/// <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 override PrecursorInfo GetPrecursorInfo(int scanNum)
{
m_spec = m_reader.GetSpectrum(scanNum);
var precursor = new PrecursorInfo();
var level = m_spec.MSLevelInfo;
if (level == MSLevel.MS)
{
precursor.MSLevel = 1;
}
else if (level == MSLevel.MSMS)
{
precursor.MSLevel = 2;
}
else
{
precursor.MSLevel = 1;
}
//this returns a list of precursor masses (not sure how there can be more than one)
var precursorMZlist = m_spec.GetPrecursorIon(out var precursorMassCount);
//if a mass is returned
if (precursorMassCount == 1)
{
//mass
precursor.PrecursorMZ = precursorMZlist[0];
//intensity
m_spec.GetPrecursorIntensity(out var precursorIntensity);
precursor.PrecursorIntensity = (float)precursorIntensity;
//charge
m_spec.GetPrecursorCharge(out var precursorCharge);
precursor.PrecursorCharge = precursorCharge;
//adjust scan number if needed
precursor.PrecursorScan = scanNum;
// TODO: Only CID possible in Agilent files?
precursor.FragmentationType = FragmentionType.CID;
}
else if (precursorMassCount > 1)
{
throw new NotImplementedException("Strange case where more than one precursor is used to generate one spectrum");
}
else
{
precursor.PrecursorMZ = 0;
precursor.PrecursorIntensity = 0;
precursor.PrecursorCharge = -1;
precursor.PrecursorScan = scanNum;
}
precursor.IonizationMode = m_spec.IonPolarity == IonPolarity.Negative ? IonizationMode.Negative : IonizationMode.Positive;
return(precursor);
}
public override int GetPrecusorCharge(int spectrumNumber, int msnOrder = 2)
{
IBDASpecData spectrum = _msdr.GetSpectrum(spectrumNumber - 1);
int precursor_charge;
spectrum.GetPrecursorCharge(out precursor_charge);
return((short)precursor_charge);
}
/// <summary>
/// Get all scans in the data file using row index. The storage mode defaults to peakElseProfile.
/// Passing null for peak filter means do not filter any peaks.
/// </summary>
/// <param name="dataAccess"></param>
private void GetAllScansUsingRowIndex(IMsdrDataReader dataAccess)
{
long totalNumScans = dataAccess.MSScanFileInformation.TotalScansPresent;
for (int i = 0; i < totalNumScans; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, null, null);//no peak filtering
}
}
/// <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!");
}
}
}
public override MZSpectrum GetSpectrum(int spectrumNumber)
{
IBDASpecData spectrum = _msdr.GetSpectrum(spectrumNumber - 1);
double[] doubleArray = new double[spectrum.YArray.Length];
for (int i = 0; i < doubleArray.Length; i++)
{
doubleArray[i] = spectrum.YArray[i];
}
return(new MZSpectrum(spectrum.XArray, doubleArray));
}
private void GetMSLevels(IMsdrDataReader dataAccess)
{
long totalNumScans = dataAccess.MSScanFileInformation.TotalScansPresent;
for (int i = 0; i < totalNumScans; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, null, null);//no peak filtering
IRange[] timeRange = spec.AcquiredTimeRange;
Console.WriteLine(timeRange[0].Start);
Console.WriteLine(i.ToString() + "\t" + spec.MSLevelInfo + "\t" + timeRange[0].Start);
}
}
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 override int GetMSLevelFromRawData(int scanNum)
{
m_spec = m_reader.GetSpectrum(scanNum);
var level = m_spec.MSLevelInfo;
if (level == MSLevel.MS)
{
return(1);
}
if (level == MSLevel.MSMS)
{
return(2);
}
return(1);
}
public static PeakList <Peak> GetPeakList(this IMsdrDataReader reader, double retentionTime, IMsdrPeakFilter peakFilter)
{
PeakList <Peak> result = new PeakList <Peak>();
IBDASpecData s = reader.GetSpectrum(retentionTime, MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, peakFilter, true);
for (int i = 0; i < s.XArray.Length; i++)
{
result.Add(new Peak(s.XArray[i], s.YArray[i]));
}
if (s.MZOfInterest.Length > 0)
{
result.PrecursorMZ = s.MZOfInterest[0].Start;
}
result.ScanTimes.Add(new ScanTime(0, retentionTime));
return(result);
}
public override MZAnalyzerType GetMzAnalyzer(int spectrumNumber)
{
IBDASpecData spectrum = _msdr.GetSpectrum(spectrumNumber - 1);
switch (spectrum.DeviceType)
{
case DeviceType.IonTrap:
return(MZAnalyzerType.IonTrap3D);
case DeviceType.Quadrupole:
case DeviceType.TandemQuadrupole:
return(MZAnalyzerType.Quadrupole);
case DeviceType.QuadrupoleTimeOfFlight:
case DeviceType.TimeOfFlight:
return(MZAnalyzerType.TOF);
default:
return(MZAnalyzerType.Unknown);
}
}
private void getAgilentSpectrum(int scanNum)
{
m_spec = m_reader.GetSpectrum(scanNum, null, null, DesiredMSStorageType.ProfileElsePeak);
}
public override MzRange GetMzRange(int spectrumNumber)
{
IBDASpecData spectrum = _msdr.GetSpectrum(spectrumNumber - 1);
return(new MzRange(spectrum.MeasuredMassRange.Start, spectrum.MeasuredMassRange.End));
}
/// <summary>
/// Get all Product Ion MS/MS scans and print out the precursor and collision energy.
/// </summary>
private void GetPrecursorInfo(IMsdrDataReader dataAccess)
{
//Create a chromatogram filter to let the scans that match
//the filter criteria to pass through
IBDAChromFilter chromFilter = new BDAChromFilter();
chromFilter.ChromatogramType = ChromType.TotalIon;
chromFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;//This means to use peak scans if available, otherwise use profile scans
chromFilter.MSLevelFilter = MSLevel.MSMS;
chromFilter.MSScanTypeFilter = MSScanType.ProductIon;
IBDAChromData[] chroms = dataAccess.GetChromatogram(chromFilter);//expect 1 chromatogram because we're not asking it to separate by scan segments, etc.
IBDAChromData chrom = chroms[0];
double[] retTime = chrom.XArray;
println("Get MS/MS spectra using retention time");
for (int i = 0; i < retTime.Length; i++)
{
//for each retention time, get the corresponding scan
//passing in null for peak filter means no peak threshold applied
IBDASpecData spec = dataAccess.GetSpectrum(retTime[i], MSScanType.ProductIon, IonPolarity.Mixed, IonizationMode.Unspecified, null);
print("RT=" + retTime[i] + ", ");
int precursorCount = 0;
double[] precursorIons = spec.GetPrecursorIon(out precursorCount);
if (precursorCount == 1)
{
print("Precursor Ions:");
for (int j = 0; j < precursorIons.Length; j++)
{
print(precursorIons[j] + " ");
}
println("");
int charge;
double intensity;
if (spec.GetPrecursorCharge(out charge))
{
println(" charge: " + charge);
}
else
{
println(" no charge avaialble");
}
if (spec.GetPrecursorIntensity(out intensity))
{
println(" intensity: " + intensity);
}
else
{
println(" no intensity available");
}
}
else
{
println("No precursor ions");
}
/*
* //Uncomment this if you want to print out x and y values of the spectrum.
* double[] mzVals = spec.XArray;
* float[] aboundanceVals = spec.YArray;
* println("RT=" + retTime[i]);
* for (int j = 0; j < mzVals.Length; j++)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
*/
}
}
