public MSScan GetAllPeaks()
{
_Scan = new MSScan(0);
int LineNumber = 0;
StreamReader sr = new StreamReader(_filepath);
string tmp;
double floatout = -0.0f, mz, intensity;
try
{
do
{
tmp = sr.ReadLine();
LineNumber++;
if (double.TryParse(tmp.Split('\t')[0], out floatout))
{
mz = Convert.ToDouble(tmp.Split('\t')[0]);
intensity = Convert.ToDouble(tmp.Split('\t')[1]);
_Scan.AddPoint(new MSPoint(mz, intensity));
}
} while (!sr.EndOfStream);
if (_Scan.MSPointList.Count == 0)
{
throw new Exception("Reading Peak in txt format error on Line:"+ LineNumber+"!! Please Check input File");
}
_Scan.ConvertHashTableToList();
return _Scan;
}
catch
{
throw new Exception("Reading Peak in txt format error!! Please Check input File");
}
finally
{
sr.Close();
}
}
private static string SendScanViaNamedPipe(MSScan argMSScan)
{
System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
MemoryStream memStream = new MemoryStream();
f.Serialize(memStream, argMSScan);
byte[] WriteBuffer = memStream.ToArray();
string responseMsg="";
CSNamedPipe.NativeNamedPipeClient.Run(@"\\.\pipe\MSScan", WriteBuffer, out responseMsg);
return responseMsg;
}
private static MSScan GetScanFromFile(int argScanNo, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge, GlypID.Readers.clsRawData Raw)
{
float[] _cidMzs = null;
float[] _cidIntensities = null;
GlypID.Peaks.clsPeak[] _cidPeaks = new GlypID.Peaks.clsPeak[1];
GlypID.Peaks.clsPeak[] _parentPeaks = new GlypID.Peaks.clsPeak[1];
GlypID.HornTransform.clsHornTransform mobjTransform = new GlypID.HornTransform.clsHornTransform();
GlypID.HornTransform.clsHornTransformParameters mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters() ;
GlypID.HornTransform.clsHornTransformResults[] _transformResult;
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessorParameters cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor() ;
GlypID.Peaks.clsPeakProcessorParameters parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
Raw.GetSpectrum(argScanNo, ref _cidMzs, ref _cidIntensities);
scan.MsLevel = Raw.GetMSLevel(Convert.ToInt32(argScanNo));
double min_peptide_intensity = 0;
scan.Time = Raw.GetScanTime(scan.ScanNo);
scan.ScanHeader = Raw.GetScanDescription(scan.ScanNo);
if (scan.MsLevel != 1)
{
float[] _parentRawMzs = null;
float[] _parentRawIntensitys = null;
string Header = Raw.GetScanDescription(argScanNo);
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
if (Header.Substring(Header.IndexOf("+") + 1).Trim().StartsWith("p"))
{
cidPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
}
// cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
// Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), false);
for (int chNum = 0; chNum < _cidMzs.Length; chNum++)
{
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_cidMzs[chNum]),
Convert.ToSingle(_cidIntensities[chNum])));
}
//for (int chNum = 0; chNum < _cidMzs.Length; chNum++)
//{
// scan.MSPeaks.Add(new MSPeak(
// Convert.ToSingle(_cidMzs[chNum]),
// Convert.ToSingle(_cidIntensities[chNum])));
//}
// Get parent information
scan.ParentScanNo = Raw.GetParentScan(scan.ScanNo);
Raw.GetSpectrum(scan.ParentScanNo, ref _parentRawMzs, ref _parentRawIntensitys);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
float _parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = false;
if (Raw.IsFTScan(scan.ParentScanNo))
{
// High resolution data
found = mobjTransform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(scan.ParentMZ), ref _transformResult);
}
if (!found)//de-isotope fail
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(scan.ScanNo);
double monoMZ = Raw.GetMonoMzFromHeader(scan.ScanNo);
List<float> ParentMzs = new List<float>(_parentRawMzs);
int CloseIdx = MassUtility.GetClosestMassIdx(ParentMzs, Convert.ToSingle(monoMZ));
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), Convert.ToInt32(_parentRawIntensitys[CloseIdx]), ref charges, ref _transformResult);
}
else
{
// instrument has no charge just store 2 and 3.
short[] charges = new short[2];
charges[0] = 2;
charges[1] = 3;
mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), Convert.ToInt32(_parentRawIntensitys[CloseIdx]), ref charges, ref _transformResult);
}
}
if (_transformResult[0].mint_peak_index == -1) //De-isotope parent scan
{
//Get parent info
MSScan _parentScan = GetScanFromFile(scan.ParentScanNo, argSingleToNoise, argPeakBackground, argPeptideBackground, argMaxCharge,Raw);
float[] _MSMzs = null;
float[] _MSIntensities = null;
Raw.GetSpectrum(scan.ParentScanNo, ref _MSMzs, ref _MSIntensities);
// Now find peaks
parentPeakParameters.SignalToNoiseThreshold = 0;
parentPeakParameters.PeakBackgroundRatio = 0.01;
parentPeakProcessor.SetOptions(parentPeakParameters);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _MSMzs, ref _MSIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
//Look for charge and mono.
float[] monoandcharge = FindChargeAndMono(_cidPeaks, Convert.ToSingle(Raw.GetParentMz(scan.ScanNo)), scan.ScanNo,Raw);
//scan.ParentMonoMW = _parentScan.MSPeaks[ClosedIdx].MonoMass;
//scan.ParentAVGMonoMW = _parentScan.MSPeaks[ClosedIdx].;
scan.ParentMZ = monoandcharge[0];
if (monoandcharge[1] == 0.0f)
{
scan.ParentCharge = Convert.ToInt32(Raw.GetMonoChargeFromHeader(scan.ParentScanNo));
}
else
{
scan.ParentCharge = Convert.ToInt32(monoandcharge[1]);
}
scan.ParentMonoMW = (monoandcharge[0] - Atoms.ProtonMass) * monoandcharge[1];
}
else
{
scan.ParentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
scan.ParentAVGMonoMW = (float)_transformResult[0].mdbl_average_mw;
scan.ParentMZ = (float)_transformResult[0].mdbl_mz;
scan.ParentCharge = (int)_transformResult[0].mshort_cs;
}
scan.IsCIDScan = Raw.IsCIDScan(argScanNo);
scan.IsFTScan = Raw.IsFTScan(argScanNo);
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
Array.Clear(_parentRawMzs, 0, _parentRawMzs.Length);
Array.Clear(_parentRawIntensitys, 0, _parentRawIntensitys.Length);
}
else //MS Scan
{
scan.ParentMZ = 0.0f;
double mdbl_current_background_intensity = 0;
// Now find peaks
parentPeakParameters.SignalToNoiseThreshold = argSingleToNoise;
parentPeakParameters.PeakBackgroundRatio = argPeakBackground;
parentPeakProcessor.SetOptions(parentPeakParameters);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
mdbl_current_background_intensity = parentPeakProcessor.GetBackgroundIntensity(ref _cidIntensities);
// Settings
min_peptide_intensity = mdbl_current_background_intensity * mobjTransformParameters.PeptideMinBackgroundRatio;
if (mobjTransformParameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < mobjTransformParameters.AbsolutePeptideIntensity)
min_peptide_intensity = mobjTransformParameters.AbsolutePeptideIntensity;
}
mobjTransformParameters.PeptideMinBackgroundRatio = argPeptideBackground;
mobjTransformParameters.MaxCharge = argMaxCharge;
mobjTransform.TransformParameters = mobjTransformParameters;
// Now perform deisotoping
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
mobjTransform.PerformTransform(Convert.ToSingle(mdbl_current_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _cidMzs, ref _cidIntensities, ref _cidPeaks, ref _transformResult);
// for getting results
for (int chNum = 0; chNum < _transformResult.Length; chNum++)
{
double sumintensity = 0.0;
double mostIntenseIntensity = 0.0;
for (int i = 0; i < _transformResult[chNum].marr_isotope_peak_indices.Length; i++)
{
sumintensity = sumintensity + _cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_intensity;
if (Math.Abs(_transformResult[chNum].mdbl_most_intense_mw -
(_cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_mz * _transformResult[chNum].mshort_cs - Atoms.ProtonMass * _transformResult[chNum].mshort_cs))
< 1.0 / _transformResult[chNum].mshort_cs)
{
mostIntenseIntensity = _cidPeaks[_transformResult[chNum].mint_peak_index].mdbl_intensity;
}
}
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_transformResult[chNum].mdbl_mono_mw),
_transformResult[chNum].mint_mono_intensity,
_transformResult[chNum].mshort_cs,
Convert.ToSingle(_transformResult[chNum].mdbl_mz),
Convert.ToSingle(_transformResult[chNum].mdbl_fit),
Convert.ToSingle(_transformResult[chNum].mdbl_most_intense_mw),
mostIntenseIntensity,
sumintensity
));
}
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
}
return scan;
}
//, float argPPM = 6, int argMinPeakCount=3)
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)
{
int mslevel = GetMsLevel(argScanNo);
tolSN = argMinSN;
MSScan scan = new MSScan(argScanNo);
scan.MsLevel = GetMsLevel(argScanNo);
scan.Time = GetRetentionTime(argScanNo);
scan.ScanHeader = GetScanDescription(argScanNo);
double[,] peakData;
if (GetMzAnalyzer(argScanNo) == ThermoMzAnalyzer.ITMS) //Low Res
{
object massList = null;
object peakFlags = null;
int arraySize = -1;
double centroidPeakWidth = double.NaN;
_rawConnection.GetMassListFromScanNum(ref argScanNo, null, 0, 0, 0,0, ref centroidPeakWidth, ref massList, ref peakFlags, ref arraySize);
peakData = (double[,])massList;
}
else
{
object labels = null;
object flags = null;
_rawConnection.GetLabelData(ref labels, ref flags, ref argScanNo);
peakData = (double[,])labels;
}
scan.RawMZs = new float[peakData.GetLength(1)];
scan.RawIntensities = new float[peakData.GetLength(1)];
if (mslevel == 1)
{
List<float> MzsAboveSN = new List<float>();
List<float> IntensitysAboveSN = new List<float>();
for (int i = 0; i < peakData.GetLength(1); i++)
{
scan.RawMZs[i] = Convert.ToSingle(peakData[(int) RawLabelDataColumn.MZ, i]);
scan.RawIntensities[i] = Convert.ToSingle(peakData[(int) RawLabelDataColumn.Intensity, i]);
if (peakData.GetLength(0) >= 4) //Data contain SN
{
double Noise = peakData[(int) RawLabelDataColumn.NoiseLevel, i];
double SN = 0;
if (Noise.Equals(0))
{
SN = float.NaN;
}
else
{
SN = scan.RawIntensities[i]/Noise;
}
if (SN >= tolSN)
{
MzsAboveSN.Add(scan.RawMZs[i]);
IntensitysAboveSN.Add(scan.RawIntensities[i]);
}
}
else
{
MzsAboveSN.Add(scan.RawMZs[i]);
IntensitysAboveSN.Add(scan.RawIntensities[i]);
}
}
scan.MZs = MzsAboveSN.ToArray();
scan.Intensities = IntensitysAboveSN.ToArray();
}
else // MS/MS
{
scan.MZs = new float[peakData.GetLength(1)];
scan.Intensities = new float[peakData.GetLength(1)];
for (int i = 0; i < peakData.GetLength(1); i++)
{
scan.MZs[i] = Convert.ToSingle(peakData[(int) RawLabelDataColumn.MZ, i]);
scan.Intensities[i] = Convert.ToSingle(peakData[(int) RawLabelDataColumn.Intensity, i]);
}
scan.ParentScanNo = GetParentScanNumber(argScanNo);
scan.ParentMZ = GetPrecusorMz(argScanNo);
scan.ParentCharge = GetPrecusorCharge(argScanNo);
//Sometime get wrong value
//scan.ParentMonoMz = Convert.ToSingle(GetExtraValue(argScanNo, "Monoisotopic M/Z:"));
//Find in raw data
scan.ParentMonoMz = GetPrecusorMz(argScanNo);
MSScan parentScan = GetScanFromFile(scan.ParentScanNo);
float peakBefore = scan.ParentMZ - (1/(float) scan.ParentCharge);
float foundPeak = parentScan.RawMZs.OrderBy(x => Math.Abs(x - peakBefore)).ToList()[0];
while (MassUtility.GetMassPPM(foundPeak, peakBefore) <= 10) //10PPM
{
//Find another
scan.ParentMonoMz = foundPeak;
peakBefore = foundPeak - (1 / (float)scan.ParentCharge);
foundPeak = parentScan.MZs.OrderBy(x => Math.Abs(x - peakBefore)).ToList()[0];
}
scan.ParentBasePeak = parentScan.MaxIntensity;
scan.ParentIntensity = parentScan.RawIntensities[parentScan.RawMZs.ToList().IndexOf(scan.ParentMonoMz)];
}
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsHCDScan = IsHCDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
return scan;
}
public static Image GetAnnotatedImage(string argPeptide, MSScan argScan, List<MSPoint> argPeaks, GlycanStructure argStructure)
{
float MaxX = argStructure.Root.FetchAllGlycanNode().OrderByDescending(o => o.IDMass).ToList()[0].IDMass;
if (MaxX + 100 > 2000.0)
{
MaxX = 2000.0f;
}
else
{
MaxX = MaxX + 100;
}
ZedGraph.GraphPane Pane = new ZedGraph.GraphPane(new RectangleF(0.0f, 0.0f, 2000.0f, 1500.0f), argScan.ScanNo.ToString(), "Mass", "Intensity");
//ZedGraph.MasterPane Pane = new ZedGraph.MasterPane(argTitle,new RectangleF(0.0f, 0.0f, 2400.0f, 1800.0f) );
Pane.XAxis.MajorTic.IsInside = false;
Pane.XAxis.MinorTic.IsInside = false;
Pane.Legend.IsVisible = false;
ZedGraph.PointPairList Peaks = new ZedGraph.PointPairList();
double MaxIntensity = 0.0;
/////////////////
//Peaks
////////////////
foreach (MSPoint p in argPeaks)
{
if (p.Intensity > MaxIntensity && p.Mass<=MaxX)
{
MaxIntensity = p.Intensity;
}
}
foreach (MSPoint p in argPeaks)
{
if (p.Mass <= MaxX)
{
Peaks.Add(p.Mass, (p.Intensity/MaxIntensity)*100.0);
}
}
Pane.AddStick("Peaks", Peaks, Color.Red);
//////////////////
//Y1 text object
//////////////////
/* ZedGraph.TextObj txtY1 = new ZedGraph.TextObj("Y1", argStructure.Y1.MZ, 102);
txtY1.FontSpec.Size = txtY1.FontSpe.cSize*0.5f;
txtY1.FontSpec.Border.IsVisible = false;
Pane.GraphObjList.Insert(0, txtY1);*/
/////////////////
//Structure
////////////////
GlycansDrawer GS;
double previousBoundary = 0;
foreach (GlycanTreeNode t in argStructure.Root.FetchAllGlycanNode().OrderBy(o => o.IDMass).ToList())
{
GS = new GlycansDrawer(t.IUPACFromRoot, false);
double glycopeptideMZ = t.IDMass;
//double glycopeptideMZ =argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfHexNac * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.HexNAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfHex*GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.Hex, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfDeHex * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.DeHex, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfNeuAc * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.NeuAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfNeuGc * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.NeuGc, FGS.Charge);
Image imgStructure = GlycanImage.RotateImage(GS.GetImage(), 270);
ZedGraph.TextObj txtGlycanMz = new ZedGraph.TextObj(glycopeptideMZ.ToString("0.000"), 100, 131);
double PositionX = glycopeptideMZ;
if (previousBoundary >= PositionX)
{
PositionX = previousBoundary + 20;
}
if (imgStructure.Width > txtGlycanMz.Location.Width)
{
previousBoundary = imgStructure.Width + PositionX;
}
else
{
previousBoundary = (float)txtGlycanMz.Location.Width + PositionX;
}
ZedGraph.ImageObj glycan = new ZedGraph.ImageObj(imgStructure, PositionX, 130, imgStructure.Width + 20, imgStructure.Height);
glycan.IsScaled = false;
glycan.Location.AlignV = ZedGraph.AlignV.Bottom;
txtGlycanMz.Location.X = glycan.Location.X + (float)glycan.Image.Width / 2 - (float)txtGlycanMz.Location.Width / 2;
txtGlycanMz.FontSpec.Size = txtGlycanMz.FontSpec.Size * 0.3f;
txtGlycanMz.FontSpec.Border.IsVisible = false;
Pane.GraphObjList.Add(txtGlycanMz);
Pane.GraphObjList.Add(glycan);
double interval = 100000;
int idx = 0;
for (int i = 0; i < Peaks.Count; i++)
{
if (Math.Abs(Peaks[i].X - glycopeptideMZ) < interval)
{
interval = Math.Abs((float)Peaks[i].X - glycopeptideMZ);
idx = i;
}
}
string mzLabelwPPM = Peaks[idx].X.ToString("0.000");// + "\n(" + Math.Abs(glycopeptideMZ - (float)Peaks[idx].X).ToString("0") + "da)";
ZedGraph.TextObj PeakLabel = new ZedGraph.TextObj(mzLabelwPPM, Peaks[idx].X, Peaks[idx].Y + 3.0);
PeakLabel.FontSpec.Size = PeakLabel.FontSpec.Size * 0.3f;
PeakLabel.FontSpec.Border.IsVisible = false;
PeakLabel.FontSpec.Fill.IsVisible = false;
Pane.GraphObjList.Add(PeakLabel);
}
Pane.AxisChange();
Pane.YAxis.Scale.Max = 145;
Pane.XAxis.Scale.Min = Convert.ToInt32(argStructure.Y1.Mass - 100);
Pane.XAxis.Scale.Max = Peaks[Peaks.Count - 1].X + 100;
////////////
//Glycan Structure
////////////
GS = new GlycansDrawer(argStructure.IUPACString, false);
Image imgStruc = RotateImage( GS.GetImage() ,180);
ZedGraph.ImageObj fullStructure = new ZedGraph.ImageObj(imgStruc, Pane.XAxis.Scale.Min + 20, 140, imgStruc.Width + 20, imgStruc.Height);
fullStructure.IsScaled = false;
Pane.GraphObjList.Add(fullStructure);
///////////////
//Glycan M/Z
//////////////
double glycopeptidemz = GlycanMass.GetGlycanMasswithCharge(argStructure.Root.GlycanType,argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
ZedGraph.TextObj txtGlycanMZ = new ZedGraph.TextObj("\n Precursor:" + argScan.ParentMZ.ToString("0.000")+"(" +argScan.ParentCharge.ToString()+")"+
"\nPeptide Sequence:" + argPeptide
, Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X2, 140);
txtGlycanMZ.FontSpec.Size = txtGlycanMZ.FontSpec.Size * 0.3f;
txtGlycanMZ.FontSpec.Border.IsVisible = false;
txtGlycanMZ.FontSpec.Fill.IsVisible = false;
Pane.GraphObjList.Add(txtGlycanMZ);
Image tmp = (Image)Pane.GetImage();
return tmp;
}
public MSScan ReadScan(int argScanNum)
{
string ScanXML = "";
if (_scanOffset != null && _scanOffset.ContainsKey(argScanNum)) //has index offset
{
using (StreamReader sr = new StreamReader(_filepath))
{
sr.BaseStream.Seek(_scanOffset[argScanNum], SeekOrigin.Begin);
string line = sr.ReadLine();
do
{
ScanXML = ScanXML + line+"\n";
line = sr.ReadLine();
} while (!line.Contains("</scan>"));
ScanXML = ScanXML + line + "\n";
}
}
else //no indexOffset
{
using (XmlReader reader = XmlReader.Create(_filepath))
{
while (reader.ReadToFollowing("scan"))
{
if (reader.GetAttribute("num") == argScanNum.ToString())
{
ScanXML = reader.ReadInnerXml();
break;
}
}
}
}
MSScan _scan =new MSScan(argScanNum);
XmlDocument doc = new XmlDocument();
doc.LoadXml(ScanXML);
XmlNode XmlScan = doc.FirstChild;
int PeakCount = 0;
foreach (XmlAttribute attribute in XmlScan.Attributes)
{
switch (attribute.Name)
{
case "msLevel":
_scan.MsLevel = Convert.ToInt32(attribute.Value);
break;
case"peaksCount":
PeakCount = Convert.ToInt32(attribute.Value);
break;
case "retentionTime":
_scan.Time = Convert.ToDouble(attribute.Value.Substring(2, attribute.Value.Length - 3)) / 60.0;
break;
}
}
//Peaks
XmlNode Peaks = XmlScan.FirstChild;
while (Peaks.Name != "peaks")
{
Peaks =Peaks.NextSibling;
}
int Precision = Convert.ToInt32(Peaks.Attributes["precision"].Value);
List<MSPoint> tmp = ParsePeakNode(Peaks.InnerText, PeakCount, Precision);
float[] mz = new float[PeakCount];
float[] intensity = new float[PeakCount];
for (int i = 0; i < PeakCount; i++)
{
mz[i] = Convert.ToSingle(tmp[i].Mass);
intensity[i] = Convert.ToSingle(tmp[i].Intensity);
}
_scan.RawMZs = mz;
_scan.RawIntensities = intensity;
_scan.MZs = mz;
_scan.Intensities = intensity;
return _scan;
}
/// <summary>
/// Merge All Peaks to Scan 0
/// </summary>
/// <returns></returns>
//public MSScan GetAllPeaks()
//{
// xmlReader = new XmlTextReader(_filepath);
// MSScan _scan = new MSScan(0);
// //List<MSPoint> _msp = new List<MSPoint>();
// xmlReader.XmlResolver = null;
// try
// {
// while (xmlReader.Read())
// {
// switch (xmlReader.NodeType)
// {
// case XmlNodeType.Element: // The node is an element.
// if (xmlReader.Name == "scan")
// {
// if (xmlReader.GetAttribute("msLevel") == "1")
// {
// int PeakCount = Convert.ToInt32(xmlReader.GetAttribute("peaksCount"));
// int ScanNum = Convert.ToInt32(xmlReader.GetAttribute("num"));
// xmlReader.Read();
// xmlReader.Read();
// if (xmlReader.Name == "peaks")
// {
// int Precision = Convert.ToInt32(xmlReader.GetAttribute("precision"));
// xmlReader.Read();
// string peakString = xmlReader.Value;
// List<MSPoint> tmp = ParsePeakNode(peakString, PeakCount);
// foreach (MSPoint p in tmp)
// {
// _scan.AddPoint(p);
// }
// }
// }
// }
// break;
// }
// }
// // _scan.ConvertHashTableToList();
// return _scan;
// }
// catch
// {
// throw new Exception("Reading Peak in mzXML format error!! Please Check input File");
// }
//}
private MSScan GetScanFromFile(int argScanNo)
{
MSScan _scan = new MSScan(argScanNo);
return _scan;
}
//, float argPPM = 6, int argMinPeakCount=3)
//private MSScan GetScanFromFile(int argScanNo)
//{
// return GetScanFromFile(argScanNo);
//}
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)
{
MSDataScan DataScan = _raw.GetMsScan(argScanNo);
tolSN = argMinSN;
//tolMinPeakCount = argMinPeakCount;
//tolPPM = argPPM;
MZPeak[] peaks;
List<ThermoLabeledPeak> TPeaks = new List<ThermoLabeledPeak>();
peaks = DataScan.MassSpectrum.GetPeaks();
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
scan.MsLevel = GetMsLevel(argScanNo);
scan.Time = _raw.GetRetentionTime(argScanNo);
scan.ScanHeader = _raw.GetScanFilter(argScanNo);
List<MSPeak> MSPsks = new List<MSPeak>();
#region MSScan
if (scan.MsLevel == 1)
{
float[] RawMz = new float[peaks.Length];
float[] RawIntensity = new float[peaks.Length];
for (int i = 0; i < peaks.Length; i++)
{
RawMz[i] = Convert.ToSingle(peaks[i].MZ);
RawIntensity[i] = Convert.ToSingle(peaks[i].Intensity);
ThermoLabeledPeak TPeak = (ThermoLabeledPeak)peaks[i];
if ( TPeak.SN >= tolSN )
{
TPeaks.Add(TPeak);
}
}
float[] Mz = new float[TPeaks.Count];
float[] Intensity = new float[TPeaks.Count];
for (int i = 0; i < TPeaks.Count; i++)
{
Mz[i] = Convert.ToSingle(TPeaks[i].MZ);
Intensity[i] = Convert.ToSingle(TPeaks[i].Intensity);
}
scan.RawMZs = RawMz;
scan.RawIntensities = RawIntensity;
scan.MZs = Mz;
scan.Intensities = Intensity;
//************************Peak Picking
//scan.MSPeaks = MSPsks;
//List<float> TPeaksMZ = new List<float>();
//for (int i = 0; i < TPeaks.Count; i++)
//{
// TPeaksMZ.Add(Convert.ToSingle(TPeaks[i].MZ));
//}
//do
//{
// ThermoLabeledPeak BasePeak = TPeaks[0];
// List<ThermoLabeledPeak> clusterPeaks = new List<ThermoLabeledPeak>();
// List<int> RemoveIdx = new List<int>();
// RemoveIdx.Add(0);
// clusterPeaks.Add(BasePeak);
// double Interval = 1 / (double)BasePeak.Charge;
// double FirstMZ = BasePeak.MZ;
// for (int i = 1; i < TPeaks.Count; i++)
// {
// if (TPeaks[i].MZ - FirstMZ > Interval * 10)
// {
// break;
// }
// List<int> ClosePeaks = MassUtility.GetClosestMassIdxsWithinPPM(TPeaksMZ.ToArray(), Convert.ToSingle(BasePeak.MZ + Interval), argPPM);
// if (ClosePeaks.Count == 1 && TPeaks[ClosePeaks[0]].Charge == BasePeak.Charge)
// {
// BasePeak = TPeaks[i];
// clusterPeaks.Add(TPeaks[i]);
// RemoveIdx.Add(i);
// }
// else if (ClosePeaks.Count > 1)
// {
// double minPPM = 100;
// int minPPMIdx = 0;
// float maxIntensity = 0;
// int maxIntensityIdx = 0;
// for (int j = 0; j < ClosePeaks.Count; j++)
// {
// if (MassUtility.GetMassPPM(BasePeak.MZ + Interval, mz[ClosePeaks[j]]) < minPPM)
// {
// minPPMIdx = ClosePeaks[j];
// minPPM = MassUtility.GetMassPPM(BasePeak.MZ + Interval, mz[ClosePeaks[j]]);
// }
// if (intensity[ClosePeaks[j]] > maxIntensity)
// {
// maxIntensity = intensity[ClosePeaks[j]];
// maxIntensityIdx = ClosePeaks[j];
// }
// }
// BasePeak = TPeaks[minPPMIdx];
// clusterPeaks.Add(TPeaks[minPPMIdx]);
// RemoveIdx.Add(minPPMIdx);
// }
// }
// if (clusterPeaks.Count < argMinPeakCount)
// {
// TPeaks.RemoveAt(RemoveIdx[0]);
// TPeaksMZ.RemoveAt(RemoveIdx[0]);
// }
// else
// {
// float MostIntenseMZ = 0.0f;
// double MostIntenseIntneisty = 0;
// double ClusterIntensity = 0;
// RemoveIdx.Reverse();
// for (int i = 0; i < RemoveIdx.Count; i++)
// {
// if (TPeaks[RemoveIdx[i]].Intensity > MostIntenseIntneisty)
// {
// MostIntenseIntneisty = TPeaks[RemoveIdx[i]].Intensity;
// MostIntenseMZ = Convert.ToSingle(TPeaks[RemoveIdx[i]].MZ);
// }
// ClusterIntensity = ClusterIntensity + TPeaks[RemoveIdx[i]].Intensity;
// TPeaks.RemoveAt(RemoveIdx[i]);
// TPeaksMZ.RemoveAt(RemoveIdx[i]);
// }
// scan.MSPeaks.Add(new MSPeak(
// Convert.ToSingle(clusterPeaks[0].MZ),
// Convert.ToSingle(clusterPeaks[0].Intensity),
// clusterPeaks[0].Charge,
// Convert.ToSingle(clusterPeaks[0].MZ),
// Convert.ToSingle(clusterPeaks[0].SN),
// MostIntenseMZ,
// MostIntenseIntneisty,
// ClusterIntensity));
// }
//} while (TPeaks.Count != 0);
}
#endregion
#region MS/MS Scan
else
{
float[] mz = new float[peaks.Length];
float[] intensity = new float[peaks.Length];
for (int i = 0; i < peaks.Length; i++)
{
mz[i] = Convert.ToSingle(peaks[i].MZ);
intensity[i] = Convert.ToSingle(peaks[i].Intensity);
//MSPsks.Add(new MSPeak(mz[i], intensity[i]));
}
scan.MZs = mz;
scan.Intensities = intensity;
//scan.MSPeaks = MSPsks;
// Get parent information
scan.ParentScanNo = _raw.GetParentSpectrumNumber(argScanNo);
scan.ParentMZ = Convert.ToSingle(_raw.GetPrecusorMz(argScanNo));
scan.ParentCharge = _raw.GetPrecusorCharge(argScanNo);
//Parent Mono
if (scan.ParentScanNo != 0)
{
MSScan ParentScan = GetScanFromFile(scan.ParentScanNo);
int ClosedIdx = MassUtility.GetClosestMassIdx(ParentScan.MZs, scan.ParentMZ);
List<int> Peaks = FindPeakIdx(ParentScan.MZs, ClosedIdx, scan.ParentCharge, 10);
scan.ParentMonoMz = ParentScan.MZs[Peaks[0]];
}
}
#endregion
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsHCDScan = IsHCDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
return scan;
}
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)
{
int isProfile = 0;
_rawConnection.IsProfileScanForScanNum(argScanNo, ref isProfile);
object labels = null;
object flags = null;
_rawConnection.GetLabelData(ref labels, ref flags, ref argScanNo);
double[,] LabeledPeaks = (double[,])labels;
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
List<ThermoLabeledPeak> FullLabeledPeak = new List<ThermoLabeledPeak>();
float[] mz = new float[LabeledPeaks.GetLength(1)];
float[] intensity = new float[LabeledPeaks.GetLength(1)];
int j = 0;
for (int i = 0; i < LabeledPeaks.GetLength(1); i++)
{
double sn = LabeledPeaks[1, i] / LabeledPeaks[4, i];
if (sn >= argMinSN)
{
mz[j] = Convert.ToSingle(LabeledPeaks[0, i]);
intensity[j] = Convert.ToSingle(LabeledPeaks[1, i]);
j++;
FullLabeledPeak.Add(new ThermoLabeledPeak(
Convert.ToSingle(LabeledPeaks[0, i]),
Convert.ToSingle(LabeledPeaks[1, i]),
Convert.ToInt32( LabeledPeaks[5, i]),
Convert.ToSingle(LabeledPeaks[4,i])));
}
}
Array.Resize(ref mz, j);
Array.Resize(ref intensity, j);
//scan.MZs = ConvertDoubleArrayToFloatArray(CSMSLScan.MassSpectrum.GetMasses());
scan.MZs = mz;
//scan.Intensities = ConvertDoubleArrayToFloatArray(CSMSLScan.MassSpectrum.GetIntensities());
scan.Intensities = intensity;
scan.MsLevel = GetMsLevel(argScanNo);
double retentionTime = 0;
_rawConnection.RTFromScanNum(argScanNo, ref retentionTime);
scan.Time = retentionTime;
scan.ScanHeader = GetScanDescription(argScanNo);
if (scan.MsLevel != 1)
{
for (int chNum = 0; chNum < scan.MZs.Length; chNum++)
{
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(scan.MZs[chNum]),
Convert.ToSingle(scan.Intensities[chNum])));
}
// Get parent information
object value = null;
_rawConnection.GetTrailerExtraValueForScanNum(argScanNo, "Master Scan Number:", ref value);
scan.ParentScanNo = Convert.ToInt32(value);
string ParentDesc = GetScanDescription(scan.ParentScanNo);
//_rawConnection.GetPrecursorInfoFromScanNum(argScanNo, ref PrecursorInfo, ref PrecursorInfoSize);
//scan.ParentMonoMW = Convert.ToSingle(PrecurorArray.);
//scan.ParentMZ = Convert.ToSingle(PrecurorArray[1,0]);
//scan.ParentCharge = Convert.ToInt32(PrecurorArray.nChargeState);
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
//Array.Clear(_transformResult, 0, _transformResult.Length);
//Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
//Array.Clear(_cidMzs, 0, _cidMzs.Length);
//Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
//Array.Clear(_parentRawMzs, 0, _parentRawMzs.Length);
//Array.Clear(_parentRawIntensitys, 0, _parentRawIntensitys.Length);
}
else //MS Scan
{
do
{
ThermoLabeledPeak BasePeak = FullLabeledPeak[0];
List<ThermoLabeledPeak> clusterPeaks = new List<ThermoLabeledPeak>();
List<int> RemoveIdx = new List<int>();
RemoveIdx.Add(0);
clusterPeaks.Add(BasePeak);
double Interval = 1 / (double)BasePeak.Charge;
double FirstMZ = BasePeak.MZ;
for (int i = 1; i < FullLabeledPeak.Count; i++)
{
if (FullLabeledPeak[i].MZ - FirstMZ > Interval * 10)
{
break;
}
if ((FullLabeledPeak[i].MZ - (BasePeak.MZ + Interval)) < 0.1 && (FullLabeledPeak[i].MZ - (BasePeak.MZ + Interval)) >= 0 && clusterPeaks[0].Charge == FullLabeledPeak[i].Charge)
{
BasePeak = FullLabeledPeak[i];
clusterPeaks.Add(FullLabeledPeak[i]);
RemoveIdx.Add(i);
}
}
if (clusterPeaks.Count < 3)
{
FullLabeledPeak.RemoveAt(RemoveIdx[0]);
}
else
{
float MostIntenseMZ =0.0f;
double MostIntenseIntneisty = 0;
double ClusterIntensity = 0;
RemoveIdx.Reverse();
for (int i = 0; i < RemoveIdx.Count; i++)
{
if(FullLabeledPeak[RemoveIdx[i]].Intensity> MostIntenseIntneisty)
{
MostIntenseIntneisty = FullLabeledPeak[RemoveIdx[i]].Intensity;
MostIntenseMZ = FullLabeledPeak[RemoveIdx[i]].MZ;
}
ClusterIntensity = ClusterIntensity + FullLabeledPeak[RemoveIdx[i]].Intensity;
FullLabeledPeak.RemoveAt(RemoveIdx[i]);
}
scan.MSPeaks.Add(new MSPeak(clusterPeaks[0].Mass, clusterPeaks[0].Intensity, clusterPeaks[0].Charge, clusterPeaks[0].MZ, clusterPeaks[0].SN, MostIntenseMZ, MostIntenseIntneisty, ClusterIntensity));
}
} while (FullLabeledPeak.Count != 0);
//Array.Clear(_transformResult, 0, _transformResult.Length);
//Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
//Array.Clear(_cidMzs, 0, _cidMzs.Length);
//Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
}
return scan;
}
private MSScan GetScanFromFile(int argScanNo)
{
MSScan scan = new MSScan(argScanNo);
float[] _cidMzs = null;
float[] _cidIntensities = null;
Raw.GetSpectrum(argScanNo, ref _cidMzs, ref _cidIntensities);
scan.MsLevel = Raw.GetMSLevel(argScanNo);
double min_peptide_intensity = 0;
scan.Time = Raw.GetScanTime(scan.ScanNo);
scan.ScanHeader = Raw.GetScanDescription(scan.ScanNo);
if (scan.MsLevel != 1)
{
float[] _parentRawMzs = null;
float[] _parentRawIntensitys = null;
scan.ParentMZ = (float)Raw.GetParentMz(argScanNo);
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), false);
for (int chNum = 0; chNum < _cidPeaks.Length; chNum++)
{
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_cidPeaks[chNum].mdbl_mz),
Convert.ToSingle(_cidPeaks[chNum].mdbl_intensity)));
}
//for (int chNum = 0; chNum < _cidMzs.Length; chNum++)
//{
// scan.MSPeaks.Add(new MSPeak(
// Convert.ToSingle(_cidMzs[chNum]),
// Convert.ToSingle(_cidIntensities[chNum])));
//}
// Get parent information
scan.ParentScanNo = Raw.GetParentScan(scan.ScanNo);
Raw.GetSpectrum(scan.ParentScanNo, ref _parentRawMzs, ref _parentRawIntensitys);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
float _parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
bool found = mobjTransform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(scan.ParentMZ), ref _transformResult);
if (Raw.IsFTScan(scan.ParentScanNo))
{
// High resolution data
found = mobjTransform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(scan.ParentMZ), ref _transformResult);
}
//if (!found) //de-isotope fail
//{
// // Low resolution data or bad high res spectra
// short cs = Raw.GetMonoChargeFromHeader(scan.ScanNo);
// if (cs > 0)
// {
// short[] charges = new short[1];
// charges[0] = cs;
// mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), ref charges, ref _transformResult);
// }
// else
// {
// // instrument has no charge just store 2 and 3.
// short[] charges = new short[2];
// charges[0] = 2;
// charges[1] = 3;
// mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), ref charges, ref _transformResult);
// }
//}
scan.ParentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
scan.ParentAVGMonoMW = (float)_transformResult[0].mdbl_average_mw;
scan.ParentCharge = (int)_transformResult[0].mshort_cs;
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
Array.Clear(_parentRawMzs, 0, _parentRawMzs.Length);
Array.Clear(_parentRawIntensitys, 0, _parentRawIntensitys.Length);
}
else //MS Scan
{
scan.ParentMZ = 0.0f;
double mdbl_current_background_intensity = 0;
// Now find peaks
parentPeakParameters.SignalToNoiseThreshold = _singleToNoiseRatio;
parentPeakParameters.PeakBackgroundRatio = _peakBackgroundRatio;
parentPeakProcessor.SetOptions(parentPeakParameters);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
mdbl_current_background_intensity = parentPeakProcessor.GetBackgroundIntensity(ref _cidIntensities);
// Settings
min_peptide_intensity = mdbl_current_background_intensity * mobjTransformParameters.PeptideMinBackgroundRatio;
if (mobjTransformParameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < mobjTransformParameters.AbsolutePeptideIntensity)
min_peptide_intensity = mobjTransformParameters.AbsolutePeptideIntensity;
}
mobjTransformParameters.PeptideMinBackgroundRatio = _peptideMinBackgroundRatio;
mobjTransformParameters.MaxCharge = _maxCharge;
mobjTransform.TransformParameters = mobjTransformParameters;
// Now perform deisotoping
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
mobjTransform.PerformTransform(Convert.ToSingle(mdbl_current_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _cidMzs, ref _cidIntensities, ref _cidPeaks, ref _transformResult);
// for getting results
for (int chNum = 0; chNum < _transformResult.Length; chNum++)
{
double sumintensity = 0.0;
double mostIntenseIntensity = 0.0;
for (int i = 0; i < _transformResult[chNum].marr_isotope_peak_indices.Length; i++)
{
sumintensity = sumintensity + _cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_intensity;
if (Math.Abs(_transformResult[chNum].mdbl_most_intense_mw -
(_cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_mz * _transformResult[chNum].mshort_cs - Atoms.ProtonMass * _transformResult[chNum].mshort_cs)
) < 1.0 / _transformResult[chNum].mshort_cs
)
{
mostIntenseIntensity = _cidPeaks[_transformResult[chNum].mint_peak_index].mdbl_intensity;
}
}
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_transformResult[chNum].mdbl_mono_mw),
_transformResult[chNum].mint_mono_intensity,
_transformResult[chNum].mshort_cs,
Convert.ToSingle(_transformResult[chNum].mdbl_mz),
Convert.ToSingle(_transformResult[chNum].mdbl_fit),
Convert.ToSingle(_transformResult[chNum].mdbl_most_intense_mw),
mostIntenseIntensity,
sumintensity));
}
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
}
return scan;
}
private MSScan GetMSScan(int argScanNo)
{
MSScan msScan = new MSScan(argScanNo);
// GlypID.Readers.clsRawData rawData = new GlypID.Readers.clsRawData() ;
GlypID.HornTransform.clsHornTransform massTransform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor peakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
// Declarations
float[] _mzs = null;
float[] _intensities = null;
GlypID.Peaks.clsPeak[] peaks;
GlypID.HornTransform.clsHornTransformResults[] _transformResults;
// Settings
peak_parameters.SignalToNoiseThreshold = 3.0;
peak_parameters.PeakBackgroundRatio = 5.0;
peakProcessor.SetOptions(peak_parameters);
peakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
transform_parameters.PeptideMinBackgroundRatio = 5.0;
transform_parameters.MaxCharge = 10;
massTransform.TransformParameters = transform_parameters;
// Load
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
if (Raw.GetMSLevel(argScanNo) == 1)
{
// Get spectra
Raw.GetSpectrum(argScanNo, ref _mzs, ref _intensities);
// Get peaks
peaks = new GlypID.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref _mzs, ref _intensities, ref peaks, Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
// Deisotope
double min_background_intensity = peakProcessor.GetBackgroundIntensity(ref _intensities);
double min_peptide_intensity = min_background_intensity * transform_parameters.PeptideMinBackgroundRatio;
_transformResults = new GlypID.HornTransform.clsHornTransformResults[1];
massTransform.PerformTransform(Convert.ToSingle(min_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _mzs, ref _intensities, ref peaks, ref _transformResults);
Array.Clear(_transformResults, 0, _transformResults.Length);
Array.Clear(peaks, 0, peaks.Length);
}
return msScan;
}
public YxList(MSScan argScan, List<ProteinInfo> argProtInfo, float argTorelance)
{
_scan = argScan;
_pInfo = argProtInfo;
_torelance = argTorelance;
}
private void ZedGraphDisplay(MSScan argScan)
{
GraphPane GP = zedGraphControl1.GraphPane;
GP.XAxis.Title.Text = "m/z";
GP.YAxis.Title.Text = "Intensity";
PointPairList pplRaw = new PointPairList();
for (int i = 0; i < argScan.MZs.Length; i++)
{
pplRaw.Add(argScan.MZs[i], argScan.Intensities[i]);
}
PointPairList pplPeak = new PointPairList();
for (int i = 0; i < argScan.MSPeaks.Count; i++)
{
pplPeak.Add(argScan.MSPeaks[i].MonoisotopicMZ,argScan.MSPeaks[i].MonoIntensity);
}
GP.AddBar("Raw", pplRaw, Color.Black);
GP.AddBar("Peak", pplPeak, Color.Blue);
zedGraphControl1.AxisChange();
}
private void ReadandDisplayScan(int argMSScan)
{
if (raw != null)
{
scan = raw.ReadScan(argMSScan);
StringBuilder SB = new StringBuilder();
SB.Append("Scan Num:" + scan.ScanNo + Environment.NewLine);
SB.Append("Scan Time:" + scan.Time + Environment.NewLine);
SB.Append("Scan header:" + scan.ScanHeader + Environment.NewLine);
SB.Append("Scan range:" + scan.MinMZ + "~" + scan.MaxMZ + Environment.NewLine);
SB.Append("Scan MS Level:" + scan.MsLevel + Environment.NewLine);
SB.Append("Scan is FT Scan:" + scan.IsFTScan + Environment.NewLine);
SB.Append("Scan is CID:" + scan.IsCIDScan + Environment.NewLine + Environment.NewLine);
if (scan.MsLevel == 2)
{
SB.Append("Parent Scan Num:" + scan.ParentScanNo + Environment.NewLine);
SB.Append("Precursor M/Z:" + scan.ParentMZ + Environment.NewLine);
SB.Append("Precursor Charge:" + scan.ParentCharge + Environment.NewLine);
SB.Append("Precursor mono mass:" + scan.ParentMonoMW + Environment.NewLine + Environment.NewLine);
}
if (scan.IsHCDScan)
{
HCDInfo HCD = ((ThermoRawReader) raw).GetHCDInfo(argMSScan);
SB.Append("HCD Score:" + HCD.HCDScore.ToString("0.00")+Environment.NewLine);
SB.Append("HCD Glycan Type:" + HCD.GlycanType + Environment.NewLine);
}
SB.Append("MS Peaks:" + scan.MSPeaks.Count + Environment.NewLine);
SB.Append("DeisotopeMZ\tPeak Intensity\tMost intense Mz\tMost intense int\t Cluster int"+Environment.NewLine);
foreach (MSPeak peak in scan.MSPeaks)
{
SB.Append(peak.DeisotopeMz + "\t\t" + peak.MonoIntensity + "\t\t" + peak.MostIntenseMass + "\t\t" + peak.MostIntenseIntensity + "\t\t" + peak.ClusterIntensity + Environment.NewLine);
}
SB.Append(Environment.NewLine + Environment.NewLine + "MZs:" + scan.MZs.Length + Environment.NewLine);
for (int i = 0; i < scan.MZs.Length; i++)
{
SB.Append("[" + i.ToString() + "]" + scan.MZs[i].ToString("0.0000") + "\t" + scan.Intensities[i].ToString("0.0000") + Environment.NewLine);
}
txtPeaks_CSMSL.Text = SB.ToString();
ZedGraphDisplay(scan);
}
}
