine("Done");
}
}
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 TestMaccoss(string specFilePath)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const string dbFilePath = @"D:\Research\Data\UW\QExactive\M_musculus_Uniprot_withContam.fasta";
const string outputDir = @"D:\Research\Data\UW\QExactive\Ic_NTT1_Mass";
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// Configure amino acid set
var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
//var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
//var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 0;
var searchModifications = new List<SearchModification>
{
carbamidomethylC,
//acetylN,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int ntt = 1; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestBottomUpSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, ntt);
}
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 TestQcShewQExactive()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// QC_Shew QE
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
const string dbFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\ID_003456_9B916A8B.fasta";
const string outputDir = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT2_Mass";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 0;
var searchModifications = new List<SearchModification>
{
//carbamidomethylC,
acetylN,
oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int ntt = 2; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = true; // true: target & decoy, false: target, null: decoy
TestBottomUpSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, ntt);
}
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 TestGetScoreDistribution()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string idFileFolder = @"D:\MassSpecFiles\training\IdScoring\MSPF_trainset";
const int scanNum = 5927;
const string protSequence = "MNKSELIEKIASGADISKAAAGRALDSFIAAVTEGLKEGDKISLVGFGTFEVRERAERTGRNPQTGEEIKIAAAKIPAFKAGKALKDAVN";
const string modStr = "";
var idFile = string.Format(@"{0}\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv", idFileFolder);
if (!File.Exists(idFile)) return;
//Console.WriteLine(dataset);
if (!File.Exists(rawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFile);
}
const int maxCharge = 20;
const int minCharge = 1;
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
//Console.WriteLine("{0}\t{1}", comparer.NumberOfBins, comparer.GetBinNumber(proteinMass));
var stopwatch = Stopwatch.StartNew();
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
stopwatch.Stop();
Console.WriteLine(@"edge generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var n = 0;
var stopwatch2 = Stopwatch.StartNew();
var sequence = Sequence.CreateSequence(protSequence, modStr, aaSet);
var proteinMass = sequence.Mass + Composition.H2O.Mass;
Console.WriteLine("Mass = {0}", proteinMass);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(spectrum, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
stopwatch.Restart();
var scorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, spectrum, tolerance, comparer);
var graph = graphFactory.CreateScoringGraph(scorer, proteinMass);
stopwatch.Stop();
Console.WriteLine(@"node generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
stopwatch.Reset();
stopwatch.Start();
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
//gf.ComputeGeneratingFunction(graph);
stopwatch.Stop();
Console.WriteLine(@"computing generation function = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var scoreDist = gf.GetScoreDistribution();
Console.WriteLine("{0}-{1}", scoreDist.MinScore, scoreDist.MaxScore);
for (var score = 45; score <= gf.MaximumScore; score++)
{
var specEvalue = gf.GetSpectralEValue(score);
Console.WriteLine("{0} : {1}", score, specEvalue);
}
stopwatch2.Stop();
Console.WriteLine(@"TOTAL computing generation function = {0:0.000} sec", (stopwatch2.ElapsedMilliseconds) / 1000.0d);
}
