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 Params()
{
_scoringParams = new GlypID.Scoring.clsScoringParameters();
_transformParams = new GlypID.HornTransform.clsHornTransformParameters();
_peakParams = new GlypID.Peaks.clsPeakProcessorParameters();
_maxUMCCoverage = 0.2;
_processOnlyNGlycopeptides = true;
_useGlycopeptideFile = false;
_printAsCSV = false;
_inGlycoMode = true;
}
public XRawReader(string argFullFilePath)
{
_fullFilePath = argFullFilePath;
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
mobjTransform = new GlypID.HornTransform.clsHornTransform(); //12KB
mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters(); //4KB
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor(); //68KB
cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
}
public XRawReader(string argFullFilePath)
{
_fullFilePath = argFullFilePath;
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
mobjTransform = new GlypID.HornTransform.clsHornTransform(); //12KB
mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters(); //4KB
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor(); //68KB
cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
}
private void btnRead_Click(object sender, EventArgs e)
{
if (rawReader == null)
{
MessageBox.Show("Load Raw data first");
return;
}
if (txtScanNo.Text == "")
{
MessageBox.Show("Input Scan number");
return;
}
txtPeaks.Text = "";
int ScanNo = Convert.ToInt32(txtScanNo.Text);
GlypID.Peaks.clsPeakProcessorParameters _peakParameter = new GlypID.Peaks.clsPeakProcessorParameters();
GlypID.HornTransform.clsHornTransformParameters _transformParameters = new GlypID.HornTransform.clsHornTransformParameters();
_transformParameters.UseAbsolutePeptideIntensity = chkPeptideMinAbso.Checked;
_transformParameters.AbsolutePeptideIntensity = 0.0;
if (_transformParameters.UseAbsolutePeptideIntensity)
{
_transformParameters.AbsolutePeptideIntensity = Convert.ToDouble(txtPeptideMinAbso.Text);
}
_transformParameters.MaxCharge = Convert.ToInt16(txtMaxCharge.Text);
_transformParameters.PeptideMinBackgroundRatio = Convert.ToDouble(txtPeptideMinRatio.Text);
_peakParameter.SignalToNoiseThreshold = Convert.ToDouble(txtSN.Text);
_peakParameter.PeakBackgroundRatio = Convert.ToDouble(txtPeakPeakBackgroundRatioRatio.Text);
rawReader.SetPeakProcessorParameter(_peakParameter);
rawReader.SetTransformParameter(_transformParameters);
for (int i = 0; i <= 10; i++)
{
MSScan GMSScan = rawReader.ReadScan(ScanNo);
List <MSPeak> deIsotopedPeaks = GMSScan.MSPeaks;
deIsotopedPeaks.Sort();
txtPeaks.Text = "Scan Number" + ScanNo.ToString() + Environment.NewLine;
txtPeaks.Text = txtPeaks.Text + "MSLevel:" + GMSScan.MsLevel.ToString() + "\t\tNumber Peaks" + deIsotopedPeaks.Count.ToString() + Environment.NewLine;
txtPeaks.Text = txtPeaks.Text + "MonoisotopicMZ\tMonoIntensity\tCharge" + Environment.NewLine;
foreach (MSPeak p in deIsotopedPeaks)
{
txtPeaks.Text = txtPeaks.Text + p.MonoisotopicMZ.ToString("0.0000") + "\t\t" + p.MonoIntensity.ToString() + "\t\t" + p.ChargeState.ToString() + Environment.NewLine;
}
}
}
public MultiNGlycanESIMultiThreads(string argGlycanCompound,
string argRawFile,
int argStartScan,
int argEndScan,
int argNoThreads,
float argMassPPM,
float argGlycanMass,
float argMergeDurationMin,
bool argPermenthylated,
bool argReducedReducingEnd,
GlypID.Peaks.clsPeakProcessorParameters argPeakProcessorPara,
GlypID.HornTransform.clsHornTransformParameters argTransformPara)
{
glycanFile = argGlycanCompound;
rawFiles = new Stack <string>();
rawFiles.Push(argRawFile);
StartScan = argStartScan;
EndScan = argEndScan;
_noOfThreads = argNoThreads;
_MassPPM = argMassPPM;
_GlycanPPM = argGlycanMass;
_MergeDurationMin = argMergeDurationMin;
_Permenthylated = argPermenthylated;
_ReducedReducingEnd = argReducedReducingEnd;
_peakParameter = argPeakProcessorPara;
_transformParameter = argTransformPara;
_pool = new Semaphore(0, _noOfThreads);
//doneEvents = new ManualResetEvent[_noOfThreads];
_multiESIThreads = new MultiNGlycanESI[_noOfThreads];
//Copy Dataset
for (int i = 1; i < _noOfThreads; i++) // only need n-1 copies
{
string newFilename = Path.GetDirectoryName(argRawFile) + "\\" + Path.GetFileNameWithoutExtension(argRawFile) + "-" + i.ToString() + Path.GetExtension(argRawFile);
File.Copy(argRawFile, newFilename);
rawFiles.Push(newFilename);
}
//Split Dataset
SplitDataset();
}
public MultiNGlycanESIMultiThreads(string argGlycanCompound,
string argRawFile,
int argStartScan,
int argEndScan,
int argNoThreads,
float argMassPPM ,
float argGlycanMass,
float argMergeDurationMin,
bool argPermenthylated,
bool argReducedReducingEnd,
GlypID.Peaks.clsPeakProcessorParameters argPeakProcessorPara,
GlypID.HornTransform.clsHornTransformParameters argTransformPara)
{
glycanFile = argGlycanCompound;
rawFiles = new Stack<string>();
rawFiles.Push(argRawFile);
StartScan = argStartScan;
EndScan = argEndScan;
_noOfThreads = argNoThreads;
_MassPPM = argMassPPM;
_GlycanPPM = argGlycanMass;
_MergeDurationMin = argMergeDurationMin;
_Permenthylated = argPermenthylated;
_ReducedReducingEnd = argReducedReducingEnd;
_peakParameter = argPeakProcessorPara;
_transformParameter = argTransformPara;
_pool = new Semaphore(0, _noOfThreads);
//doneEvents = new ManualResetEvent[_noOfThreads];
_multiESIThreads = new MultiNGlycanESI[_noOfThreads];
//Copy Dataset
for (int i = 1; i < _noOfThreads; i++) // only need n-1 copies
{
string newFilename = Path.GetDirectoryName(argRawFile) + "\\" + Path.GetFileNameWithoutExtension(argRawFile) + "-" + i.ToString() + Path.GetExtension(argRawFile);
File.Copy(argRawFile, newFilename);
rawFiles.Push(newFilename);
}
//Split Dataset
SplitDataset();
}
public MapCreator()
{
_GlycoMap = new Classes.MapRecord() ;
_utils = new Utilities();
_glycopeptides = new List<GlycopeptideRecord> ();
_TransformParameters = new GlypID.HornTransform.clsHornTransformParameters() ;
_ParentPeakProcessorParams = new GlypID.Peaks.clsPeakProcessorParameters() ;
_MSMSPeakProcessorParams = new GlypID.Peaks.clsPeakProcessorParameters() ;
_ScoringParameters = new GlypID.Scoring.clsScoringParameters();
_HornTransform = new GlypID.HornTransform.clsHornTransform() ;
_ParentPeakProcessor = new GlypID.Peaks.clsPeakProcessor() ;
_MSMSPeakProcessor = new GlypID.Peaks.clsPeakProcessor() ;
_ParentPeaks = new GlypID.Peaks.clsPeak[1] ;
_MSMSPeaks = new GlypID.Peaks.clsPeak[1];
_ParentTransformResults = new GlypID.HornTransform.clsHornTransformResults[1];
_dGlycopeptides = new Dictionary<int, List<GlycopeptideRecord>>();
_CIDScoring = new GlypID.CIDScoring.clsCIDScoring();
_HCDScoring = new GlypID.HCDScoring.clsHCDScoring();
_ETDScoring = new GlypID.ETDScoring.clsETDScoring();
}
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;
}
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);
}
public Class1(string argFileName, int argScanNo)
{
_scanNum = argScanNo;
_filename = argFileName;
GlypID.HornTransform.clsHornTransform Transform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
Raw = new GlypID.Readers.clsRawData(_filename, GlypID.Readers.FileType.FINNIGAN);
Raw.GetSpectrum(_scanNum, ref _cidMzs, ref _cidIntensities);
Transform.TransformParameters = transform_parameters;
_msLevel = Raw.GetMSLevel(_scanNum);
if (_msLevel > 1)
{
_parentScanNum = Raw.GetParentScan(_scanNum);
_parentMz = (float)Raw.GetParentMz(_scanNum);
}
else
{
return; //MS scan
}
Raw.GetSpectrum(_parentScanNum, ref _parentRawMzs, ref _parentRawIntensitys);
_cidPeaks = new GlypID.Peaks.clsPeak[1];
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), false);
_parentPeaks = new GlypID.Peaks.clsPeak[1];
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
_parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
double min_peptide_intensity = _parentBackgroundIntensity * transform_parameters.PeptideMinBackgroundRatio;
if (transform_parameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < transform_parameters.AbsolutePeptideIntensity)
{
min_peptide_intensity = transform_parameters.AbsolutePeptideIntensity;
}
}
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
if (Raw.IsFTScan(_parentScanNum))
{
// High resolution data
found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
}
if (!found)
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(_scanNum);
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500, 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;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500, ref charges, ref _transformResult);
}
}
_parentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
_parentCharge = (int)_transformResult[0].mshort_cs;
MaxIntensityPeak();
Raw.Close();
}
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 GlypID.Peaks.clsPeakProcessorParameters PeakProcessorParameter
//{
// set
// {
// _singleToNoiseRatio = value.SignalToNoiseThreshold;
// _peakBackgroundRatio = value.PeakBackgroundRatio;
// }
//}
public void SetPeakProcessorParameter(GlypID.Peaks.clsPeakProcessorParameters argPeakProcessorParameter)
{
_singleToNoiseRatio = argPeakProcessorParameter.SignalToNoiseThreshold;
_peakBackgroundRatio = argPeakProcessorParameter.PeakBackgroundRatio;
}
public void LoadParameters(GlycoFragworkDLL.Classes.Params thisParams)
{
_TransformParameters = thisParams.TransformParams;
_ParentPeakProcessorParams = thisParams.PeakParams ;
_MSMSPeakProcessorParams = thisParams.PeakParams;
_HCDScoring.ScoringParameters = _CIDScoring.ScoringParameters = _ETDScoring.ScoringParameters = thisParams.ScoringParams;
InitParameters();
_PPM_Diff = thisParams.ScoringParams.PPMTolerance;
}
public Class1(string argFileName,int argScanNo)
{
_scanNum = argScanNo;
_filename = argFileName;
GlypID.HornTransform.clsHornTransform Transform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
Raw = new GlypID.Readers.clsRawData(_filename, GlypID.Readers.FileType.FINNIGAN);
Raw.GetSpectrum(_scanNum, ref _cidMzs, ref _cidIntensities);
Transform.TransformParameters = transform_parameters;
_msLevel = Raw.GetMSLevel(_scanNum);
if (_msLevel > 1)
{
_parentScanNum = Raw.GetParentScan(_scanNum);
_parentMz = (float)Raw.GetParentMz(_scanNum);
}
else
{
return; //MS scan
}
Raw.GetSpectrum(_parentScanNum, ref _parentRawMzs, ref _parentRawIntensitys);
_cidPeaks = new GlypID.Peaks.clsPeak[1];
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), false);
_parentPeaks = new GlypID.Peaks.clsPeak[1];
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
_parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
double min_peptide_intensity = _parentBackgroundIntensity * transform_parameters.PeptideMinBackgroundRatio;
if (transform_parameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < transform_parameters.AbsolutePeptideIntensity)
min_peptide_intensity = transform_parameters.AbsolutePeptideIntensity;
}
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
if (Raw.IsFTScan(_parentScanNum))
{
// High resolution data
found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
}
if (!found)
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(_scanNum);
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz),500, 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;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500,ref charges, ref _transformResult);
}
}
_parentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
_parentCharge = (int)_transformResult[0].mshort_cs;
MaxIntensityPeak();
Raw.Close();
}
private void btnRead_Click(object sender, EventArgs e)
{
if (rawReader == null)
{
MessageBox.Show("Load Raw data first");
return;
}
if (txtScanNo.Text == "")
{
MessageBox.Show("Input Scan number");
return;
}
txtPeaks.Text = "";
int ScanNo = Convert.ToInt32(txtScanNo.Text);
GlypID.Peaks.clsPeakProcessorParameters _peakParameter = new GlypID.Peaks.clsPeakProcessorParameters();
GlypID.HornTransform.clsHornTransformParameters _transformParameters = new GlypID.HornTransform.clsHornTransformParameters();
_transformParameters.UseAbsolutePeptideIntensity = chkPeptideMinAbso.Checked;
_transformParameters.AbsolutePeptideIntensity = 0.0;
if (_transformParameters.UseAbsolutePeptideIntensity)
{
_transformParameters.AbsolutePeptideIntensity = Convert.ToDouble(txtPeptideMinAbso.Text);
}
_transformParameters.MaxCharge = Convert.ToInt16(txtMaxCharge.Text);
_transformParameters.PeptideMinBackgroundRatio = Convert.ToDouble(txtPeptideMinRatio.Text);
_peakParameter.SignalToNoiseThreshold = Convert.ToDouble(txtSN.Text);
_peakParameter.PeakBackgroundRatio = Convert.ToDouble(txtPeakPeakBackgroundRatioRatio.Text);
rawReader.SetPeakProcessorParameter(_peakParameter);
rawReader.SetTransformParameter(_transformParameters);
for (int i = 0; i <= 10; i++)
{
MSScan GMSScan = rawReader.ReadScan(ScanNo);
List<MSPeak> deIsotopedPeaks = GMSScan.MSPeaks;
deIsotopedPeaks.Sort();
txtPeaks.Text = "Scan Number" + ScanNo.ToString() + Environment.NewLine;
txtPeaks.Text = txtPeaks.Text + "MSLevel:" + GMSScan.MsLevel.ToString() + "\t\tNumber Peaks" + deIsotopedPeaks.Count.ToString() + Environment.NewLine;
txtPeaks.Text = txtPeaks.Text + "MonoisotopicMZ\tMonoIntensity\tCharge" + Environment.NewLine;
foreach (MSPeak p in deIsotopedPeaks)
{
txtPeaks.Text = txtPeaks.Text + p.MonoisotopicMZ.ToString("0.0000") + "\t\t" + p.MonoIntensity.ToString() + "\t\t" + p.ChargeState.ToString() + Environment.NewLine;
}
}
}
