protected IsobaricPeptideStatisticBuilderOptions GetStatisticOption()
{
var option = new IsobaricPeptideStatisticBuilderOptions();
option.PeptideFile = peptideFile.FullName;
option.DesignFile = designFile.FullName;
option.Mode = modes.SelectedItem;
option.ModifiedAminoacids = modifiedAminoacids.Text;
option.PerformNormalizition = normalize.Checked;
if (option.Mode == QuantifyMode.qmModificationSite)
{
option.MinimumSiteProbability = minimumSiteProbability.Value;
}
return(option);
}
public void TestFilterSpectraByQuantifyMode()
{
var options = new IsobaricPeptideStatisticBuilderOptions()
{
ModifiedAminoacids = "STY",
MinimumSiteProbability = 0.8
};
//For all spectra, nothing will be filtered
options.Mode = QuantifyMode.qmAll;
var isoSpectra = InitializeSpectra();
new IsobaricPeptideStatisticBuilder(options).FilterSpectraByQuantifyMode(isoSpectra);
Assert.AreEqual(3, isoSpectra.Count);
//Unmodified spectra
options.Mode = QuantifyMode.qmUnmodifiedPeptide;
isoSpectra = InitializeSpectra();
new IsobaricPeptideStatisticBuilder(options).FilterSpectraByQuantifyMode(isoSpectra);
Assert.AreEqual(1, isoSpectra.Count);
Assert.AreEqual("^AAAQLLQSQAQQSGAQQTK@", isoSpectra[0].Sequence);
//modified spectra, not filter site probability
options.Mode = QuantifyMode.qmModificationSite;
options.MinimumSiteProbability = -0.1;
isoSpectra = InitializeSpectra();
new IsobaricPeptideStatisticBuilder(options).FilterSpectraByQuantifyMode(isoSpectra);
Assert.AreEqual(2, isoSpectra.Count);
Assert.IsTrue(isoSpectra.All(m => !m.Sequence.Equals("^AAAQLLQSQAQQSGAQQTK@")));
//modified spectra, filter site probability
options.MinimumSiteProbability = 0.8;
isoSpectra = InitializeSpectra();
new IsobaricPeptideStatisticBuilder(options).FilterSpectraByQuantifyMode(isoSpectra);
Assert.AreEqual(1, isoSpectra.Count);
Assert.AreEqual("^AAADTGAS*PR", isoSpectra[0].Sequence);
}
public IsobaricPeptideStatisticBuilder(IsobaricPeptideStatisticBuilderOptions options)
{
this.options = options;
}