/// <summary>
///
/// </summary>
/// <param name="argPeaks"></param>
/// <returns></returns>
public double CalculateHCDScorePValue(List <MSPeak> argPeaks)
{
identified_peak_indices.Clear();
int num_hcd_present = 0;
double del_mz_bin = 0.1;
double del_mz_range = mdbl_max_mz - mdbl_min_mz;
double p = (2 * del_mz_bin) / del_mz_range;
double p_value = 0;
double[] mzs = new double[argPeaks.Count];
double[] intensities = new double[argPeaks.Count];
List <int> mint_peak_indices = new List <int>();
for (int i = 0; i < argPeaks.Count; i++)
{
mzs[i] = argPeaks[i].MonoisotopicMZ;
intensities[i] = argPeaks[i].MonoIntensity;
}
for (int i = 0; i < 7; i++)
{
double this_mz = marr_theoretical_peaks[i];
int ClosedIdx = MassUtility.GetClosestMassIdx(argPeaks, Convert.ToSingle(mzs[i]));
if (Math.Abs(this_mz - mzs[ClosedIdx]) < 0.1)
{
num_hcd_present++;
mint_peak_indices.Add(ClosedIdx);
}
}
if (num_hcd_present > mint_min_number_peaks)
{
for (int i = 0; i < mint_peak_indices.Count; i++)
{
identified_peak_indices.Add(mint_peak_indices[i]);
}
// Start calculating p value
long N_factorial = Factorial(7);
for (int x = num_hcd_present; x <= 7; x++)
{
long x_factorial = Factorial(x);
long N_x_factorial = Factorial(7 - x);
double N_choose_x = (double)(N_factorial / (x_factorial * N_x_factorial));
double pX = N_choose_x * Math.Pow(p, x) * Math.Pow(1 - p, 7 - x);
p_value += pX;
}
}
else
{
p_value = 0;
}
return(p_value);
}
public double CalculateHCDScore(List <MSPeak> argPeaks)
{
if (argPeaks.Count == 0)
{
return(0);
}
identified_peak_indices.Clear();
int num_hcd_present = 0;
double hcd_score = 0;
double[] mzs = new double[argPeaks.Count];
double[] intensities = new double[argPeaks.Count];
List <int> mint_peak_indices = new List <int>();
for (int i = 0; i < argPeaks.Count; i++)
{
mzs[i] = argPeaks[i].MonoMass;
intensities[i] = argPeaks[i].MonoIntensity;
}
for (int i = 0; i < 7; i++)
{
double this_mz = marr_theoretical_peaks[i];
int ClosedIdx = MassUtility.GetClosestMassIdx(argPeaks, Convert.ToSingle(this_mz));
if (Math.Abs(this_mz - mzs[ClosedIdx]) < 0.1)
{
num_hcd_present++;
mint_peak_indices.Add(ClosedIdx);
}
}
if (num_hcd_present > mint_min_number_peaks)
{
for (int i = 0; i < mint_peak_indices.Count; i++)
{
identified_peak_indices.Add(mint_peak_indices[i]);
}
}
hcd_score = (double)num_hcd_present / (double)6;
if (hcd_score > 1)
{
hcd_score = 1;
}
return(hcd_score);
}
public enumGlycanType DetermineGlycanType(List <MSPeak> argPeaks)
{
enumGlycanType GType = enumGlycanType.NA;
// Function that attempts to categorize the glycan type by calculating cross correlation
//First find peaks and get p value
int num_hcd_present = 0;
double hcd_score = 0;
double del_mz_bin = 0.015;
double del_mz_range = mdbl_max_mz - mdbl_min_mz;
double p = (2 * del_mz_bin) / del_mz_range;
double p_value = 0;
double[] mzs = new double[argPeaks.Count];
double[] intensities = new double[argPeaks.Count];
List <int> mint_peak_indices = new List <int>();
for (int i = 0; i < argPeaks.Count; i++)
{
mzs[i] = argPeaks[i].MonoisotopicMZ;
intensities[i] = argPeaks[i].MonoIntensity;
}
float[] obs_intensities = new float[7];
double maxintensity = 0;
for (int j = 0; j < 7; j++)
{
obs_intensities[j] = 0;
}
mint_peak_indices.Clear();
for (int j = 0; j < 7; j++)
{
double this_mz = marr_theoretical_peaks[j];
int ClosedIdx = MassUtility.GetClosestMassIdx(argPeaks, Convert.ToSingle(mzs[j]));
if (Math.Abs(mzs[ClosedIdx] - this_mz) < del_mz_bin)
{
if (intensities[ClosedIdx] > obs_intensities[j]) //Anoop jan 2011, make sure you get teh highest intensity
{
num_hcd_present++;
mint_peak_indices.Add(ClosedIdx);
obs_intensities[j] = (float)intensities[ClosedIdx];
if (intensities[ClosedIdx] > maxintensity)
{
maxintensity = intensities[ClosedIdx];
}
}
}
}
// Normalizing
for (int j = 0; j < 7; j++)
{
obs_intensities[j] = (float)(obs_intensities[j] / maxintensity);
}
if (num_hcd_present >= mint_min_number_peaks)
{
for (int i = 0; i < mint_peak_indices.Count; i++)
{
identified_peak_indices.Add(mint_peak_indices[i]);
}
// Start calculating p value
long N_factorial = Factorial(7);
if (num_hcd_present > 7)
{
num_hcd_present = 7;
}
for (int x = num_hcd_present; x <= 7; x++)
{
long x_factorial = Factorial(x);
long N_x_factorial = Factorial(7 - x);
double N_choose_x = (double)(N_factorial / (x_factorial * N_x_factorial));
double pX = N_choose_x * Math.Pow(p, x) * Math.Pow(1 - p, 7 - x);
p_value += pX;
}
//Now do a correlation with each class
float corr_HM = 0;
float corr_CA = 0;
float corr_CS = 0;
float corr_Hybrid = 0;
float max_corr = 0;
//Anoop Jan 2011, performing the glycan type detection in two stages,
//if NeuAc peak (or its water equivalent) is present, a distinction between hybrid and sialylated structures is made
// else only look for high mannose and complex_asialylated
if ((obs_intensities[4] > 0) || (obs_intensities[3] > 0))
{
corr_CS = Correlation(obs_intensities, marr_theoretical_cs, 0);
corr_Hybrid = Correlation(obs_intensities, marr_theoretical_hybrid, 0);
corr_HM = 0;
corr_CA = 0;
}
else
{
corr_CS = 0;
corr_Hybrid = 0;
corr_HM = Correlation(obs_intensities, marr_theoretical_hm, 0);
corr_CA = Correlation(obs_intensities, marr_theoretical_ca, 0);
}
max_corr = Math.Max(Math.Max(Math.Max(corr_HM, corr_CA), corr_CS), corr_Hybrid);
if (max_corr == corr_HM)
{
GType = enumGlycanType.HM;
}
if (max_corr == corr_CA)
{
GType = enumGlycanType.CA;
}
if (max_corr == corr_CS)
{
GType = enumGlycanType.CS;
}
if (max_corr == corr_Hybrid)
{
GType = enumGlycanType.HY;
}
}
else
{
p_value = 1;
GType = enumGlycanType.NA;
}
return(GType);
}
//private MSScan GetScanFromFile(int argScanNo)
//{
// return GetScanFromFile(argScanNo);
//}
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)//, float argPPM = 6, int argMinPeakCount=3)
{
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)
{
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;
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);
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);
//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 = _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);
}
