private static MSPeak ConvertDeconPeakToMSPeak(Decon2LS.Peaks.clsPeak deconPeak)
{
MSPeak msPeak = new MSPeak();
msPeak.Intensity = deconPeak.mdbl_intensity;
msPeak.PeakWidth = deconPeak.mdbl_FWHM;
msPeak.MZ = deconPeak.mdbl_mz;
return msPeak;
}
private IList<MSPeak> GenerateTestPeakList()
{
IList<MSPeak> msPeaklist = new List<MSPeak>();
MSPeak mspeak1 = new MSPeak(500, 100, 0.5);
MSPeak mspeak2 = new MSPeak(501, 50, 0.5);
MSPeak mspeak3 = new MSPeak(502, 10, 0.5);
MSPeak mspeak4 = new MSPeak(503, 1, 0.5);
msPeaklist.Add(mspeak1);
msPeaklist.Add(mspeak2);
msPeaklist.Add(mspeak3);
msPeaklist.Add(mspeak4);
return msPeaklist;
}
private void GenerateTheoreticalIsotopicPeakList(RunResult runResult)
{
MSPeak mspeak1 = new MSPeak(500, 100, 0.5);
MSPeak mspeak2 = new MSPeak(501, 44.25, 0.5);
MSPeak mspeak3 = new MSPeak(502, 7.34, 0.5);
MSPeak mspeak4 = new MSPeak(503, 1.22, 0.5);
MSPeak mspeak5 = new MSPeak(504, 0.65, 0.5);
runResult.TheoreticalIsotopicPeakList.Add(mspeak1);
runResult.TheoreticalIsotopicPeakList.Add(mspeak2);
runResult.TheoreticalIsotopicPeakList.Add(mspeak3);
runResult.TheoreticalIsotopicPeakList.Add(mspeak4);
runResult.TheoreticalIsotopicPeakList.Add(mspeak5);
}
private void AssertMSPeak(MSPeak peak, double expectedMz, double expectedIntensity)
{
Assert.AreEqual(expectedMz, peak.MZ);
Assert.AreEqual(Math.Round(expectedIntensity, 5), Math.Round(peak.Intensity, 5));
}
private void GenerateIsotopicPeakList(RunResult runResult)
{
MSPeak mspeak1 = new MSPeak(500, 100, 0.5);
MSPeak mspeak2 = new MSPeak(501, 50, 0.5);
MSPeak mspeak3 = new MSPeak(502, 10, 0.5);
MSPeak mspeak4 = new MSPeak(503, 1, 0.5);
runResult.IsotopicPeakList.Add(mspeak1);
runResult.IsotopicPeakList.Add(mspeak2);
runResult.IsotopicPeakList.Add(mspeak3);
runResult.IsotopicPeakList.Add(mspeak4);
}
private static int CalculatePeaksInCalculation(RunResult result)
{
// determine max intensity
MSPeak mostIntensePeak = new MSPeak();
foreach (MSPeak peak in result.IsotopicPeakList)
{
if (peak.Intensity > mostIntensePeak.Intensity)
{
mostIntensePeak = peak;
}
}
bool foundPeakaboveThreshold = false;
int returnedIndex = 0;
for (int i = 0; i < result.IsotopicPeakList.Count; i++)
{
// start at Mono
// add peaks if they are above the deutDistThreshold
// Stop adding peaks if they are below the deutDistThreshold
if (result.IsotopicPeakList[i].Intensity / mostIntensePeak.Intensity * 100 > result.ActualDeutDistThreshold)
{
foundPeakaboveThreshold = true;
}
if (foundPeakaboveThreshold && result.IsotopicPeakList[i].Intensity / mostIntensePeak.Intensity * 100 < result.ActualDeutDistThreshold)
{
returnedIndex = i;
break;
}
returnedIndex = i;
}
return returnedIndex;
}
// TODO: This method is redudant with the one below. Collapse it so it uses the method below.
public void GetIsotopicProfile(RunResult result, bool addProton, int numberOfIsotopesInProfile, bool addNTerminalProteon, bool addCTerminalFreeAcid)
{
Peptide peptide = result.Peptide;
if (IsPeptideSequenceValid(peptide.Sequence))
{
// the dimensions change once used by the MolecularWeightCalculator
double[,] isotopeData = new double[100, 2];
string threeLetterCodedPeptide = GetPeptideThreeLetterCode(peptide.Sequence, false, addNTerminalProteon, addCTerminalFreeAcid, string.Empty);
if (addProton)
{
threeLetterCodedPeptide += "H";
}
string resultsString = string.Empty;
int numResults = 0;
mw.ComputeIsotopicAbundances(ref threeLetterCodedPeptide, (short)peptide.ChargeState, ref resultsString, ref isotopeData, ref numResults, string.Empty, string.Empty, string.Empty, string.Empty);
for (int i = 1; i < isotopeData.GetLength(0); i++)
{
MSPeak peak = new MSPeak();
peak.MZ = isotopeData[i, 0];
peak.Intensity = isotopeData[i, 1];
result.TheoreticalIsotopicPeakList.Add(peak);
}
if (result.TheoreticalIsotopicPeakList.Count < numberOfIsotopesInProfile)
{
for (int i = result.TheoreticalIsotopicPeakList.Count; i < numberOfIsotopesInProfile; i++)
{
result.TheoreticalIsotopicPeakList.Add(new MSPeak(0, 0, 0));
}
}
}
}
public void GetIsotopicProfileForFragmentIon(RunResult result, int numberOfIsotopesInProfile)
{
if (IsPeptideSequenceValid(result.Peptide.Sequence))
{
// the dimensions change once used by the MolecularWeightCalculator
double[,] isotopeData = new double[100, 2];
string threeLetterCodedPeptide;
switch (result.FragmentIon.FragmentIonType)
{
case Hydra.Core.FragmentIonType.Parent:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, true, true, string.Empty);
break;
case Hydra.Core.FragmentIonType.BFragment:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, false, false, string.Empty);
break;
case Hydra.Core.FragmentIonType.YFragment:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, true, true, string.Empty);
break;
case Hydra.Core.FragmentIonType.AFragment:
throw new System.ArgumentException("Code not yet written for a-ions");
case Hydra.Core.FragmentIonType.BMinusH2O:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, false, false, ">H2O");
break;
case Hydra.Core.FragmentIonType.YMinusH2O:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, true, true, ">H2O");
break;
case Hydra.Core.FragmentIonType.BMinusNH3:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, false, false, ">NH3");
break;
case Hydra.Core.FragmentIonType.YMinusNH3:
threeLetterCodedPeptide = GetPeptideThreeLetterCode(result.FragmentIon.Sequence, true, true, true, ">NH3");
break;
default:
throw new System.ArgumentException("Invalid fragment ion Type");
}
string resultsString = string.Empty;
int numResults = 0;
mw.ComputeIsotopicAbundances(ref threeLetterCodedPeptide, (short)result.FragmentIon.ChargeState, ref resultsString, ref isotopeData, ref numResults, string.Empty, string.Empty, string.Empty, string.Empty);
for (int i = 1; i < isotopeData.GetLength(0); i++)
{
MSPeak peak = new MSPeak();
peak.MZ = isotopeData[i, 0];
peak.Intensity = isotopeData[i, 1];
result.TheoreticalIsotopicPeakList.Add(peak);
}
if (result.TheoreticalIsotopicPeakList.Count < numberOfIsotopesInProfile)
{
for (int i = result.TheoreticalIsotopicPeakList.Count; i < numberOfIsotopesInProfile; i++)
{
result.TheoreticalIsotopicPeakList.Add(new MSPeak(0, 0, 0));
}
}
}
}
public IList<MSPeak> GetIsotopicProfile(string peptideSequence, int chargeState, bool addProton, int numberOfIsotopesInProfile, bool addNTerminalProteon, bool addCTerminalFreeAcid, string tag)
{
if (IsPeptideSequenceValid(peptideSequence))
{
// the dimensions change once used by the MolecularWeightCalculator
double[,] isotopeData = new double[100, 2];
string resultsString = string.Empty;
int numResults = 0;
IList<MSPeak> theoreticalIsotopicProfilePeaks = new List<MSPeak>();
string threeLetterCodedPeptide = GetPeptideThreeLetterCode(peptideSequence, false, addNTerminalProteon, addCTerminalFreeAcid, string.Empty);
if (addProton)
{
threeLetterCodedPeptide += "H";
}
threeLetterCodedPeptide = threeLetterCodedPeptide + tag;
mw.ComputeIsotopicAbundances(ref threeLetterCodedPeptide, (short)chargeState, ref resultsString, ref isotopeData, ref numResults, string.Empty, string.Empty, string.Empty, string.Empty);
for (int i = 1; i < isotopeData.GetLength(0); i++)
{
MSPeak peak = new MSPeak();
peak.MZ = isotopeData[i, 0];
peak.Intensity = isotopeData[i, 1];
theoreticalIsotopicProfilePeaks.Add(peak);
}
if (theoreticalIsotopicProfilePeaks.Count < numberOfIsotopesInProfile)
{
for (int i = theoreticalIsotopicProfilePeaks.Count; i < numberOfIsotopesInProfile; i++)
{
theoreticalIsotopicProfilePeaks.Add(new MSPeak(0, 0, 0));
}
}
return theoreticalIsotopicProfilePeaks;
}
return null;
}