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);
}
/// <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 TargetPeptide(string argPeptide, string argProteinName, float argPeptideMass, float argStartTime, float argEndTime)
{
_PeptideSeq = argPeptide;
_ProteinName = argProteinName;
if (argPeptideMass == 0)
{
AminoAcidMass AAMS = new AminoAcidMass();
_PeptideMass = AAMS.GetMonoMW(_PeptideSeq, true);
}
else
{
_PeptideMass = argPeptideMass;
}
_StartTime = argStartTime;
_EndTime = argEndTime;
}
private void bgWorker_Process_DoWork(object sender, DoWorkEventArgs e)
{
AAMW = new AminoAcidMass();
this.lblStatus.SafeBeginInvoke(new Action(() => lblStatus.Text = "Begin initial raw file"));
Raw = new ThermoRawReader(_rawFile);
this.lblStatus.SafeBeginInvoke(new Action(() => lblStatus.Text = "Initial raw file completed"));
List <GlycanSequencing> lstGS = new List <GlycanSequencing>();
if (_UseGlycanList)
{
_GlycanCompounds = ReadGlycanListFromFile.ReadGlycanList(_glycanFile, false, _Human, false);
_MassGlycanMapping = new Dictionary <double, GlycanCompound>();
_GlycanCompoundMassList = new List <float>();
foreach (GlycanCompound G in _GlycanCompounds)
{
if (!_MassGlycanMapping.ContainsKey(G.AVGMass))
{
_MassGlycanMapping.Add(G.AVGMass, G);
_GlycanCompoundMassList.Add((float)G.AVGMass);
}
}
}
for (int i = 0; i < lstScans.Count; i++)
{
int ScanNo = lstScans[i];
if (Raw.GetMsLevel(ScanNo) == 1)
{
CurrentScan = ScanNo;
int ProcessReport = Convert.ToInt32((i / (float)lstScans.Count) * 100);
//Console.WriteLine("Scan:" + ScanNo.ToString()+"\t Peptide:" + Peptide + " completed");
bgWorker_Process.ReportProgress(ProcessReport);
this.lblStatus.SafeBeginInvoke(new Action(() => lblStatus.Text = "MS scan pass:"******"Scan:" + ScanNo.ToString()+"\t Peptide:" + Peptide + " completed");
bgWorker_Process.ReportProgress(ProcessReport);
this.lblStatus.SafeBeginInvoke(new Action(() => lblStatus.Text = "Not CID scan pass:"******"ms2")+4, _scan.ScanHeader.IndexOf("@") - _scan.ScanHeader.IndexOf("ms2")-3) + "hcd";
do
{
CheckScanNO++;
// if (Raw.GlypIDReader.GetScanDescription(CheckScanNO).Contains(ScanHeader))
// {
// HCDScanNo = CheckScanNO;
// HCD = new HCDInfo(Raw.GlypIDReader, HCDScanNo);
// break;
// }
if (Raw.GetHCDInfo(CheckScanNO) != null)
{
HCD = Raw.GetHCDInfo(CheckScanNO);
break;
}
} while (Raw.GetMsLevel(CheckScanNO) != 1); //Check Until hit Next Full MS
//CA: Complex Asialyated, CS:Complex Sialylated, HM:High mannose, HY:Hybrid and NA
}
if (HCD != null)
{
Console.WriteLine("CID Scan No:" + ScanNo.ToString() + "\tHCD Scan No:" + HCDScanNo.ToString() + "\tGlycanType:" + HCD.GlycanType.ToString());
}
this.lblStatus.SafeBeginInvoke(new Action(() => lblStatus.Text = "Sequencing:" + ScanNo.ToString()));
foreach (string Peptide in _Peptides)
{
float PeptideMass = AAMW.GetMonoMW(Peptide, true);
for (int j = PrecursorCharge - 1; j <= PrecursorCharge; j++)
{
int Y1ChargeSt = j;
if (j == 0)
{
continue;
}
float PredictedY1 = 0.0f;
PredictedY1 = (float)(PeptideMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.HexNAc) + COL.MassLib.Atoms.ProtonMass * Y1ChargeSt) / Y1ChargeSt;
GlycanSequencing GS = null;
if (_UseGlycanList)
{
float GlycanMonoMass = (_scan.ParentMZ - Atoms.ProtonMass) * _scan.ParentCharge - AAMW.GetAVGMonoMW(Peptide, true);
float PrecursorMono = _scan.ParentMonoMW;
//if (_scan.ParentAVGMonoMW != 0.0)
//{
// GlycanMonoMass = _scan.ParentAVGMonoMW - PeptideMass + (Atoms.HydrogenAVGMass * 2 + Atoms.OxygenAVGMass);
// PrecursorMono = _scan.ParentAVGMonoMW;
//}
//else
//{
// GlycanMonoMass = (_scan.ParentMZ - Atoms.ProtonMass) * _scan.ParentCharge - PeptideMass + (Atoms.HydrogenAVGMass * 2 + Atoms.OxygenAVGMass);
// PrecursorMono = _scan.ParentMonoMW;
//}
List <GlycanCompound> ClosedGlycans = new List <GlycanCompound>();
foreach (float gMass in _GlycanCompoundMassList)
{
if (Math.Abs(gMass - GlycanMonoMass) < 100.0f)
{
ClosedGlycans.Add(_GlycanCompounds[MassUtility.GetClosestMassIdx(_GlycanCompoundMassList, gMass)]);
}
}
//if (HCD != null)
//{
// if ((HCD.GlycanType == GlypID.enmGlycanType.CA && ClosedGlycan.NoOfSia>0) ||
// (HCD.GlycanType == GlypID.enmGlycanType.HM && (ClosedGlycan.NoOfSia!=0||ClosedGlycan.NoOfHexNAc!=2 || ClosedGlycan.NoOfDeHex!=0) ) ||
// (HCD.GlycanType == GlypID.enmGlycanType.CS && ClosedGlycan.NoOfSia==0))
// {
// continue;
// }
//}
//if (Math.Abs(ClosedGlycan.AVGMass - GlycanMonoMass) <= _MSMSTol)
foreach (GlycanCompound ClosedGlycan in ClosedGlycans)
{
if (_Human) //NeuAc
{
int NoOfSia = ClosedGlycan.NoOfSia;
int NoOfDeHex = ClosedGlycan.NoOfDeHex;
if (HCD != null && HCD.GlycanType == COL.MassLib.enumGlycanType.CA && ClosedGlycan.NoOfSia > 0)
{
NoOfDeHex = NoOfDeHex + NoOfSia * 2;
NoOfSia = 0;
}
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, ClosedGlycan.NoOfHex, ClosedGlycan.NoOfHexNAc, NoOfDeHex, NoOfSia, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
else //NeuGc
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, ClosedGlycan.NoOfHex, ClosedGlycan.NoOfHexNAc, ClosedGlycan.NoOfDeHex, 0, ClosedGlycan.NoOfSia, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
GS.NumbersOfPeaksForSequencing = 140;
GS.UseAVGMass = _AverageMass;
GS.CreatePrecursotMZ = true;
if (!_CompletedOnly)
{
GS.RewardForCompleteStructure = 0.0f;
}
if (HCD != null)
{
GS.GlycanType = HCD.GlycanType;
}
GS.StartSequencing();
if (_CompletedOnly && GS.FullSequencedStructures.Count == 0)
{
continue;
}
lstGS.Add(GS);
CurrentScan = ScanNo;
CurrentPeptide = GS.PeptideSeq;
int ProcessReport = Convert.ToInt32((i / (float)lstScans.Count) * 100);
//Console.WriteLine("Scan:" + ScanNo.ToString()+"\t Peptide:" + Peptide + " completed");
bgWorker_Process.ReportProgress(ProcessReport);
}
}
else // no list
{
if (_Human) //NeuAc
{
if (HCD != null)
{
//CA: Complex Asialyated, CS:Complex Sialylated, HM:High mannose, HY:Hybrid and NA
if (HCD.GlycanType == enumGlycanType.CA)
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, 0, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
else if (HCD.GlycanType == enumGlycanType.HM)
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, 2, 0, 0, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
else
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, _NoSia, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
}
else
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, _NoSia, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
}
else //NeuGc
{
if (HCD != null)
{
//CA: Complex Asialyated, CS:Complex Sialylated, HM:High mannose, HY:Hybrid and NA
if (HCD.GlycanType == enumGlycanType.CA)
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, 0, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
else if (HCD.GlycanType == enumGlycanType.HM)
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, 2, 0, 0, 0, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
else
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, 0, _NoSia, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
}
else
{
GS = new GlycanSequencing(_scan, Peptide, true, Y1ChargeSt, _NoHex, _NoHexNAc, _NoDeHex, 0, _NoSia, @"d:\tmp", _NGlycan, _MSMSTol, _PrecursorTol);
}
}
GS.NumbersOfPeaksForSequencing = 140;
GS.UseAVGMass = _AverageMass;
GS.CreatePrecursotMZ = true;
if (!_CompletedOnly)
{
GS.RewardForCompleteStructure = 0.0f;
}
if (HCD != null)
{
GS.GlycanType = HCD.GlycanType;
}
GS.StartSequencing();
if (_CompletedOnly && GS.FullSequencedStructures.Count == 0)
{
continue;
}
lstGS.Add(GS);
CurrentScan = ScanNo;
CurrentPeptide = GS.PeptideSeq;
int ProcessReport = Convert.ToInt32((i / (float)lstScans.Count) * 100);
//Console.WriteLine("Scan:" + ScanNo.ToString()+"\t Peptide:" + Peptide + " completed");
bgWorker_Process.ReportProgress(ProcessReport);
}
} //Foreach charge
} //Foreach peptide
if (lstGS.Count > 0)
{
GenerateReportBody(lstGS);
}
}//Foreach Scan
}
private void btnLoad_Click(object sender, EventArgs e)
{
openFileDialog1.Filter = "Raw files (*.RAW,*.mzXML)|*.RAW;*.mzXML";
openFileDialog1.RestoreDirectory = true;
if (txtScanNo.Text == "" || txtPeptideSeq.Text == "")
{
MessageBox.Show("Please fill the information");
return;
}
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
_torelance = Convert.ToSingle(txtPeaKTol.Text);
_precursorTorelance = Convert.ToSingle(txtPrecusorTol.Text);
dtTrees.Rows.Clear();
int ScanNo = 0;
if (Int32.TryParse(txtScanNo.Text, out ScanNo) == false)
{
MessageBox.Show("Input Scan Number Error");
return;
}
if (Path.GetExtension(openFileDialog1.FileName).ToLower() == ".raw")
{
ThermoRawReader RawReader = new COL.MassLib.ThermoRawReader(openFileDialog1.FileName);
/*GlypID.Peaks.clsPeakProcessorParameters clsParameters = new GlypID.Peaks.clsPeakProcessorParameters();
* clsParameters.SignalToNoiseThreshold = 0.0f;
* clsParameters.PeakBackgroundRatio = 0.01f;*/
//RawReader.SetPeakProcessorParameter(2, 2);
scan = RawReader.ReadScan(ScanNo);
}
else
{
//scan = new mzXMLReader(openFileDialog1.FileName).ReadScan(ScanNo);
}
int NoNeuAc = 0;
int NoNeuGc = 0;
if (rdoNeuAc.Checked)
{
NoNeuAc = Convert.ToInt32(txtSia.Text);
}
else
{
NoNeuGc = Convert.ToInt32(txtSia.Text);
}
List <int> SequenceParameters = new List <int>();
SequenceParameters.Add(Convert.ToInt32(txtTopPeaks_i.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopDiagPeaks_j.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopCorePeaks_k.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopBrancingPeaks_l.Text));
SequenceParameters.Add(Convert.ToInt32(txtMaxGlycansToCompleteStruct_m.Text));
GS = new GlycanSequencing_MultipleScoring(scan, scan.ParentCharge, Convert.ToInt32(txtHex.Text), Convert.ToInt32(txtHexNAc.Text), Convert.ToInt32(txtdeHex.Text), NoNeuAc, NoNeuGc, @"D:\tmp", true, 0.8f, 10, SequenceParameters, Peptides.ReadFastaFile(txtPeptideSeq.Text));
GS.NumbersOfPeaksForSequencing = 140;
GS.UseAVGMass = true;
//GS.DebugMode(@"E:\temp\SeqTmp\");
GS.CreatePrecursotMZ = true;
GS.RewardForCompleteStructure = 3;
GS.StartSequencing();
GS.GetTopRankScoreStructre(1);
//lstPeak.Items.Add("Top " + GS.FilteredPeaks.Count.ToString() + " peaks");
//lstPeak.Items.Add("m/z / normailzed intensity ");
//foreach (MSPoint p in GS.FilteredPeaks)
//{
// lstPeak.Items.Add(p.Mass.ToString("0.0000") +"/" + p.Intensity.ToString("0.0000"));
//}
bool isFullSeq = false;
ReportStructure = GS.SequencedStructures;
if (ReportStructure.Count == 0)
{
MessageBox.Show("No Structure Found");
return;
}
if (GS.FullSequencedStructures.Count != 0)
{
ReportStructure = GS.FullSequencedStructures;
isFullSeq = true;
}
AminoAcidMass AA = new AminoAcidMass();
for (int i = 0; i < ReportStructure.Count; i++)
{
GlycanStructure gt = ReportStructure[i];
DataRow row = dtTrees.NewRow();
//row.Add(new Object[] (gt.Mass.ToString("0.0000"), gt.Score.ToString("0.0000"),gt.GetIUPACString()));
row["ID"] = i.ToString();
row["Glycan Mass"] = gt.GlycanAVGMonoMass.ToString("0.0000");
row["Y1"] = gt.Y1.Mass.ToString("0.0000");;
row["Core Score"] = Convert.ToSingle((gt.CoreScore).ToString("0.00"));
row["Branch Score"] = Convert.ToSingle((gt.BranchScore).ToString("0.00"));
row["Append Glycan Score"] = Convert.ToSingle((gt.InCompleteScore).ToString("0.00"));
if (gt.IsCompleteByPrecursorDifference)
{
row["PPM"] =
Convert.ToSingle(
MassUtility.GetMassPPM(
gt.GlycanMonoMass + AA.GetMonoMW(gt.PeptideSequence, true) +
GetGlycanMassByGlycanString(gt.RestGlycanString), GS.PrecusorMonoMass)
.ToString("0.00"));
}
else
{
row["PPM"] =
Convert.ToSingle(
MassUtility.GetMassPPM(
gt.GlycanMonoMass + AA.GetMonoMW(gt.PeptideSequence, true), GS.PrecusorMonoMass).ToString("0.00"));
}
row["Peptide"] = gt.PeptideSequence;
row["Append Glycan"] = gt.RestGlycanString;
row["IUPAC"] = gt.IUPACString;
GlycansDrawer GDRaw = new GlycansDrawer(gt.IUPACString, false);
Image tmpImg = GDRaw.GetImage();
row["Structure"] = tmpImg;
dtTrees.Rows.Add(row);
}
////GS.SequencStructures[0].TheoreticalFragment
dtTrees.DefaultView.Sort = "Glycan Mass DESC";
for (int i = 0; i < dgView.Rows.Count; i++)
{
this.dgView.AutoResizeRow(i);
if (Convert.ToSingle(dgView.Rows[i].Cells["PPM"].Value) <= Convert.ToSingle(txtPrecusorTol.Text))
{
dgView.Rows[i].DefaultCellStyle.BackColor = Color.Red;
}
}
}
}
