public Xic GetProductExtractedIonChromatogram(double productIonMz, double precursorIonMz, Tolerance tolerance, int minScanNum, int maxScanNum)
{
var productXic = new Xic();
for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
continue;
}
var productSpec = _scanNumSpecMap[scanNum] as ProductSpectrum;
if (productSpec == null)
{
continue;
}
if (!productSpec.IsolationWindow.Contains(precursorIonMz))
{
continue;
}
var peak = productSpec.FindPeak(productIonMz, tolerance);
if (peak != null)
{
productXic.Add(new XicPoint(scanNum, peak.Mz, peak.Intensity));
}
}
return(productXic);
}
private static Xic GetXicPointsWithin(double minMz, double maxMz, List <LcMsPeak> peakList)
{
var xic = new Xic();
var index = peakList.BinarySearch(new LcMsPeak((minMz + maxMz) / 2, 0, 0));
if (index < 0)
{
index = ~index;
}
// go down
var i = index - 1;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz <= minMz)
{
break;
}
xic.Add(new XicPoint(peak));
--i;
}
// go up
i = index;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz >= maxMz)
{
break;
}
xic.Add(new XicPoint(peak));
++i;
}
return(xic);
}
/// <summary>
/// Gets the extracted ion chromatogram of the specified m/z range (using only MS2 spectra)
/// </summary>
/// <param name="minMz">min m/z</param>
/// <param name="maxMz">max m/z</param>
/// <param name="precursorIonMz">precursor m/z of the precursor ion</param>
/// <param name="minScanNum">minimum scan number (inclusive)</param>
/// <param name="maxScanNum">maximum scan number (inclusive)</param>
/// <returns>XIC as an Xic object</returns>
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz, int minScanNum, int maxScanNum)
{
var xic = new Xic();
//for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
foreach (var scanNum in GetFragmentationSpectraScanNums(precursorIonMz))
{
if (scanNum < minScanNum || scanNum > maxScanNum)
{
continue;
}
var spec = GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null)
{
continue;
}
var peak = spec.FindPeak(minMz, maxMz);
xic.Add(peak != null ? new XicPoint(scanNum, peak.Mz, peak.Intensity) : new XicPoint(scanNum, 0, 0));
}
return(xic);
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0) index = ~index;
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return xicSegment;
}
private static Xic GetXicPointsWithin(double minMz, double maxMz, List<LcMsPeak> peakList)
{
var xic = new Xic();
var index = peakList.BinarySearch(new LcMsPeak((minMz + maxMz) / 2, 0, 0));
if (index < 0) index = ~index;
// go down
var i = index - 1;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz <= minMz) break;
xic.Add(new XicPoint(peak));
--i;
}
// go up
i = index;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz >= maxMz) break;
xic.Add(new XicPoint(peak));
++i;
}
return xic;
}
public Xic GetProductExtractedIonChromatogram(double productIonMz, double precursorIonMz, Tolerance tolerance, int minScanNum, int maxScanNum)
{
var productXic = new Xic();
for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) continue;
var productSpec = _scanNumSpecMap[scanNum] as ProductSpectrum;
if (productSpec == null) continue;
if (!productSpec.IsolationWindow.Contains(precursorIonMz)) continue;
var peak = productSpec.FindPeak(productIonMz, tolerance);
if (peak != null) productXic.Add(new XicPoint(scanNum, peak.Mz, peak.Intensity));
}
return productXic;
}
/// <summary>
/// Gets the extracted ion chromatogram of the specified m/z range (using only MS2 spectra)
/// </summary>
/// <param name="minMz">min m/z</param>
/// <param name="maxMz">max m/z</param>
/// <param name="precursorIonMz">precursor m/z of the precursor ion</param>
/// <param name="minScanNum">minimum scan number (inclusive)</param>
/// <param name="maxScanNum">maximum scan number (inclusive)</param>
/// <returns>XIC as an Xic object</returns>
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz, int minScanNum, int maxScanNum)
{
var xic = new Xic();
//for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
foreach (var scanNum in GetFragmentationSpectraScanNums(precursorIonMz))
{
if (scanNum < minScanNum || scanNum > maxScanNum) continue;
var spec = GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null) continue;
var peak = spec.FindPeak(minMz, maxMz);
xic.Add(peak != null ? new XicPoint(scanNum, peak.Mz, peak.Intensity) : new XicPoint(scanNum, 0, 0));
}
return xic;
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0)
{
index = ~index;
}
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return(xicSegment);
}
