/// <summary>
/// Illustrate how to make calls to deisotope a spectrum.
/// </summary>
/// <param name="dataAccess"></param>
private void DeisotopeTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;//no limit on max number of peaks
IMsdrChargeStateAssignmentFilter csaFilter = new MsdrChargeStateAssignmentFilter();
IBDASpecFilter f = new BDASpecFilter();
f.SpectrumType = SpecType.MassSpectrum;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
int nNonEmptyCount = 0; // just deisotope the first 10 non-empty spectra
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1);//same peak filter used for both MS and MS2 spectra (you can pass in 2 different filters)
println("Original spectrum has " + spec.TotalDataPoints + " points");
if (spec.XArray.Length > 0)
{
++nNonEmptyCount;
}
if (nNonEmptyCount > 10)
{
break;
}
dataAccess.Deisotope(spec, csaFilter);
println(" Deisotoped spectrum has " + spec.TotalDataPoints + " points");
}
}
public static PeakList <Peak> GetPeakList(this IMsdrDataReader reader, double retentionTime, double minPeakIntensity, int maxNumPeaks)
{
IMsdrPeakFilter peakFilter = new MsdrPeakFilter();
peakFilter.AbsoluteThreshold = minPeakIntensity;
peakFilter.RelativeThreshold = 0;
peakFilter.MaxNumPeaks = maxNumPeaks;
return(GetPeakList(reader, retentionTime, peakFilter));
}
/// <summary>
/// Illustrate how to use
/// GetSpectrum(double retentionTime, MSScanType scanType, IonPolarity ionPolarity, IonizationMode ionMode, IMsdrPeakFilter peakFilter, bool peakFilterOnCentroid);
/// Get a TIC, and then use the retention time array to access each scan.
/// </summary>
/// <param name="dataAccess"></param>
private void DoSpectrumExtractionTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;
IBDAChromFilter chromFilter = new BDAChromFilter();
chromFilter.ChromatogramType = ChromType.TotalIon;
chromFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;
IBDAChromData[] chroms = dataAccess.GetChromatogram(chromFilter);
IBDAChromData chrom = chroms[0];
double[] retTime = chrom.XArray;
for (int i = 0; i < retTime.Length; i++)
{
println("Extract spectrum at RT=" + retTime[i]);
//Get a spectrum without doing peak filtering if the spectrum is centroid
//The peak filter passed in will be applied to profile spectrum, but not
//centroid spectrum, because the flag peakFilterOnCentroid=false
IBDASpecData spec = dataAccess.GetSpectrum(retTime[i], MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, filter1, false);//peakFilterOnCentroid=false
/*//uncomment this section if you want to print out spectrum points
* double[] mzVals = spec.XArray;
* float[] aboundanceVals = spec.YArray;
* for (int j = 0; j < mzVals.Length; j++)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
*/
//Get a spectrum and apply peak filtering to it regardless profile or centroid
IBDASpecData spec2 = dataAccess.GetSpectrum(retTime[i], MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, filter1, true);//peakFilterOnCentroid=true
/*
* mzVals = spec.XArray;
* aboundanceVals = spec.YArray;
* for (int j = 0; j < mzVals.Length; j++)
* {
* if (aboundanceVals[j] > 5000)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
* }
*/
if (spec2.TotalDataPoints > spec.TotalDataPoints)
{//since spec2 is always thresholded, it must have less than or equal # of points as spec
println(" Error: filtered spectrum contains more points than unfiltered spectrum!");
}
}
}
private void DoSpectrumExtractionTestWithStorage(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1, DesiredMSStorageType.PeakElseProfile);
println("Spectrum " + i.ToString() + "has " + spec.TotalDataPoints + " points");
}
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary <int, IBDASpecData> ms1s;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
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(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock (agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if (scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock (agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if (agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if (agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if (agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if (polarity < 0)
{
charge = -charge;
}
List <MSPeak> peaks = null;
if (!assignChargeStates)
{
peaks = new List <MSPeak>(agilent_spectrum.TotalDataPoints);
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
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++)
{
if (assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock (csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List <MSPeak>(num_peaks);
HashSet <int> observed_peak_clusters = new HashSet <int>();
for (int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if (!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if (peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, 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 / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if (new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary<int, IBDASpecData> ms1s;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
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(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock(agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if(scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock(agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if(agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if(agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if(agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if(polarity < 0)
{
charge = -charge;
}
List<MSPeak> peaks = null;
if(!assignChargeStates)
{
peaks = new List<MSPeak>(agilent_spectrum.TotalDataPoints);
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
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++)
{
if(assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock(csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List<MSPeak>(num_peaks);
HashSet<int> observed_peak_clusters = new HashSet<int>();
for(int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if(!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if(peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, 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 / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}
