/// <summary>
/// Get the spectrum intensity.
/// </summary>
/// <param name="rawFile">the RAW file object</param>
/// <param name="precursorScanNumber">the precursor scan number</param>
/// <param name="precursorMass">the precursor mass</param>
/// <param name="retentionTime">the retention time</param>
/// <param name="isolationWidth">the isolation width</param>
protected static double? GetPrecursorIntensity(IRawDataPlus rawFile, int precursorScanNumber,
double precursorMass, double retentionTime, double? isolationWidth)
{
double? precursorIntensity = null;
// Get the scan from the RAW file
var scan = Scan.FromFile(rawFile, precursorScanNumber);
// Check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
var centroidStream = rawFile.GetCentroidStream(precursorScanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
if (Math.Abs(precursorMass - centroidStream.Masses[i]) < Tolerance)
{
//Console.WriteLine(Math.Abs(precursorMass - centroidStream.Masses[i]));
//Console.WriteLine(precursorMass + " - " + centroidStream.Masses[i] + " - " +
// centroidStream.Intensities[i]);
precursorIntensity = centroidStream.Intensities[i];
break;
}
}
}
}
else
{
rawFile.SelectInstrument(Device.MS, 1);
var component = new Component
{
MassRange = new Limit
{
Low = (double) (precursorMass - isolationWidth / 2),
High = (double) (precursorMass + isolationWidth / 2)
},
RtRange = new Limit
{
Low = rawFile.RetentionTimeFromScanNumber(precursorScanNumber),
High = rawFile.RetentionTimeFromScanNumber(precursorScanNumber)
}
};
;
IChromatogramSettings[] allSettings =
{
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = Component.Filter,
MassRanges = new[]
{
new Range(component.MassRange.Low, component.MassRange.High)
}
}
};
var rtFilteredScans = rawFile.GetFilteredScansListByTimeRange("",
component.RtRange.Low,
component.RtRange.High);
var data = rawFile.GetChromatogramData(allSettings, rtFilteredScans[0],
rtFilteredScans[rtFilteredScans.Count - 1]);
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
}
return precursorIntensity;
}
