private void ListFragementStructure(GlycanStructure argStructure)
{
//dgDetail
DataTable dtDetail = new DataTable();
DataColumn dcID = new DataColumn("ID", Type.GetType("System.Int32"));
DataColumn dcMass = new DataColumn("Mass", Type.GetType("System.Single"));
DataColumn dcScore = new DataColumn("Score", Type.GetType("System.Single"));
DataColumn dcStructure = new DataColumn("Structure", typeof(Image));
dtDetail.Columns.Add(dcID);
dtDetail.Columns.Add(dcMass);
dtDetail.Columns.Add(dcScore);
dtDetail.Columns.Add(dcStructure);
//dgDetail.DataSource = dtDetail;
//dgDetail.Columns[0].Width = 30;
//dgDetail.Columns[1].Width = 70;
//dgDetail.Columns[2].Width = 50;
//dgDetail.Columns[3].Width = 315;
dtDetail.DefaultView.Sort = "Mass";
int idx = 0;
float TotalScore = 0.0f;
GlycansDrawer GDRaw;
foreach (GlycanTreeNode frm in argStructure.TheoreticalFragment)
{
DataRow row = dtDetail.NewRow();
row[0] = idx;
float glycanmass = COL.GlycoLib.GlycanMass.GetGlycanMasswithCharge(frm.GlycanType, argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
int closepeakidx = MassUtility.GetClosestMassIdx(scan.MSPeaks, glycanmass);
row[1] = glycanmass;
if (MassUtility.GetMassPPM(glycanmass, scan.MSPeaks[closepeakidx].MonoisotopicMZ) < _torelance)
{
row[2] = scan.MSPeaks[closepeakidx].MonoIntensity / scan.MaxIntensity;
}
else
{
row[2] = 0.0f;
}
GDRaw = new GlycansDrawer(frm.GetIUPACString(), false);
row[3] = GDRaw.GetImage();
idx++;
dtDetail.Rows.Add(row);
TotalScore = TotalScore + Convert.ToSingle(row[2]);
}
DataRow dtrow = dtDetail.NewRow();
dtrow[0] = idx;
dtrow[1] = GlycanMass.GetGlycanMasswithCharge(argStructure.Root.GlycanType, argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
dtrow[2] = TotalScore;
GDRaw = new GlycansDrawer(argStructure.IUPACString, false);
dtrow[3] = GDRaw.GetImage();
dtDetail.Rows.Add(dtrow);
}
/// <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 YxFinder(List <MSPeak> argSpectrum, float argY1, int argCharge, float argTolerance)
{
_y1 = argY1;
_YxCount = 0;
_charge = argCharge;
GeneratedYxPeak();
_YxMzIdx = new float[5];
for (int i = 0; i <= 4; i++)
{
_YxMzIdx[i] = -1;
}
for (int i = 1; i <= 4; i++)
{
int idx = MassUtility.GetClosestMassIdx(argSpectrum, _YxMz[i]);
if (MassUtility.GetMassPPM(argSpectrum[idx].MonoMass, _YxMz[i]) < argTolerance)
{
_YxMzIdx[i] = idx;
_YxCount++;
}
}
}
private void button1_Click(object sender, EventArgs e)
{
MassUtility.GetMassPPM(697.006653, 697.0557);
}
private List<int> FindPeakIdx(float[] argMZAry, int argTargetIdx, int argCharge, float argPPM)
{
List<int> Peak = new List<int>();
float Interval = 1 / (float)argCharge;
float FirstMZ = argMZAry[argTargetIdx];
int CurrentIdx = argTargetIdx;
Peak.Add(argTargetIdx);
//Forward Peak
for (int i = argTargetIdx - 1; i >= 0; i--)
{
if (argMZAry[argTargetIdx] - argMZAry[i] >= Interval * 10)
{
break;
}
List<int> ClosedPeaks = MassUtility.GetClosestMassIdxsWithinPPM(argMZAry, argMZAry[CurrentIdx] - Interval, argPPM);
if (ClosedPeaks.Count == 1)
{
CurrentIdx = ClosedPeaks[0];
Peak.Insert(0, ClosedPeaks[0]);
}
else if (ClosedPeaks.Count > 1)
{
double minPPM = 100;
int minPPMIdx = 0;
for (int j = 0; j < ClosedPeaks.Count; j++)
{
if (MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] - Interval) < minPPM)
{
minPPMIdx = ClosedPeaks[j];
minPPM = MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval);
}
}
CurrentIdx = minPPMIdx;
Peak.Insert(0, CurrentIdx);
}
}
//Backward Peak
CurrentIdx = argTargetIdx;
for (int i = argTargetIdx + 1; i < argMZAry.Length; i++)
{
if (argMZAry[i] - argMZAry[argTargetIdx] >= Interval * 10)
{
break;
}
List<int> ClosedPeaks = MassUtility.GetClosestMassIdxsWithinPPM(argMZAry, argMZAry[CurrentIdx] + Interval, argPPM);
if (ClosedPeaks.Count == 1)
{
CurrentIdx = ClosedPeaks[0];
Peak.Add(ClosedPeaks[0]);
}
else if (ClosedPeaks.Count > 1)
{
double minPPM = 100;
int minPPMIdx = 0;
for (int j = 0; j < ClosedPeaks.Count; j++)
{
if (MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval) < minPPM)
{
minPPMIdx = ClosedPeaks[j];
minPPM = MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval);
}
}
CurrentIdx = minPPMIdx;
Peak.Add(CurrentIdx);
}
}
return Peak;
}
public static void Processing(ref MultiGlycanESI argMultiGlycan)
{
try
{
List <string> identifiedGlycan = argMultiGlycan.IdentifiedGlycanCompounds.Select(x => x.GlycanKey).Distinct().ToList();
Dictionary <string, List <int> > dictGlycanKeySearchRange = new Dictionary <string, List <int> >();
int LastScan = argMultiGlycan.RawReader.NumberOfScans;
foreach (string glycanKey in identifiedGlycan)
{
List <int> identifedScans =
argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition.GlycanKey == glycanKey)
.Select(y => y.ScanNum)
.ToList();
identifedScans.Sort();
int frontEdge = identifedScans[0];
double FirstIdentifiedTime = argMultiGlycan.RawReader.ReadScan(frontEdge).Time;
while (frontEdge > 1)
{
frontEdge -= 1;
if (argMultiGlycan.RawReader.GetMsLevel(frontEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(frontEdge);
if (FirstIdentifiedTime - s.Time > 5)
{
break;
}
}
int backEdge = identifedScans[identifedScans.Count - 1];
double LastIdentifedTime = argMultiGlycan.RawReader.ReadScan(backEdge).Time;
while (backEdge < LastScan)
{
backEdge += 1;
if (argMultiGlycan.RawReader.GetMsLevel(backEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(backEdge);
if (s.Time - LastIdentifedTime > 5)
{
break;
}
}
dictGlycanKeySearchRange.Add(glycanKey, new List <int>()
{
frontEdge, backEdge
});
}
List <MSScan> msScans = new List <MSScan>();
string previousGlycanKey = "";
foreach (GlycanCompound g in argMultiGlycan.GlycanList.OrderBy(x => x.GlycanKey))
{
if (!identifiedGlycan.Contains(g.GlycanKey))
{
continue;
}
if (previousGlycanKey != g.GlycanKey)
{
msScans.Clear();
//Read Scans
int startScan = dictGlycanKeySearchRange[g.GlycanKey][0] >= 1 ? dictGlycanKeySearchRange[g.GlycanKey][0] : 1;
int endScan = dictGlycanKeySearchRange[g.GlycanKey][1] <= LastScan ? dictGlycanKeySearchRange[g.GlycanKey][1] : LastScan;
msScans.AddRange(argMultiGlycan.RawReader.ReadScanWMSLevel(startScan, endScan, 1));
previousGlycanKey = g.GlycanKey;
}
//FindPeaks
int charge = g.Charge;
List <List <MSScan> > scanSectionsContainPeaks = new List <List <MSScan> >();
for (int i = 0; i < msScans.Count; i++)
{
MSScan scan = msScans[i];
int closedIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
if (MassUtility.GetMassPPM(scan.MZs[closedIdx], g.MZ) <= argMultiGlycan.MassPPM)
{
List <int> peaks = FindPeakIdx(scan.MZs, closedIdx, charge, argMultiGlycan.IsotopePPM);
if (peaks.Count - peaks.IndexOf(closedIdx) < argMultiGlycan.MininumIsotopePeakCount)
{
continue;
}
//Found peaks
if (scanSectionsContainPeaks.Count > 0)
{
MSScan lastSectionLastScan = scanSectionsContainPeaks.Last().Last();
if (scan.Time - lastSectionLastScan.Time > 2.5)
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
else
{
scanSectionsContainPeaks.Last().Add(scan);
}
}
else
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
}
}
//If scans can form an elution profile add to identifed result;
foreach (List <MSScan> sectionScans in scanSectionsContainPeaks)
{
if (sectionScans.Count < 3)
{
continue;
}
else
{
//Add matched peak
foreach (MSScan s in sectionScans)
{
int PeakIdx = MassUtility.GetClosestMassIdx(s.MZs, (float)g.MZ);
MatchedGlycanPeak mPeak = new MatchedGlycanPeak(s.ScanNo, s.Time, s.MSPeaks[PeakIdx], g);
List <int> peaks = FindPeakIdx(s.MZs, PeakIdx, charge, argMultiGlycan.IsotopePPM);
int startIdx = peaks.IndexOf(PeakIdx);
List <MSPoint> lstIsotopes = new List <MSPoint>();
for (int i = startIdx; i < peaks.Count; i++)
{
lstIsotopes.Add(new MSPoint(s.MZs[peaks[i]], s.Intensities[peaks[i]]));
}
mPeak.MSPoints = lstIsotopes;
if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
{
argMultiGlycan.MatchedPeakInScan.Add(mPeak);
}
}
}
}
}
//foreach (GlycanCompound g in argMultiGlycan.IdentifiedGlycanCompounds)
//{
// processed = g;
// //Search Peak in front of the peak
// ThermoRawReader raw = (ThermoRawReader)argMultiGlycan.RawReader;
// List<int> identifedScans = argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition == g).Select(y => y.ScanNum).ToList();
// for (int i = 0; i < identifedScans.Count; i++)
// {
// int identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum -= 1;
// if (identifiedScanNum < 1 || raw.GetRetentionTime(identifedScans[i]) - raw.GetRetentionTime(identifiedScanNum) > argMultiGlycan.MaxLCFrontMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f/g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum += 1;
// if (identifiedScanNum > raw.NumberOfScans || raw.GetRetentionTime(identifiedScanNum) - raw.GetRetentionTime(identifedScans[i]) > argMultiGlycan.MaxLCBackMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f / g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// }
//}
}
catch (Exception ex)
{
throw ex;
}
}
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;
}
}
}
}