public virtual void Analyze(int scan)
{
IGlycoPeptideScoreResultProduct result = resultTable[scan];
(analyzer as IGlycoPeptideScoreResultAnalyzer).SetResultProduct(result);
analyzer.Analyze();
}
protected void ProduceResult(IDataPoints data, ISpectrum spectrum, List <IGlycoPeptide> precursor)
{
List <IGlycoPeptideScore> glycoPeptideScores = new List <IGlycoPeptideScore>();
List <NGlycoPeptideNode> nodes = GetMaxNodes(data);
//score precursor
foreach (IGlycoPeptide glycoPeptide in precursor)
{
string seq = glycoPeptide.GetPeptide().GetSequence();
ITableNGlycan glycan = glycoPeptide.GetGlycan() as ITableNGlycan;
PeakScore score = new PeakScore();
foreach (NGlycoPeptideNode node in nodes)
{
if (node.GetPeptide().GetSequence() == seq &&
IsGlycanMatch(node.GetNGlycan(), glycan))
{
score.Merge(node);
}
}
if (score.GetScore() > 0)
{
glycoPeptideScores.Add(new GeneralGlycoPeptideScore(glycoPeptide, score.GetScore()));
}
}
result = new GeneralGlycoPeptideScoreResultProduct(spectrum, glycoPeptideScores);
}
public void AddFDRResult(IGlycoPeptideScoreResultProduct product)
{
product.MaxScore();
List <IGlycoPeptideScore> results = product.GetResults();
if (results.Count > 0)
{
negatives.Add(results[0].GetScore());
}
}
public override void Run()
{
IDoubleDigestionPeptidesSearchRun pepRunner = new DoubleDigestionFastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new DoubleDigestionPeptideCreator()));
IPeptideCreatorParameter parameter = new GeneralPeptideCreatorParameter(Proteases.Trypsin, 2, 7);;
pepRunner.AddPeptideParameter(parameter);
//parameter = new GeneralPeptideCreatorParameter(Proteases.GluC, 2, 7);
//pepRunner.AddPeptideParameter(parameter);
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\Human_ReviewedCanonical_20201Entries_25thJuly_2017.fasta");
IGlycanCreator glyRunner = new BruteForceNGlycanCreator();
List <IGlycan> glycans = glyRunner.Generate();
//IGlycanGenerator glyRunner = new SimpleGlycanGenerator();
//List<IGlycan> glycans = glyRunner.Generate();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
//specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
specRunner.Run(@"C:\Users\iruiz\Downloads\1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
Console.Write("scan, ");
Console.Write("peptide, ");
Console.Write("glycan, ");
Console.Write("score, ");
Console.Write("mz, ");
Console.WriteLine("charge");
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IMonoMassSpectrumRun monoRunner = new BinSearchMonoMassSpectrumRun();
double pretol = 20;
IPrecursorMatcher precursorMatcher = new Y1PeptidesFilterPrecursorMatcher(
new GlycoPeptidePrecursorMatcher(peptides, glycans, pretol), peptides);
IGlycoPeptideScoreFactory searchRunner = new DPSearchSpectrumCID();
for (int i = 10621; i < 10628; i++)
//for (int i = 1; i < specRunner.GetLastScan(); i++)
{
ISpectrum spectrum = specRunner.GetSpectrum(i);
if (spectrum.GetMSnOrder() == 1)
{
monoRunner.SetMS1Spectrum(spectrum);
continue;
}
if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.CID)
{
continue;
}
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
monoRunner.Run(spectrum as ISpectrumMSn);
double mass = monoRunner.GetMonoMass();
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum, mass);
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
result.MaxScore();
result.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public void SetResultProduct(IGlycoPeptideScoreResultProduct product)
{
this.product = product;
}
public void Search(ISpectrum spectrum, List <IGlycoPeptide> glycoPeptides)
{
List <IGlycoPeptideScore> results = MatchSpectrum(spectrum, glycoPeptides);
result = new GeneralGlycoPeptideScoreResultProduct(spectrum, results);
}
public override void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
FastaSearchRunPeptides pepRunner = new FastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new GeneralPeptideCreator()));
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\ms_fasta.fasta");
//List<IPeptide> peptides = pepRunner.Run(@"C:\Users\rz20\Downloads\ms_fasta.fasta");
Console.WriteLine(peptides.Count);
IAccumulatedMSNGlycanCreator glyRunner = new AccumulatedMSBruteForceNGlycanCreator();
List <IAccumulatedGlycanMassProxy> glycans = glyRunner.GenerateSpecific();
IAccumulatedStructNGlycanCreator glyRunner2 = new AccumulatedStructBruteForceNGlycanCreator();
List <IAccumulatedGlycanStructureProxy> glycans2 = glyRunner2.GenerateSpecific();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
//for (int i = 1; i < specRunner.GetLastScan(); i++)
//{
ISpectrum spectrum = specRunner.GetSpectrum(3361);
//if (spectrum.GetMSnOrder() == 1) continue;
//if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.ETD) continue;
List <IGlycan> glycanSet = new List <IGlycan>();
glycanSet.AddRange(glycans);
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
double pretol = 20;
IAccumulatedPrecursorMatcher precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycanSet, pretol);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);
IGlycoPeptideScoreFactory searchRunner = new BinSearchSpectrumEThcD();
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
List <IGlycoPeptideScore> results = result.GetResults();
IAnnotatedPeakFactory annotator = new BinSearchAnnotatedSpectrumEThcD(glycans2, 20);
foreach (IGlycoPeptideScore r in results)
{
annotator.Annotate(spectrum, r);
IAnnotatedPeakResultProduct peaks = annotator.GetResult();
peaks.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
}
public override void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IDoubleDigestionPeptidesSearchRun pepRunner = new DoubleDigestionFastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new DoubleDigestionPeptideCreator()));
IPeptideCreatorParameter parameter = new GeneralPeptideCreatorParameter(Proteases.Trypsin, 2, 7);;
pepRunner.AddPeptideParameter(parameter);
parameter = new GeneralPeptideCreatorParameter(Proteases.GluC, 2, 7);
pepRunner.AddPeptideParameter(parameter);
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\HP.fasta");
IAccumulatedMSNGlycanCreator glyRunner = new AccumulatedMSBruteForceNGlycanCreator();
List <IAccumulatedGlycanMassProxy> glycans = glyRunner.GenerateSpecific();
//IGlycanGenerator glyRunner = new SimpleGlycanGenerator();
//List<IGlycan> glycans = glyRunner.Generate();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
Console.Write("scan, ");
Console.Write("peptide, ");
Console.Write("glycan, ");
Console.Write("score, ");
Console.Write("mz, ");
Console.WriteLine("charge");
for (int i = 7861; i < 7862; i++)
{
ISpectrum spectrum = specRunner.GetSpectrum(i);
if (spectrum.GetMSnOrder() == 1)
{
continue;
}
if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.ETD)
{
continue;
}
List <IGlycan> glycanSet = new List <IGlycan>();
glycanSet.AddRange(glycans);
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
double pretol = 20;
IAccumulatedPrecursorMatcher precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycanSet, pretol);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);
IGlycoPeptideScoreFactory searchRunner = new BinSearchSpectrumEThcD();
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
result.MaxScore();
result.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
}
