/// <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 static IBDAChromData GetChromData(this IMsdrDataReader reader)
{
IBDAChromFilter chroFilter = new BDAChromFilter();
chroFilter.ChromatogramType = ChromType.TotalIon;
chroFilter.DoCycleSum = false;
chroFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;
IBDAChromData[] chro = reader.GetChromatogram(chroFilter);
return(chro[0]);
}
private static ITICData DOReadTICTest1(string FileName) // data file name, such as c:\temp\mydata.d
{
IDataAccess dataAccessor = new DataAccess() as IDataAccess;
string sFileName = string.Empty;
try
{
double[] m_allRtArray = null; // RT x-value
float[] m_allTicYArray = null; // TIC y-values
sFileName = FileName;
dataAccessor.OpenDataFile(sFileName);
var m_BDADataAccess = dataAccessor.BaseDataAccess;
IBDAChromFilter psetfilter = new BDAChromFilter();
psetfilter.ChromatogramType = ChromType.TotalIon;
IBDAChromData[] chromarray = m_BDADataAccess.GetChromatogram(psetfilter);
m_allRtArray = chromarray[0].XArray;
m_allTicYArray = chromarray[0].YArray;
TICData tICData = new TICData();
tICData.SetTICData(m_allRtArray, m_allTicYArray);
return(tICData);
}
catch (Exception ex)
{
// MessageBox.Show(ex.Message);
throw;
}
finally
{
if (!string.IsNullOrEmpty(sFileName))
{
dataAccessor.CloseDataFile(); // make sure the data file will be closed
}
}
}
// Examine triggered MRM data file transition chromatograms to see which are
// for primary transitions.
private void TestIsPrimaryChrom(string tMrmFilePath)
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(tMrmFilePath);
IBDAChromFilter filter = new BDAChromFilter();
filter.ChromatogramType = ChromType.MultipleReactionMode;
filter.MSScanTypeFilter = MSScanType.MultipleReaction;
filter.ExtractOneChromatogramPerScanSegment = true;
filter.DoCycleSum = false;
IBDAChromData[] chroms = dataReader.GetChromatogram(filter);
foreach (IBDAChromData chrom in chroms)
{
bool val = chrom.IsPrimaryMrm;
string s = string.Format("{0}->{1}, {2}", chrom.MZOfInterest[0].Start, chrom.MeasuredMassRange[0].Start,
val);
println(s);
}
dataReader.CloseDataFile();
}
private void GetAxisInformation(IMsdrDataReader dataAccess)
{
DataUnit chromunit;
DataValueType chromvalueType;
IBDAChromFilter filter = new BDAChromFilter();
filter.ChromatogramType = ChromType.TotalIon;
IBDAChromData[] chroms = dataAccess.GetChromatogram(filter);
if (chroms.Length > 0)
{
chroms[0].GetXAxisInfoChrom(out chromunit, out chromvalueType);
println("X Axis");
println("======");
println("Data Unit: " + BaseUtilities.GetEnumString(chromunit, true));
println("Data Value type: " + BaseUtilities.GetEnumString(chromvalueType, true));
chroms[0].GetYAxisInfoChrom(out chromunit, out chromvalueType);
println("Y Axis");
println("======");
println("Data Unit: " + BaseUtilities.GetEnumString(chromunit, true));
println("Data Value type: " + BaseUtilities.GetEnumString(chromvalueType, true));
println(string.Empty);
}
}
/// <summary>
/// EIC Extraction
/// </summary>
/// <param name="dataAccess"></param>
private void ExtractEIC(IMsdrDataReader dataAccess)
{
IBDAChromFilter filter = new BDAChromFilter();
filter.ChromatogramType = ChromType.ExtractedIon;
IRange[] ranges = new IRange[1];
ranges[0] = new CenterWidthRange(158, 1);//EC: center mass is 158 Da, with a 1 Da window
// ranges[0] = new MinMaxRange(157.5, 158.5);//EC: this is another way to do the same thing
filter.IncludeMassRanges = ranges;
IBDAChromData[] chroms = dataAccess.GetChromatogram(filter);
println("\n EIC EXTRACTION\n");
string chromDesc = string.Empty;
for (int i = 0; i < chroms.Length; i++)
{
chromDesc = "Chromatogram extracted with : Chromatogram type =" + chroms[i].ChromatogramType.ToString()
+ " and Total Datapoints = " + chroms[i].TotalDataPoints.ToString()
+ " for range = " + chroms[i].AcquiredTimeRange[0].Start.ToString()
+ "-" + chroms[i].AcquiredTimeRange[0].End.ToString()
+ Environment.NewLine;
println(chromDesc);
}
}
/// <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]);
* }
*/
}
}
