/// <summary>
/// Returns a 'peak-to-the-left' of the monoisotopic peak if: 1) it exists and 2) it is above the user provided relative intensity
/// </summary>
/// <param name="monoPeak"></param>
/// <param name="chargeState"></param>
/// <param name="peakList"></param>
/// <param name="minRelIntensityForFlag"></param>
/// <returns></returns>
public MSPeak LookforPeakToTheLeftOfMonoPeak(MSPeak monoPeak, int chargeState, List <Peak> peakList, double minRelIntensityForFlag)
{
double mzTol = monoPeak.Width;
var targetMZ = monoPeak.XValue - (1.003 / (double)chargeState);
var foundLeftOfMonoPeaks = PeakUtilities.GetPeaksWithinTolerance(peakList, targetMZ, mzTol);
//if found a peak to the left, will return that peak. If
if (foundLeftOfMonoPeaks.Count == 0)
{
return(null);
}
var peakToTheLeft = foundLeftOfMonoPeaks.OrderByDescending(p => p.Height).First() as MSPeak;
if (peakToTheLeft == null)
{
return(null);
}
if (peakToTheLeft.Height > monoPeak.Height * MinRatioToGiveFlag)
{
return(peakToTheLeft);
}
return(null);
}
private List <Peak> FilterPeaksBasedOnBasePeakList(List <Peak> basePeaklist, List <Peak> inputPeakList)
{
var trimmedPeakList = new List <Peak>();
foreach (var peak in basePeaklist)
{
var mzTolerance = _toleranceInPPM * peak.XValue / 1e6;
var foundPeaks = PeakUtilities.GetPeaksWithinTolerance(inputPeakList, peak.XValue,
mzTolerance);
if (foundPeaks.Count == 1)
{
trimmedPeakList.Add(foundPeaks.First());
}
else if (foundPeaks.Count > 1)
{
trimmedPeakList.Add(foundPeaks.OrderByDescending(p => p.Height).First());
}
}
//if we can't find any observed peaks, we won't trim anything. Just return the original list
if (!trimmedPeakList.Any())
{
return(basePeaklist);
}
return(trimmedPeakList);
}
public void FindPeaksWithinTolerance_highMZRangeTest()
{
List <IPeak> peakList = TestUtilities.GeneratePeakList(new ScanSet(6005));
List <IPeak> filteredList = PeakUtilities.GetPeaksWithinTolerance(peakList, 1500, 100);
Assert.AreEqual(809, peakList.Count);
TestUtilities.DisplayPeaks(filteredList);
Assert.AreEqual(115, filteredList.Count);
}
private void GetIsotopicProfilePeaks(List <Peak> peakList, int chargeState, double monoMass, ref IsotopicProfile inputProfile)
{
double toleranceInPPM = 20;
var tff = new BasicTFF(toleranceInPPM);
var theorProfile = new IsotopicProfile();
theorProfile.MonoIsotopicMass = monoMass;
theorProfile.ChargeState = chargeState;
theorProfile.MonoPeakMZ = monoMass / chargeState + Globals.PROTON_MASS;
//a hack to guess how many peaks to include in the theor isotopic profile
int numPeaksToIncludeInProfile = (int)Math.Round(Math.Max(3, 3 + (monoMass - 1000) / 1000));
double monoPeakMZ = monoMass / chargeState + Globals.PROTON_MASS;
for (int i = 0; i < numPeaksToIncludeInProfile; i++)
{
var peak = new MSPeak();
peak.XValue = monoPeakMZ + i * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
if (i == 0)
{
peak.Height = 1;
}
else
{
peak.Height = 0;
}
theorProfile.Peaklist.Add(peak);
}
var foundIso = tff.FindMSFeature(peakList, theorProfile);
if (foundIso == null)
{
var monoPeak = PeakUtilities.GetPeaksWithinTolerance(peakList, monoPeakMZ, toleranceInPPM).OrderByDescending(p => p.Height).FirstOrDefault();
if (monoPeak != null)
{
inputProfile.Peaklist.Add((MSPeak)monoPeak);
}
}
else
{
inputProfile.Peaklist = new List <MSPeak>(foundIso.Peaklist);
}
}
/// <summary>
/// Calculates mass error based on the theoretical most intense peak.
/// </summary>
/// <returns> This returns the mass error between a theoretical and observed peak. Nota bene the is MASS, not m/z
/// If no peak is detected, we return the mass error 999999. This should be interpreted as a null value.</returns>
protected double TheorMostIntensePeakMassError(IsotopicProfile theoreticalIso, IsotopicProfile observedIso, int chargeState)
{
var theoreticalMostIntensePeak = theoreticalIso.getMostIntensePeak();
//find peak in obs data
var mzTolerance = WorkflowParameters.MSToleranceInPPM * theoreticalMostIntensePeak.XValue / 1e6;
var foundPeaks = PeakUtilities.GetPeaksWithinTolerance(new List <Peak>(observedIso.Peaklist), theoreticalMostIntensePeak.XValue, mzTolerance);
if (foundPeaks.Count == 0)
{
return(999999);
}
var obsXValue = foundPeaks.OrderByDescending(p => p.Height).First().XValue; //order the peaks and take the first (most intense) one.
return((theoreticalMostIntensePeak.XValue * chargeState) - (obsXValue * chargeState));
}
private List <Peak> ApplySmartTrimming(List <Peak> theorPeakList, List <Peak> massSpectrumPeakList)
{
var trimmedPeakList = new List <Peak>();
foreach (var peak in theorPeakList)
{
var mzTolerance = _toleranceInPPM * peak.XValue / 1e6;
var foundPeaks = PeakUtilities.GetPeaksWithinTolerance(massSpectrumPeakList, peak.XValue,
mzTolerance);
if (foundPeaks.Any())
{
trimmedPeakList.Add(peak);
}
}
//if we can't find any observed peaks, we won't trim anything. Just return the original list
if (!trimmedPeakList.Any())
{
return(theorPeakList);
}
return(trimmedPeakList);
}
public double GetFit(
List <Peak> theorPeakList,
List <Peak> observedPeakList,
double minIntensityForScore,
double toleranceInPPM,
int numPeaksToTheLeftForScoring,
out int ionCountUsed)
{
Utilities.IqLogger.IqLogger.LogTrace("Min Intensity For Scoring: " + minIntensityForScore);
Utilities.IqLogger.IqLogger.LogTrace("PPM Tolerance: " + toleranceInPPM);
ionCountUsed = 0;
var theorIntensitiesUsedInCalc = new List <double>();
var observedIntensitiesUsedInCalc = new List <double>();
//first gather all the intensities from theor and obs peaks
var maxTheorIntensity = double.MinValue;
foreach (var peak in theorPeakList)
{
if (peak.Height > maxTheorIntensity)
{
maxTheorIntensity = peak.Height;
}
}
for (var index = 0; index < theorPeakList.Count; index++)
{
var peak = theorPeakList[index];
var overrideMinIntensityCutoff = index < numPeaksToTheLeftForScoring;
if (peak.Height > minIntensityForScore || overrideMinIntensityCutoff)
{
theorIntensitiesUsedInCalc.Add(peak.Height);
Utilities.IqLogger.IqLogger.LogTrace("Theoretical Peak Selected! Peak Height: "+ peak.Height + " Peak X-Value: " + peak.XValue);
//find peak in obs data
var mzTolerance = toleranceInPPM * peak.XValue / 1e6;
var foundPeaks = PeakUtilities.GetPeaksWithinTolerance(observedPeakList, peak.XValue, mzTolerance);
double obsIntensity;
if (foundPeaks.Count == 0)
{
Utilities.IqLogger.IqLogger.LogTrace("No Observed Peaks Found Within Tolerance");
obsIntensity = 0;
}
else if (foundPeaks.Count == 1)
{
obsIntensity = foundPeaks.First().Height;
Utilities.IqLogger.IqLogger.LogTrace("Observed Peak Selected! Peak Height: "+ foundPeaks[0].Height + " Peak X-Value " + foundPeaks[0].XValue);
}
else
{
obsIntensity = foundPeaks.OrderByDescending(p => p.Height).First().Height;
Utilities.IqLogger.IqLogger.LogTrace("Observed Peak Selected! Peak Height: "+ foundPeaks[0].Height + " Peak X-Value " + foundPeaks[0].XValue);
}
observedIntensitiesUsedInCalc.Add(obsIntensity);
}
else
{
Utilities.IqLogger.IqLogger.LogTrace("Theoretical Peak Not Selected! Peak Height: "+ peak.Height + " Peak X-Value: " + peak.XValue);
}
}
//the minIntensityForScore is too high and no theor peaks qualified. This is bad. But we don't
//want to throw errors here
if (theorIntensitiesUsedInCalc.Count == 0)
{
Utilities.IqLogger.IqLogger.LogTrace("No peaks meet minIntensityForScore.");
return(1.0);
}
var maxObs = observedIntensitiesUsedInCalc.Max();
if (Math.Abs(maxObs) < float.Epsilon)
{
maxObs = double.PositiveInfinity;
}
Utilities.IqLogger.IqLogger.LogTrace("Max Observed Intensity: " + maxObs);
var normalizedObs = observedIntensitiesUsedInCalc.Select(p => p / maxObs).ToList();
var maxTheor = theorIntensitiesUsedInCalc.Max();
var normalizedTheor = theorIntensitiesUsedInCalc.Select(p => p / maxTheor).ToList();
Utilities.IqLogger.IqLogger.LogTrace("Max Theoretical Intensity: " + maxTheor);
//foreach (var val in normalizedObs)
//{
// Console.WriteLine(val);
//}
//Console.WriteLine();
//foreach (var val in normalizedTheor)
//{
// Console.WriteLine(val);
//}
double sumSquareOfDiffs = 0;
double sumSquareOfTheor = 0;
for (var i = 0; i < normalizedTheor.Count; i++)
{
var diff = normalizedObs[i] - normalizedTheor[i];
sumSquareOfDiffs += (diff * diff);
sumSquareOfTheor += (normalizedTheor[i] * normalizedTheor[i]);
Utilities.IqLogger.IqLogger.LogTrace("Normalized Observed: " + normalizedObs[i]);
Utilities.IqLogger.IqLogger.LogTrace("Normalized Theoretical: " + normalizedTheor[i]);
Utilities.IqLogger.IqLogger.LogTrace("Iterator: " + i + " Sum of Squares Differences: " + sumSquareOfDiffs + " Sum of Squares Theoretical: " + sumSquareOfTheor);
}
ionCountUsed = normalizedTheor.Count;
var fitScore = sumSquareOfDiffs / sumSquareOfTheor;
if (double.IsNaN(fitScore) || fitScore > 1)
{
fitScore = 1;
}
else
{
// Future possibility (considered in January 2014):
// Normalize the fit score by the number of theoretical ions
// fitScore /= ionCountUsed;
}
Utilities.IqLogger.IqLogger.LogTrace("Fit Score: " + fitScore);
return(fitScore);
}
public virtual IsotopicProfile FindMSFeature(List <Peak> peakList, IsotopicProfile theorFeature)
{
Check.Require(theorFeature != null, "Theoretical feature hasn't been defined.");
if (theorFeature == null)
{
return(null);
}
Check.Require(theorFeature.Peaklist != null && theorFeature.Peaklist.Count > 0, "Theoretical feature hasn't been defined.");
var outFeature = new IsotopicProfile
{
ChargeState = theorFeature.ChargeState
};
var indexOfMaxTheorPeak = theorFeature.GetIndexOfMostIntensePeak();
var toleranceInMZ = theorFeature.getMonoPeak().XValue *ToleranceInPPM / 1e6;
var foundMatchingMaxPeak = false;
double massDefect = 0; // this is the m/z diff between the max peak of theor feature and the max peak of the experimental feature
var failedResult = false;
for (var i = indexOfMaxTheorPeak; i >= 0; i--)
{
//find experimental peak(s) within range
var peaksWithinTol = PeakUtilities.GetPeaksWithinTolerance(peakList, theorFeature.Peaklist[i].XValue, toleranceInMZ);
if (i == indexOfMaxTheorPeak)
{
foundMatchingMaxPeak = peaksWithinTol.Count > 0;
}
if (!foundMatchingMaxPeak) // can't even find the observed peak that matches the most intense theor peak.
{
failedResult = true;
break;
}
if (peaksWithinTol.Count == 0)
{
if (NeedMonoIsotopicPeak)
{
//here, we are looking to the left of most intense theor peak. If we have the prerequisite of finding the monoIsotopic peak and fail here, we'll return a failed result
failedResult = true;
}
break; // stop looking to the left of the most intense peak.
}
if (peaksWithinTol.Count == 1)
{
if (outFeature.Peaklist.Count == 0)
{
outFeature.Peaklist.Add((MSPeak)peaksWithinTol[0]);
}
else
{
outFeature.Peaklist.Insert(0, (MSPeak)peaksWithinTol[0]);
}
}
else // when we have several peaks within tolerance, we'll need to decide what to do
{
MSPeak bestPeak;
if (i == indexOfMaxTheorPeak) //when matching to most intense peak, we will use the most intense peak
{
bestPeak = (MSPeak)findMostIntensePeak(peaksWithinTol);
}
else
{
bestPeak = (MSPeak)findClosestToXValue(peaksWithinTol, theorFeature.Peaklist[i].XValue - massDefect);
}
if (outFeature.Peaklist.Count == 0)
{
outFeature.Peaklist.Add(bestPeak);
}
else
{
outFeature.Peaklist.Insert(0, bestPeak);
}
}
if (i == indexOfMaxTheorPeak) //when matching to most intense peak, we will get the mass defect using the most intense peak
{
massDefect = theorFeature.Peaklist[i].XValue - outFeature.Peaklist[0].XValue;
}
}
//------------------------- look right -------------------------------------------
for (var i = indexOfMaxTheorPeak + 1; i < theorFeature.Peaklist.Count; i++) //start one peak to the right of the max intense theor peak
{
var peaksWithinTol = PeakUtilities.GetPeaksWithinTolerance(peakList, theorFeature.Peaklist[i].XValue, toleranceInMZ);
if (peaksWithinTol.Count == 0)
{
if (i == indexOfMaxTheorPeak + 1) // first peak to the right of the max peak. We need this one or we declare it to be a failure (= null)
{
failedResult = true;
}
break; // finished. Exit loop.
}
if (peaksWithinTol.Count == 1)
{
outFeature.Peaklist.Add((MSPeak)peaksWithinTol[0]); //here, we tack peaks onto the profile
}
else //two or more peaks are within tolerance. Need to get the best one, which is based on the distance from the
{
outFeature.Peaklist.Add((MSPeak)findClosestToXValue(peaksWithinTol, theorFeature.Peaklist[i].XValue - massDefect));
}
}
//for higher mass peptides, we will return the profile if there is 2 or more peaks, regardless if none are found to the right of the most abundant
if (indexOfMaxTheorPeak > 0 && outFeature.Peaklist.Count > 1)
{
failedResult = false;
}
if (failedResult)
{
return(null); // return a null Isotopic profile, indicating a failed result
}
addMassInfoToIsotopicProfile(theorFeature, outFeature);
return(outFeature);
}
public static int GetChargeState(XYData rawData, List <Peak> peakList, MSPeak peak)
{
//look in rawData to the left (-0.1) and right (+1.1) of peak
var minus = 0.1;
var plus = 1.1;
double fwhm = peak.Width;
var leftIndex = MathUtils.GetClosest(rawData.Xvalues, peak.XValue - fwhm - minus);
var rightIndex = MathUtils.GetClosest(rawData.Xvalues, peak.XValue + fwhm + plus);
var filteredXYData = getFilteredXYData(rawData, leftIndex, rightIndex);
var minMZ = filteredXYData.Xvalues[0];
var maxMZ = filteredXYData.Xvalues[filteredXYData.Xvalues.Length - 1];
double sumOfDiffsBetweenValues = 0;
double pointCounter = 0;
for (var i = 0; i < filteredXYData.Xvalues.Length - 1; i++)
{
var y1 = filteredXYData.Yvalues[i];
var y2 = filteredXYData.Yvalues[i + 1];
if (y1 > 0 && y2 > 0)
{
var x1 = filteredXYData.Xvalues[i];
var x2 = filteredXYData.Xvalues[i + 1];
sumOfDiffsBetweenValues += (x2 - x1);
pointCounter++;
}
}
int numL;
if (pointCounter > 5)
{
var averageDiffBetweenPoints = sumOfDiffsBetweenValues / pointCounter;
numL = (int)Math.Ceiling((maxMZ - minMZ) / averageDiffBetweenPoints);
numL = (int)(numL + numL * 0.1);
//numL = 445;
}
else
{
var numPoints = rightIndex - leftIndex + 1;
var desiredNumPoints = 256;
var pointMultiplier = (int)Math.Ceiling(desiredNumPoints / (double)numPoints);
if (numPoints < 5)
{
return(-1);
}
if (numPoints < desiredNumPoints)
{
pointMultiplier = Math.Max(5, pointMultiplier);
numL = pointMultiplier * numPoints;
}
else
{
numL = numPoints;
}
}
//Console.WriteLine("Number of points in interpolated data= " + numL);
var interpolationFunction = new alglib.spline1d.spline1dinterpolant();
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
alglib.spline1d.spline1dbuildcubic(
filteredXYData.Xvalues, filteredXYData.Yvalues, filteredXYData.Xvalues.Length,
1, +1, 1, -1, interpolationFunction);
sw.Stop();
//Console.WriteLine("spline time = " + sw.ElapsedMilliseconds);
// DisplayXYVals(filteredXYData);
var evenlySpacedXYData = new XYData
{
Xvalues = new double[numL],
Yvalues = new double[numL]
};
for (var i = 0; i < numL; i++)
{
var xVal = (minMZ + ((maxMZ - minMZ) * i) / numL);
var yVal = alglib.spline1d.spline1dcalc(interpolationFunction, xVal);
evenlySpacedXYData.Xvalues[i] = xVal;
evenlySpacedXYData.Yvalues[i] = yVal;
}
//Console.WriteLine();
//DisplayXYVals(evenlySpacedXYData);
var autoCorrScores = ACss(evenlySpacedXYData.Yvalues);
//var tempXYData = new XYData
//{
// Xvalues = autoCorrScores,
// Yvalues = autoCorrScores
//};
// DisplayXYVals(tempXYData);
var startingIndex = 0;
while (startingIndex < numL - 1 && autoCorrScores[startingIndex] > autoCorrScores[startingIndex + 1])
{
startingIndex++;
}
double bestAutoCorrScore = -1;
var bestChargeState = -1;
GetHighestChargeStatePeak(minMZ, maxMZ, startingIndex, autoCorrScores, MaxCharge, ref bestAutoCorrScore, ref bestChargeState);
if (bestChargeState == -1)
{
return(-1);
}
var returnChargeStateVal = -1;
var chargeStateList = new List <int>();
GenerateChargeStateData(minMZ, maxMZ, startingIndex, autoCorrScores, MaxCharge, bestAutoCorrScore, chargeStateList);
for (var i = 0; i < chargeStateList.Count; i++)
{
var tempChargeState = chargeStateList[i];
var skip = false;
for (var j = 0; j < i; j++)
{
if (chargeStateList[j] == tempChargeState)
{
skip = true;
break;
}
}
if (skip)
{
continue;
}
if (tempChargeState > 0)
{
var anotherPeak = peak.XValue + (1.003d / tempChargeState);
var foundPeak = PeakUtilities.GetPeaksWithinTolerance(peakList, anotherPeak, peak.Width).Count > 0;
if (foundPeak)
{
returnChargeStateVal = tempChargeState;
if (peak.XValue * tempChargeState < 3000)
{
break;
}
return(tempChargeState);
}
}
}
return(returnChargeStateVal);
//StringBuilder sb = new StringBuilder();
//foreach (var item in chargeStatesAndScores)
//{
// sb.Append(item.Key + "\t" + item.Value + "\n");
//}
//Console.WriteLine(sb.ToString());
//StringBuilder sb = new StringBuilder();
//foreach (var item in autoCorrScores)
//{
// sb.Append(item);
// sb.Append(Environment.NewLine);
//}
//Console.WriteLine(sb.ToString());
//then extract AutoCorrelation scores (ACss)
//determine highest charge state peak (?)
}
public void AppendO16O18PeakInfo(List <Peak> peakList, List <IsosResult> resultList)
{
//iterate over each ms feature
foreach (var isosResult in resultList)
{
if (!(isosResult is O16O18IsosResult msFeature))
{
continue;
}
if (msFeature.IsotopicProfile == null)
{
continue;
}
var monoMZ = msFeature.IsotopicProfile.GetMZ();
var mzMinusDaltons = monoMZ - (MASS_UNIT_BETWEEN_ISO * 4 / msFeature.IsotopicProfile.ChargeState);
var mzPlusDaltons = monoMZ + (MASS_UNIT_BETWEEN_ISO * 4 / msFeature.IsotopicProfile.ChargeState);
var mzPlusTwoDaltons = monoMZ + (MASS_UNIT_BETWEEN_ISO * 2 / msFeature.IsotopicProfile.ChargeState);
double toleranceInPPM = 50;
var toleranceInMZ = toleranceInPPM * monoMZ / 1e6;
var minusPeaksWithinTol = PeakUtilities.GetPeaksWithinTolerance(peakList, mzMinusDaltons, toleranceInMZ);
var plusPeaksWithinTol = PeakUtilities.GetPeaksWithinTolerance(peakList, mzPlusDaltons, toleranceInMZ);
var twoDaltonsPlusPeaksWithinTol = PeakUtilities.GetPeaksWithinTolerance(peakList, mzPlusTwoDaltons, toleranceInMZ);
var fourDaltonsMinusPeak = GetBestPeak(minusPeaksWithinTol, mzMinusDaltons);
var fourDaltonsPlusPeak = GetBestPeak(plusPeaksWithinTol, mzPlusDaltons);
var twoDaltonsPlusPeak = GetBestPeak(twoDaltonsPlusPeaksWithinTol, mzPlusTwoDaltons);
if (fourDaltonsMinusPeak != null)
{
msFeature.MonoMinus4Abundance = fourDaltonsMinusPeak.Height;
}
else
{
msFeature.MonoMinus4Abundance = 0;
}
if (fourDaltonsPlusPeak != null)
{
msFeature.MonoPlus4Abundance = fourDaltonsPlusPeak.Height;
}
else
{
msFeature.MonoPlus4Abundance = 0;
}
if (twoDaltonsPlusPeak != null)
{
msFeature.MonoPlus2Abundance = twoDaltonsPlusPeak.Height;
}
else
{
msFeature.MonoPlus2Abundance = 0;
}
}
}