private static double GetMonoisotopicMZ(IXRawfile2 raw, int scanNumber, string scanFilter)
{
object labels_obj = null;
object values_obj = null;
int array_size = -1;
raw.GetTrailerExtraForScanNum(scanNumber, ref labels_obj, ref values_obj, ref array_size);
string[] labels = (string[])labels_obj;
string[] values = (string[])values_obj;
for (int i = labels.GetLowerBound(0); i <= labels.GetUpperBound(0); i++)
{
if (labels[i].StartsWith("Monoisotopic M/Z"))
{
double monoisotopic_mz = double.Parse(values[i], CultureInfo.InvariantCulture);
if (monoisotopic_mz > 0.0)
{
return(monoisotopic_mz);
}
else
{
break;
}
}
}
return(GetIsolationMZ(scanFilter));
}
/// <summary>
/// Get fragmentation data from RAW data.
/// </summary>
/// <param name="raw"></param>
/// <param name="scanNumber"></param>
/// <param name="scanFilter"></param>
/// <returns></returns>
private double[,] GetFragmentationData(IXRawfile2 raw, int scanNumber, string scanFilter)
{
double[,] data;
if (scanFilter.ToLower().Contains("ftms") && isCentroided)
{
//get the FT-PROFILE labels as the centroided peaks;
object labelsObj = null;
object flagsObj = null;
raw.GetLabelData(ref labelsObj, ref flagsObj, ref scanNumber);
data = (double[, ])labelsObj;
}
else
{
int centroidStatus = isCentroided ? 1 : 0;
double centroidPeakWidth = double.NaN;
object massList = null;
object peakFlags = null;
int arraySize = -1;
raw.GetMassListFromScanNum(scanNumber, null, 0, 0, 0, centroidStatus, ref centroidPeakWidth, ref massList, ref peakFlags, ref arraySize);
data = (double[, ])massList;
}
return(data);
}
public FullPeptideHit(string line, string sequence, string dynamicModifications, double eValueScore, bool decoy,
Peptide peptide,
IXRawfile2 raw, int scanNumber, int firstScanNumber,
int charge)
: base(sequence, dynamicModifications, eValueScore, decoy, peptide, raw, scanNumber, firstScanNumber, charge)
{
this.line = line;
lineHasExtendedInformation = false;
}
public FullPeptideHit(string line, string sequence, string dynamicModifications, double eValueScore, bool decoy,
Peptide peptide,
IXRawfile2 raw, int scanNumber, int firstScanNumber,
int charge)
: base(sequence, dynamicModifications, eValueScore, decoy, peptide, raw, scanNumber, firstScanNumber, charge)
{
this.line = line;
lineHasExtendedInformation = false;
}
protected void CalculatePrecursorMassError(IXRawfile2 raw, int scanNumber, int firstScanNumber, int charge)
{
int survey_scan_number = scanNumber;
while (survey_scan_number >= firstScanNumber)
{
string temp_survey_scan_filter = null;
raw.GetFilterForScanNum(survey_scan_number, ref temp_survey_scan_filter);
if (!temp_survey_scan_filter.Contains(" ms ") || !temp_survey_scan_filter.Contains("FTMS"))
{
survey_scan_number--;
}
else
{
break;
}
}
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref survey_scan_number);
double[,] labels = (double[, ])labels_obj;
byte[,] flags = (byte[, ])flags_obj;
string scan_filter = null;
raw.GetFilterForScanNum(scanNumber, ref scan_filter);
string temp_scan_filter = scan_filter.Substring(0, scan_filter.IndexOf('@'));
isolationMZ = double.Parse(temp_scan_filter.Substring(temp_scan_filter.LastIndexOf(' ') + 1));
int?isolation_index = null;
for (int i = labels.GetLowerBound(1); i <= labels.GetUpperBound(1); i++)
{
if (!isolation_index.HasValue || Math.Abs(labels[(int)RawLabelDataColumn.MZ, i] - isolationMZ) < Math.Abs(labels[(int)RawLabelDataColumn.MZ, isolation_index.Value] - isolationMZ))
{
isolation_index = i;
}
}
if (!isolation_index.HasValue)
{
throw new Exception("Could not find isolated precursor peak.");
}
isolationMZ = labels[(int)RawLabelDataColumn.MZ, isolation_index.Value];
isolationMass = MassFromMZAndCharge(isolationMZ, charge);
double mass_error = isolationMass - theoreticalNeutralMass;
double mass_offset = Math.Round(mass_error / C12_C13_MASS_DIFFERENCE) * C12_C13_MASS_DIFFERENCE;
experimentalNeutralMass = isolationMass - mass_offset;
mass_error = experimentalNeutralMass - theoreticalNeutralMass;
precursorMassError = mass_error / theoreticalNeutralMass * 1e6;
}
public PeptideHit(string sequence, string dynamicModifications, double eValueScore, bool decoy,
Peptide peptide, IXRawfile2 raw, int scanNumber, int firstScanNumber, int charge)
{
this.sequence = sequence;
this.dynamicModifications = dynamicModifications;
this.eValueScore = eValueScore;
this.decoy = decoy;
this.theoreticalNeutralMass = peptide.Mass;
CalculatePrecursorMassError(raw, scanNumber, firstScanNumber, charge);
this.qValue = double.NaN;
}
public PeptideHit(string sequence, string dynamicModifications, double eValueScore, bool decoy,
Peptide peptide, IXRawfile2 raw, int scanNumber, int firstScanNumber, int charge)
{
this.sequence = sequence;
this.dynamicModifications = dynamicModifications;
this.eValueScore = eValueScore;
this.decoy = decoy;
this.theoreticalNeutralMass = peptide.Mass;
CalculatePrecursorMassError(raw, scanNumber, firstScanNumber, charge);
this.qValue = double.NaN;
}
private static void GetPrecursor(IDictionary <int, double[, ]> ms1s, IXRawfile2 raw, int scanNumber, string scanFilter, int firstScanNumber, out double mz, out double intensity)
{
if (PRECURSOR_MASS_TYPE == PrecursorMassType.Isolation)
{
mz = GetIsolationMZ(scanFilter);
}
else if (PRECURSOR_MASS_TYPE == PrecursorMassType.Monoisotopic)
{
mz = GetMonoisotopicMZ(raw, scanNumber, scanFilter);
}
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, raw, scanNumber, firstScanNumber, ref mz, out intensity);
}
else
{
intensity = double.NaN;
}
}
private static int DeterminePrecursorCharge(IXRawfile2 raw, int scanNumber)
{
object trailer_labels_obj = null;
object trailer_values_obj = null;
int trailer_array_size = -1;
raw.GetTrailerExtraForScanNum(scanNumber, ref trailer_labels_obj, ref trailer_values_obj, ref trailer_array_size);
string[] trailer_labels = (string[])trailer_labels_obj;
string[] trailer_values = (string[])trailer_values_obj;
int charge = -1;
for (int trailer_index = trailer_labels.GetLowerBound(0); trailer_index <= trailer_labels.GetUpperBound(0); trailer_index++)
{
if (trailer_labels[trailer_index].StartsWith("Charge"))
{
charge = int.Parse(trailer_values[trailer_index]);
}
}
return(charge);
}
private static double[,] GetFragmentationData(IXRawfile2 raw, int scanNumber, string scanFilter)
{
double[,] data;
if (scanFilter.Contains("FTMS"))
{
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
data = (double[, ])labels_obj;
}
else
{
double centroid_peak_width = double.NaN;
object mass_list = null;
object peak_flags = null;
int array_size = -1;
raw.GetMassListFromScanNum(scanNumber, null, 0, 0, 0, 1, ref centroid_peak_width, ref mass_list, ref peak_flags, ref array_size);
data = (double[, ])mass_list;
}
return(data);
}
private void DeterminePrecursorParams(IXRawfile2 raw, int scanNumber, out int charge, out double ionInjectTime)
{
object trailer_labels_obj = null;
object trailer_values_obj = null;
int trailer_array_size = -1;
raw.GetTrailerExtraForScanNum(scanNumber, ref trailer_labels_obj, ref trailer_values_obj, ref trailer_array_size);
string[] trailer_labels = (string[])trailer_labels_obj;
string[] trailer_values = (string[])trailer_values_obj;
charge = -1;
ionInjectTime = -1.0;
for (int trailer_index = trailer_labels.GetLowerBound(0); trailer_index <= trailer_labels.GetUpperBound(0); trailer_index++)
{
if (trailer_labels[trailer_index].StartsWith("Charge"))
{
charge = int.Parse(trailer_values[trailer_index]);
}
if (trailer_labels[trailer_index].Contains("Ion Injection"))
{
ionInjectTime = double.Parse(trailer_values[trailer_index]);
}
}
}
protected void CalculatePrecursorMassError(IXRawfile2 raw, int scanNumber, int firstScanNumber, int charge)
{
int survey_scan_number = scanNumber;
while(survey_scan_number >= firstScanNumber)
{
string temp_survey_scan_filter = null;
raw.GetFilterForScanNum(survey_scan_number, ref temp_survey_scan_filter);
if(!temp_survey_scan_filter.Contains(" ms ") || !temp_survey_scan_filter.Contains("FTMS"))
{
survey_scan_number--;
}
else
{
break;
}
}
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref survey_scan_number);
double[,] labels = (double[,])labels_obj;
byte[,] flags = (byte[,])flags_obj;
string scan_filter = null;
raw.GetFilterForScanNum(scanNumber, ref scan_filter);
string temp_scan_filter = scan_filter.Substring(0, scan_filter.IndexOf('@'));
isolationMZ = double.Parse(temp_scan_filter.Substring(temp_scan_filter.LastIndexOf(' ') + 1));
int? isolation_index = null;
for(int i = labels.GetLowerBound(1); i <= labels.GetUpperBound(1); i++)
{
if(!isolation_index.HasValue || Math.Abs(labels[(int)RawLabelDataColumn.MZ, i] - isolationMZ) < Math.Abs(labels[(int)RawLabelDataColumn.MZ, isolation_index.Value] - isolationMZ))
{
isolation_index = i;
}
}
if(!isolation_index.HasValue)
{
throw new Exception("Could not find isolated precursor peak.");
}
isolationMZ = labels[(int)RawLabelDataColumn.MZ, isolation_index.Value];
isolationMass = MassFromMZAndCharge(isolationMZ, charge);
double mass_error = isolationMass - theoreticalNeutralMass;
double mass_offset = Math.Round(mass_error / C12_C13_MASS_DIFFERENCE) * C12_C13_MASS_DIFFERENCE;
experimentalNeutralMass = isolationMass - mass_offset;
mass_error = experimentalNeutralMass - theoreticalNeutralMass;
precursorMassError = mass_error / theoreticalNeutralMass * 1e6;
}
private static void GetPrecursor(IDictionary<int, double[,]> ms1s, IXRawfile2 raw, int scanNumber, string scanFilter, int firstScanNumber, out double mz, out double intensity)
{
if(PRECURSOR_MASS_TYPE == PrecursorMassType.Isolation)
{
mz = GetIsolationMZ(scanFilter);
}
else if(PRECURSOR_MASS_TYPE == PrecursorMassType.Monoisotopic)
{
mz = GetMonoisotopicMZ(raw, scanNumber, scanFilter);
}
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, raw, scanNumber, firstScanNumber, ref mz, out intensity);
}
else
{
intensity = double.NaN;
}
}
private static double GetMonoisotopicMZ(IXRawfile2 raw, int scanNumber, string scanFilter)
{
object labels_obj = null;
object values_obj = null;
int array_size = -1;
raw.GetTrailerExtraForScanNum(scanNumber, ref labels_obj, ref values_obj, ref array_size);
string[] labels = (string[])labels_obj;
string[] values = (string[])values_obj;
for(int i = labels.GetLowerBound(0); i <= labels.GetUpperBound(0); i++)
{
if(labels[i].StartsWith("Monoisotopic M/Z"))
{
double monoisotopic_mz = double.Parse(values[i], CultureInfo.InvariantCulture);
if(monoisotopic_mz > 0.0)
{
return monoisotopic_mz;
}
else
{
break;
}
}
}
return GetIsolationMZ(scanFilter);
}
private static double[,] GetFragmentationData(IXRawfile2 raw, int scanNumber, string scanFilter)
{
double[,] data;
if(scanFilter.Contains("FTMS"))
{
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
data = (double[,])labels_obj;
}
else
{
double centroid_peak_width = double.NaN;
object mass_list = null;
object peak_flags = null;
int array_size = -1;
raw.GetMassListFromScanNum(scanNumber, null, 0, 0, 0, 1, ref centroid_peak_width, ref mass_list, ref peak_flags, ref array_size);
data = (double[,])mass_list;
}
return data;
}
private static bool GetAccurateMZAndIntensity(IDictionary<int, double[,]> ms1s, IXRawfile2 raw, int scanNumber, int firstScanNumber, ref double mz, out double intensity)
{
scanNumber--;
while(scanNumber >= firstScanNumber)
{
string scan_filter = null;
raw.GetFilterForScanNum(scanNumber, ref scan_filter);
if(scan_filter.Contains(" ms "))
{
double[,] ms1;
lock(ms1s)
{
if(!ms1s.TryGetValue(scanNumber, out ms1))
{
if(scan_filter.Contains("FTMS"))
{
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
ms1 = (double[,])labels_obj;
}
else
{
double centroid_peak_width = double.NaN;
object mass_list = null;
object peak_flags = null;
int array_size = -1;
raw.GetMassListFromScanNum(scanNumber, null, 0, 0, 0, 1, ref centroid_peak_width, ref mass_list, ref peak_flags, ref array_size);
ms1 = (double[,])mass_list;
}
ms1s.Add(scanNumber, ms1);
}
}
int index = -1;
for(int i = ms1.GetLowerBound(1); i <= ms1.GetUpperBound(1); i++)
{
if(index < 0 || Math.Abs(ms1[0, i] - mz) < Math.Abs(ms1[0, index] - mz))
{
index = i;
}
}
if(index >= 0)
{
mz = ms1[0, index];
intensity = ms1[1, index];
return true;
}
else
{
break;
}
}
else
{
scanNumber--;
}
}
intensity = double.NaN;
return false;
}
private static int DeterminePrecursorCharge(IXRawfile2 raw, int scanNumber)
{
object trailer_labels_obj = null;
object trailer_values_obj = null;
int trailer_array_size = -1;
raw.GetTrailerExtraForScanNum(scanNumber, ref trailer_labels_obj, ref trailer_values_obj, ref trailer_array_size);
string[] trailer_labels = (string[])trailer_labels_obj;
string[] trailer_values = (string[])trailer_values_obj;
int charge = -1;
for(int trailer_index = trailer_labels.GetLowerBound(0); trailer_index <= trailer_labels.GetUpperBound(0); trailer_index++)
{
if(trailer_labels[trailer_index].StartsWith("Charge"))
{
charge = int.Parse(trailer_values[trailer_index]);
}
}
return charge;
}
public void Load(string rawFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IXRawfile2 raw = (IXRawfile2) new MSFileReader_XRawfile();
raw.Open(rawFilepath);
raw.SetCurrentController(0, 1);
Dictionary <int, double[, ]> ms1s;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, double[, ]>();
}
int first_scan_number = -1;
raw.GetFirstSpectrumNumber(ref first_scan_number);
int last_scan_number = -1;
raw.GetLastSpectrumNumber(ref last_scan_number);
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(first_scan_number, last_scan_number + 1, scan_number =>
{
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
if (!scan_filter.Contains(" ms "))
{
string spectrum_id = "controllerType=0 controllerNumber=1 scan=" + scan_number.ToString();
double retention_time_minutes = double.NaN;
raw.RTFromScanNum(scan_number, ref retention_time_minutes);
int polarity = DeterminePolarity(scan_filter);
string fragmentation_method = GetFragmentationMethod(scan_filter);
double precursor_mz;
double precursor_intensity;
GetPrecursor(ms1s, raw, scan_number, scan_filter, first_scan_number, out precursor_mz, out precursor_intensity);
int charge = DeterminePrecursorCharge(raw, scan_number);
if (polarity < 0)
{
charge = -charge;
}
double[,] label_data = GetFragmentationData(raw, scan_number, scan_filter);
List <MSPeak> peaks = new List <MSPeak>(label_data.GetLength(1));
for (int peak_index = label_data.GetLowerBound(1); peak_index <= label_data.GetUpperBound(1); peak_index++)
{
peaks.Add(new MSPeak(label_data[(int)RawLabelDataColumn.MZ, peak_index],
label_data[(int)RawLabelDataColumn.Intensity, peak_index],
assignChargeStates && (int)RawLabelDataColumn.Charge < label_data.GetLength(0) ? (int)label_data[(int)RawLabelDataColumn.Charge, peak_index] : 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if (peaks.Count > 0)
{
for (int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(rawFilepath, scan_number, spectrum_id, null, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock (this)
{
Add(spectrum);
}
}
}
}
lock (progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / (last_scan_number - first_scan_number + 1) * 100);
if (new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
raw.Close();
}
private static bool GetAccurateMZAndIntensity(IDictionary <int, double[, ]> ms1s, IXRawfile2 raw, int scanNumber, int firstScanNumber, ref double mz, out double intensity)
{
scanNumber--;
while (scanNumber >= firstScanNumber)
{
string scan_filter = null;
raw.GetFilterForScanNum(scanNumber, ref scan_filter);
if (scan_filter.Contains(" ms "))
{
double[,] ms1;
lock (ms1s)
{
if (!ms1s.TryGetValue(scanNumber, out ms1))
{
if (scan_filter.Contains("FTMS"))
{
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
ms1 = (double[, ])labels_obj;
}
else
{
double centroid_peak_width = double.NaN;
object mass_list = null;
object peak_flags = null;
int array_size = -1;
raw.GetMassListFromScanNum(scanNumber, null, 0, 0, 0, 1, ref centroid_peak_width, ref mass_list, ref peak_flags, ref array_size);
ms1 = (double[, ])mass_list;
}
ms1s.Add(scanNumber, ms1);
}
}
int index = -1;
for (int i = ms1.GetLowerBound(1); i <= ms1.GetUpperBound(1); i++)
{
if (index < 0 || Math.Abs(ms1[0, i] - mz) < Math.Abs(ms1[0, index] - mz))
{
index = i;
}
}
if (index >= 0)
{
mz = ms1[0, index];
intensity = ms1[1, index];
return(true);
}
else
{
break;
}
}
else
{
scanNumber--;
}
}
intensity = double.NaN;
return(false);
}
