private void CalculateTICisolationWindow(RawScan previousFullMS, double precursormz, double window)
{
double intensitySum = 0.0;
double relativeIntensity = 0.0;
if (previousFullMS != null)
{
double[,] msscan = previousFullMS.Data;
int msscanLength = msscan.GetLength(1);
double lowerbound = precursormz - window / 2;
double upperbound = precursormz + window / 2;
for (int i = 0; i < msscanLength; i++)
{
if (msscan[0, i] > lowerbound && msscan[0, i] < upperbound)
{
intensitySum += msscan[1, i];
}
}
if (intensitySum > 0)
{
relativeIntensity = this.Tic / intensitySum;
}
}
this.IsolationWindowTic = intensitySum;
this.IsolationWindowTicRelative = relativeIntensity;
}
public Ms2Scan(RawScan rawScan, double signalToNoiseThreshold, RawScan previousFullMS) : base(rawScan, signalToNoiseThreshold)
{
SetPrecursorMass(rawScan.Precursormz);
CalculateSignalPartAbove(rawScan.Data, rawScan.Precursormz, IsolationWindow);//parameter here to shift outside precursor window?
CalculateTICisolationWindow(previousFullMS, rawScan.Precursormz, IsolationWindow);
IsPrecursorBP(rawScan.Precursormz, rawScan.BasePeakMass);
}
/// <summary>
/// Reads raw data. Puts spectra into a thread safe queue. Closes queue when done. Parses the rawfile-log into the statusLog object
/// </summary>
/// <param name="raw">Raw file</param>
/// <param name="rawScanQueue">Thread safe queue</param>
private void ReadRawFile(IXRawfile5 raw, BlockingCollection <RawScan> rawScanQueue)
{
int firstScanNumber = -1;
raw.GetFirstSpectrumNumber(ref firstScanNumber);
int lastScanNumber = -1;
raw.GetLastSpectrumNumber(ref lastScanNumber);
for (int scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
string scanFilter = null;
raw.GetFilterForScanNum(scanNumber, ref scanFilter);
//read scan header into key/value arrays
object keyRef = null;
object valueRef = null;
int indexRef = 0;
raw.GetTrailerExtraForScanNum(scanNumber, ref keyRef, ref valueRef, ref indexRef);
string[] trailerKeys = (string[])keyRef;
string[] trailerValues = (string[])valueRef;
//read tic and base peak mass using dummy variables
double tic = 0.0;
int int1 = 0;
int int2 = 0;
int int3 = 0;
double double1 = 0.0;
double double2 = 0.0;
double double3 = 0.0;
double basePeakMass = 0.0;
double double5 = 0.0;
double double6 = 0.0;
raw.GetScanHeaderInfoForScanNum(scanNumber, ref int1, ref double1, ref double2, ref double3, ref tic, ref basePeakMass, ref double5, ref int2, ref int3, ref double6);
//read data (mz,int,...) using dummy variables
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
double[,] data = (double[, ])labels_obj;
//read precursorMz
double precursorMz = 0.0;
raw.GetPrecursorMassForScanNum(scanNumber, 2, ref precursorMz);
RawScan rawScan = new RawScan(scanNumber, scanFilter, tic, trailerKeys, trailerValues, data, precursorMz, basePeakMass);
rawScanQueue.Add(rawScan);
//read status log
double rtLog = 0.0;
object statuslogKeys = null;
object statuslogValues = null;
int statuslogN = 0;
raw.GetStatusLogForScanNum(scanNumber, ref rtLog, ref statuslogKeys, ref statuslogValues, ref statuslogN);
statusLog.Add(rtLog, (string[])statuslogKeys, (string[])statuslogValues);
}
rawScanQueue.CompleteAdding();
Log.Information("Read all spectra in base module");
}
protected void ParseScanHeader(RawScan rawScan)
{
double _injectionTime = 0.0;
double _ionCountFromRawOvFtT = 0.0;
double _isolationWidth = 0.0;
int _chargeState = 0;
double _ctcd = 0.0;
int _lockMassNo = 0;
double _lockMassCorr = 0.0;
string[] theStringKeys = (string[])rawScan.TrailerExtraKeys;
string[] theStringValues = (string[])rawScan.TrailerExtraValues;
for (int i = 0; i < theStringKeys.Length; i++)
{
string trimmed = theStringKeys[i].Trim(new Char[] { ' ', '*', '.', ';', ':' });
switch (trimmed)
{
case "Ion Injection Time (ms)":
Double.TryParse(theStringValues[i], out _injectionTime);
break;
case "RawOvFtT":
Double.TryParse(theStringValues[i], out _ionCountFromRawOvFtT);
break;
case "Charge State":
Int32.TryParse(theStringValues[i], out _chargeState);
break;
case "MS2 Isolation Width":
Double.TryParse(theStringValues[i], out _isolationWidth);
break;
case "LM m/z-Correction (ppm)":
Double.TryParse(theStringValues[i], out _lockMassCorr);
break;
case "CTCD Comp":
Double.TryParse(theStringValues[i], out _ctcd);
break;
case "PrOSA Comp":
Double.TryParse(theStringValues[i], out _ctcd);
break;
}
}
this.ScanNumber = rawScan.ScanNumber;
this.InjectionTime = _injectionTime;
this.IonCountFromRawOvFtT = _ionCountFromRawOvFtT;
this.ChargeState = _chargeState;
this.IsolationWindow = _isolationWidth;
this.LockMassCorr = _lockMassCorr;
this.LockMassNo = _lockMassNo;
this.Ctcd = _ctcd;
this.Tic = rawScan.Tic;
}
public MsScan(RawScan rawScan, double signalToNoiseThreshold, List <Tuple <int, double, int> > polymerTargetList, int polymerCount, List <Adduct> adducts, double massError) : base(rawScan, signalToNoiseThreshold)
{
Tuple <double, int> maxMz = GetMaxIntensity(rawScan.Data);
if (maxMz.Item2 > 0)
{
List <Tuple <int, double, int> > targetList = new List <Tuple <int, double, int> >();
targetList.AddRange(polymerTargetList);
int precursorIndex, adductIndex;
ExtractAdducts(polymerCount, adducts, maxMz, targetList, out precursorIndex, out adductIndex);
double[] targetIntensities = GetIntensityByMatching(rawScan, massError, targetList);
SetPolymersAndAdducts(polymerCount, targetList, precursorIndex, adductIndex, targetIntensities);
}
else
{
this.Polymer = new double[polymerCount];
this.Adduct = new double[adducts.Count];
}
}
private static double[] GetIntensityByMatching(RawScan rawScan, double massError, List <Tuple <int, double, int> > targetList)
{
double[] targetIntensities = new double[targetList.Count];
int sortedMzAscendingLength = targetList.Count;
double[,] msscan = rawScan.Data;
int msscanLength = msscan.GetLength(1);
int t = 0;
int o = 0;
int charge = (int)(msscan[5, o] + 0.5);
while (t < sortedMzAscendingLength && o < msscanLength)
{
int specificScan = o;
double[] curscan = new double[] { msscan[0, specificScan], msscan[1, specificScan], msscan[2, specificScan], msscan[3, specificScan], msscan[4, specificScan], msscan[5, specificScan] };
double mass_difference = (msscan[0, o] - targetList[t].Item2) / targetList[t].Item2 * 1e6;
if (Math.Abs(mass_difference) <= massError && targetList[t].Item3 == charge)
{
if (msscan[1, o] > targetIntensities[t])
{
targetIntensities[t] = msscan[1, o];
}
t++;
}
else if (mass_difference < 0)
{
o++;
if (o < msscanLength)
{
charge = (short)(msscan[5, o] + 0.5);
}
}
else if (mass_difference >= 0)
{
t++;
}
}
return(targetIntensities);
}
// Relies on assumption that the rawscans are sorted, i.e. the currentFullMS is set for each ms2 scan
private Tuple <List <MsScan>, List <Ms2Scan> > ParseSpectra(BlockingCollection <RawScan> rawScanQueue, SettingsForAnalysis fixedSettings)
{
List <Tuple <int, double, int> > polymerTargetList = ExtractPolymers(fixedSettings.Polymers);
List <MsScan> msScanList = new List <MsScan>(1000);
List <Ms2Scan> ms2ScanList = new List <Ms2Scan>(1000);
RawScan currentFullMS = null;
foreach (RawScan rawScan in rawScanQueue.GetConsumingEnumerable())
{
if (rawScan.IsMS2())
{
ms2ScanList.Add(new Ms2Scan(rawScan, fixedSettings.StoNthreshold, currentFullMS));
}
else
{
currentFullMS = rawScan;
msScanList.Add(new MsScan(rawScan, fixedSettings.StoNthreshold, polymerTargetList, fixedSettings.Polymers.Count, fixedSettings.Adducts, fixedSettings.BaseMassTolerance));
}
}
return(new Tuple <List <MsScan>, List <Ms2Scan> >(msScanList, ms2ScanList));
}
public MsScanAbstract(RawScan rawScan, double signalToNoiseThreshold)
{
ParseScanHeader(rawScan);
SetSignalToNoiseAsAverageAboveThreshold(signalToNoiseThreshold, rawScan.Data);
}
