/// <summary>
/// Scan No,Charge,Peptide Seq, MaxMz,Y1Mz,Y1Intensity,Y2Mz,Y2Intensity,Y3Mz,Y3Intensity,Y4Mz,Y4Intensity
/// </summary>
/// <returns></returns>
public List<string> Process(int argMissCleavage)
{
List<string> result = new List<string>();
AminoAcidMass AAMW = new AminoAcidMass();
foreach (ProteinInfo p in _pInfo)
{
p.CreateCleavage(argMissCleavage);
List<string> Glycopeptide = p.Glycopeptide(0);
foreach (string Pep in Glycopeptide)
{
for (int i = 0; i <= 2; i++)
{
float PeptideMass = AAMW.GetMonoMW(Pep, true);
List<float> Peakmz = GetPeakCluster(PeptideMass, _scan.ParentCharge - i);
List<int> ClosePeakIdx = new List<int>();
int foundpeak = 0;
double MaxIntensity = 0.0;
double MaxMz = 0.0;
foreach (float peak in Peakmz)
{
int closepeakidx = MassUtility.GetClosestMassIdx(_scan.MSPeaks,peak);
ClosePeakIdx.Add(closepeakidx);
if (MassUtility.GetMassPPM(peak, _scan.MSPeaks[closepeakidx].MonoMass) < _torelance)
{
if (_scan.MSPeaks[closepeakidx].MonoIntensity > MaxIntensity)
{
MaxIntensity = _scan.MSPeaks[closepeakidx].MonoIntensity;
MaxMz = _scan.MSPeaks[closepeakidx].MonoMass;
}
foundpeak++;
}
}
if (foundpeak >= 3)
{
string tmp = _scan.ScanNo + "," + Convert.ToString(_scan.ParentCharge - i) + "," + Pep + "," + MaxMz.ToString() + ",";
for (int j = 0; j < 4; j++)
{
if (MassUtility.GetMassPPM(_scan.MSPeaks[ClosePeakIdx[j]].MonoMass, Peakmz[j]) < _torelance)
{
tmp = tmp + _scan.MSPeaks[ClosePeakIdx[j]].MonoMass + "," + (_scan.MSPeaks[ClosePeakIdx[j]].MonoIntensity / MaxIntensity) + ",";
}
else
{
tmp = tmp + ",,";
}
}
result.Add(tmp);
}
}
}
}
return result;
}
public static float GetGlycopeptideMZ(string argPeptide, GlycanStructure argGlycan, int argCharge)
{
float TotalMZ = 0.0f;
AminoAcidMass AAMS = new AminoAcidMass();
float PeptideMonoMass = AAMS.GetAVGMonoMW(argPeptide, true);
float GlycanMass = 0.0f;
GlycanMass = GlycanMass + argGlycan.NoOfHex*GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.Hex);
GlycanMass = GlycanMass + argGlycan.NoOfHexNac * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.HexNAc);
GlycanMass = GlycanMass + argGlycan.NoOfDeHex * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.DeHex);
GlycanMass = GlycanMass + argGlycan.NoOfNeuAc * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuAc);
GlycanMass = GlycanMass + argGlycan.NoOfNeuGc * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuGc);
TotalMZ = (PeptideMonoMass + GlycanMass + MassLib.Atoms.ProtonMass*argCharge)/argCharge;
return TotalMZ;
}
private void btnGetPeptideMass_Click(object sender, EventArgs e)
{
AminoAcidMass AAMS = new AminoAcidMass();
lblPeptideMass.Text = " Mass:" + AAMS.GetMonoMW(txtPeptideSeq.Text, chkCYS_CAM.Checked) + "\nAvg Mass:" +
AAMS.GetAVGMonoMW(txtPeptideSeq.Text, chkCYS_CAM.Checked);
}
