public virtual void Analyze()
{
if (product == null)
{
return;
}
product.MaxScore();
ISpectrum spectrum = product.GetSpectrum();
HashSet <string> seen = new HashSet <string>();
foreach (IGlycoPeptideScore g in product.GetResults())
{
// remove redudant
string structure = string.Join("_", g.GetGlycoPeptide().GetGlycan().GetStructure());
string seq = g.GetGlycoPeptide().GetPeptide().GetSequence();
if (!seen.Contains(structure + seq))
{
seen.Add(structure + seq);
}
else
{
continue;
}
writer.Write(spectrum.GetScanNum().ToString() + ", ");
writer.Write(seq + ", ");
writer.Write(structure + ", ");
writer.Write(g.GetScore().ToString() + ", ");
writer.Write((spectrum as ISpectrumMSn).GetParentMZ().ToString() + ", ");
writer.WriteLine((spectrum as ISpectrumMSn).GetParentCharge().ToString());
}
}
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 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");
}
