private void btnLoadRawCSMSL_Click(object sender, EventArgs e)
{
if (openFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
COL.MassLib.ThermoRawReader raw = new ThermoRawReader(openFileDialog1.FileName);
}
}
public Form1()
{
InitializeComponent();
//StreamReader SR = new StreamReader(@"D:\Data\Jacobson Tang Meeting\bkdsub_smooth_centroid RNASE5.txt");
//List<double> mzs = new List<double>();
//List<double> intensities = new List<double>();
//do
//{
// string tmp = SR.ReadLine();
// mzs.Add(Convert.ToDouble(tmp.Split('\t')[0]));
// intensities.Add(Convert.ToDouble(tmp.Split('\t')[1]));
//} while (!SR.EndOfStream);
//SR.Close();
//GraphPane gp = zedGraphControl1.GraphPane;
//PointPairList ppl = new PointPairList(mzs.ToArray(), intensities.ToArray());
//gp.AddBar("X-Y", ppl, Color.Black);
//gp.AxisChange();
//zedGraphControl1.Refresh();
//List<Protease.Type> proteasList = new List<Protease.Type>();
//proteasList.Add(Protease.Type.Trypsin);
//List<ProteinInfo> PInfos = FastaReader.ReadFasta(@"E:\Dropbox\@Paper\MyPaper\GlycanSeq_AC\Data\H1N1\H1N1.fasta");
//List<string> Peptides = PInfos[0].NGlycopeptide(0, proteasList, enumPeptideMutation.NoMutation);
//List<string> MutaPeptides = PInfos[0].NGlycopeptide(0, proteasList,enumPeptideMutation.DtoN);
//Console.WriteLine(Peptides.Count);
//Console.WriteLine(MutaPeptides.Count);
COL.GlycoLib.ReadGlycanListFromFile.ReadGlycanList(@"D:\!Git\MultiGlycan\lib\Default_Combination.csv", true,
false, false, true, true);
COL.MassLib.ThermoRawReader Raw = new ThermoRawReader(@"E:\Dropbox\@Paper\MyPaper\GlycanSeq_AC\Data\H1N1\P-Glu-C_IU_090710_HCD.RAW");
List <MSScan> Scan = Raw.ReadScanWMSLevel(13107, 13127, 1);
Console.WriteLine(Raw.NumberOfScans.ToString());
List <MSScan> MS1 = Raw.ReadScanWMSLevel(1, Raw.NumberOfScans, 1);
List <MSScan> MS2 = Raw.ReadScanWMSLevel(1, Raw.NumberOfScans, 2);
int CIDCount = 0;
int HCDCount = 0;
foreach (var m in MS2)
{
if (m.IsCIDScan)
{
CIDCount++;
}
if (m.IsHCDScan)
{
HCDCount++;
}
}
Console.WriteLine(CIDCount.ToString());
}
private void button3_Click(object sender, EventArgs e)
{
MassLib.ThermoRawReader Raw = new ThermoRawReader(@"E:\Dropbox\Chuan-Yih\PerMethQuant\RiboB_7plex_05302014.raw");
List <MSScan> scans = Raw.ReadScans(766, 1066);
List <MSPeak> Peaks = new List <MSPeak>();
foreach (MSScan s in scans)
{
foreach (MSPeak p in s.MSPeaks)
{
if (p.ChargeState == 2)
{
Peaks.Add(p);
}
//if (p.MonoisotopicMZ >= 834.62 && p.MonoisotopicMZ <= 834.65)
//{
// Peaks.Add(p);
//}
}
}
}
private void button1_Click(object sender, EventArgs e)
{
ThermoRawReader TRaw = (ThermoRawReader)raw;
string[] TagArray = TRaw.GetTrailerExtraLabelArray(1);
//Title
int msCount = 0;
int msmsCount = 0;
int CIDcount = 0;
int msCount = 0;
int msmsCount = 0;
int CIDcount = 0;
int HCDcount = 0;
int HCDcount = 0;
for (int i = 1; i <= raw.NumberOfScans; i++)
{
if (TRaw.GetMsLevel(i) == 1)
{
msCount += 1;
msCount += 1;
}
else
{
msmsCount += 1;
msmsCount += 1;
if (TRaw.IsCIDScan(i))
{
CIDcount += 1;
}
else
{
HCDcount += 1;
}
}
}
}
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
}
