private void lookForMissingPeaksAndInsertZeroIntensityPeaksWhenMissing(IsotopicProfile o16o18Profile, IsotopicProfile theorFeature)
{
if (o16o18Profile.Peaklist.Count == 0)
{
return;
}
var mzDistanceBetweenIsotopes = 1.003 / o16o18Profile.ChargeState;
var monoMZ = theorFeature.getMonoPeak().XValue;
var indexOfLastPeak = o16o18Profile.Peaklist.Count - 1;
var toleranceInDa = 0.1;
//this will iterate over the first five expected m/z values of a theoretical profile
//and loosely try to the corresponding peak within the observed profile.
//If missing, will add one at the expected m/z. This ensures no missing peaks within the O16O18 profile
//so that looking up the first peak will always give you the intensity of the O16 peak (even if
//it never existed in the real data - in this case the intensity is 0);
for (var i = 0; i < 6; i++)
{
var currentMZ = monoMZ + mzDistanceBetweenIsotopes * i;
var peaksWithinTol = PeakUtilities.GetMSPeaksWithinTolerance(o16o18Profile.Peaklist, currentMZ, toleranceInDa);
if (peaksWithinTol.Count == 0) //
{
o16o18Profile.Peaklist.Insert(i, new MSPeak(currentMZ, 0, 0, 0));
}
}
}
private bool findPeakWithinMSFeatureResults(List <IsosResult> msFeatureList, MSPeakResult peakResult, double scanTolerance)
{
double toleranceInPPM = 5;
var toleranceInMZ = toleranceInPPM / 1e6 * peakResult.MSPeak.XValue;
foreach (var msfeature in msFeatureList)
{
if (msfeature.IsotopicProfile == null || msfeature.IsotopicProfile.Peaklist == null || msfeature.IsotopicProfile.Peaklist.Count == 0)
{
continue;
}
//check target peak is within an allowable scan tolerance
var targetPeakIsWithinScanTol = Math.Abs(msfeature.ScanSet.PrimaryScanNumber - peakResult.Scan_num) <= scanTolerance;
if (!targetPeakIsWithinScanTol)
{
continue;
}
var peaksWithinTol = PeakUtilities.GetMSPeaksWithinTolerance(msfeature.IsotopicProfile.Peaklist, peakResult.MSPeak.XValue, toleranceInMZ);
if (peaksWithinTol.Count == 0)
{
continue;
}
else
{
return(true);
}
}
return(false);
}
private void addIsotopePeaks(IsotopicProfile foundO16O18Profile, IsotopicProfile profileToAdd, int numIsotopePeaksToAdd)
{
if (profileToAdd?.Peaklist == null || profileToAdd.Peaklist.Count == 0)
{
return;
}
for (var i = 0; i < numIsotopePeaksToAdd; i++)
{
if (i < profileToAdd.Peaklist.Count)
{
var peakMz = profileToAdd.Peaklist[i].XValue;
var toleranceInMZ = ToleranceInPPM / 1e6 * peakMz;
var peaksAlreadyThere = PeakUtilities.GetMSPeaksWithinTolerance(foundO16O18Profile.Peaklist, peakMz, toleranceInMZ);
if (peaksAlreadyThere == null || peaksAlreadyThere.Count == 0)
{
foundO16O18Profile.Peaklist.Add(profileToAdd.Peaklist[i]);
}
}
else // if profileToAdd doesn't have enough peaks
{
break;
}
}
foundO16O18Profile.Peaklist = foundO16O18Profile.Peaklist.OrderBy(p => p.XValue).ToList();
}
private IsosResult getMSFeatureForCurrentSourcePeak(MSPeakResult peakResult, Run run)
{
if (run.ResultCollection.IsosResultBin == null || run.ResultCollection.IsosResultBin.Count == 0)
{
return(null);
}
var isosResultPossiblyContainingSourcePeak = new Dictionary <IsosResult, double>(); //store possible isosResult, along with it's difference with the peakResult
for (var i = 0; i < run.ResultCollection.IsosResultBin.Count; i++)
{
var msfeature = run.ResultCollection.IsosResultBin[i];
double toleranceInMZ = peakResult.MSPeak.Width / 2;
var peaksWithinTolerance = PeakUtilities.GetMSPeaksWithinTolerance(msfeature.IsotopicProfile.Peaklist, peakResult.MSPeak.XValue, toleranceInMZ);
if (peaksWithinTolerance == null || peaksWithinTolerance.Count == 0)
{
}
else
{
var diff = Math.Abs(peaksWithinTolerance[0].XValue - peakResult.MSPeak.XValue);
isosResultPossiblyContainingSourcePeak.Add(msfeature, diff);
}
}
if (isosResultPossiblyContainingSourcePeak.Count == 0)
{
return(null);
}
else if (isosResultPossiblyContainingSourcePeak.Count == 1)
{
return(isosResultPossiblyContainingSourcePeak.First().Key);
}
else
{
return(isosResultPossiblyContainingSourcePeak.Keys.OrderByDescending(p => p.IntensityAggregate).First());
}
}
