public O18QuantificationSummaryItem()
{
this.SpeciesAbundance = new SpeciesAbundanceInfo();
this.SampleAbundance = new SampleAbundanceInfo();
this.ObservedEnvelopes = new List <O18QuanEnvelope>();
this.ScanStartPercentage = 0.0;
this.ScanEndPercentage = 1.0;
}
/**
* the whole labelling procedure contains two steps
* first one is caused by enzyme and labelled the peptide with one O18.
* the efficiency of this step is 100%.
* second one is add one O18 on peptide
* the efficiency of this step is unknown.
* let's assume the abundance from O16 sample is x,
* the abundance from O18 labelled sample is y,
* the purity of O18 H2O is p,
* the efficiency of second step is k (here k must be less than or equal to p)
* only one replacement from O16 to O18 for each peptide occurs in second step,
* then the final abundance of O16, Single O18, Double O18 have those formula:
* O16 = x + (1 - k) * (1 - p) * y
* O181 = (k(1-p) + p(1-k)) * y
* O182 = p * k * y
**/
#region ISampleAbundanceCalculator Members
public SampleAbundanceInfo Calculate(SpeciesAbundanceInfo speciesAbundance)
{
double o16 = speciesAbundance.O16;
double o18_1 = speciesAbundance.O181;
double o18_2 = speciesAbundance.O182;
//Console.Out.WriteLine("{0:0.00}\t{1:0.00}\t{2:0.00}", o16, o18_1, o18_2);
double k;
if (this.fixedEfficiency)
{
k = purityOfO18Water; //consider k equals to p
}
else
{
//Consider that O16 cannot be labelled to O18 in second step to decrease the complexibility
//I(O18_1)/I(O18_2) = ((1-p)k + (1-k)p) /pk
//k = 1 / (2 + O181/O182 - 1/p)
k = 1 / (2 + o18_1 / o18_2 - 1 / purityOfO18Water);
Console.Out.WriteLine("k=" + k);
if (k > purityOfO18Water || k <= 0)
{
k = purityOfO18Water; //consider k equals to p
}
}
//then, calculate the intensity from O18 labelled sample, assume as y
//I(O18_1) + I(O18_2) = (1-k)py + (1-p)ky + pky
//y = (I(O18_1) + I(O18_2)) / ((1-k)p + (1-p)k + pk)
double y = (o18_1 + o18_2) / ((1 - k) * purityOfO18Water + (1 - purityOfO18Water) * k + purityOfO18Water * k);
//finally, calculate the intensity from O16 labelled sample, assume as x
//I(O16) = x + (1-k)(1-purity) * y
//x = I(O16) - (1-k)(1-purity) * y
double x = o16 - (1 - k) * (1 - purityOfO18Water) * y;
if (x < 0) // it cannot be fixed, just use simple formula
{
x = o16;
y = o18_1 + o18_2;
k = purityOfO18Water;
}
var result = new SampleAbundanceInfo();
result.O16 = x;
result.O18 = y;
result.LabellingEfficiency = k;
result.CalculateRatio();
return(result);
}
public void CalculateFromProfile(List <Peak> profile, ISampleAbundanceCalculator calc)
{
var top2percentage = profile[0].Intensity + profile[1].Intensity;
this.SpeciesAbundance = new SpeciesAbundanceInfo();
this.SpeciesAbundance.O16 = (this[0].Intensity + this[1].Intensity) / top2percentage;
var intensity3 = Math.Max(0, this[2].Intensity - this.SpeciesAbundance.O16 * profile[2].Intensity);
var intensity4 = Math.Max(0, this[3].Intensity - this.SpeciesAbundance.O16 * profile[3].Intensity);
this.SpeciesAbundance.O181 = (intensity3 + intensity4) / top2percentage;
var intensity5 = Math.Max(0, this[4].Intensity - this.SpeciesAbundance.O16 * profile[4].Intensity - this.SpeciesAbundance.O181 * profile[2].Intensity);
var intensity6 = Math.Max(0, this[5].Intensity - this.SpeciesAbundance.O16 * profile[5].Intensity - this.SpeciesAbundance.O181 * profile[3].Intensity);
this.SpeciesAbundance.O182 = (intensity5 + intensity6) / top2percentage;
this.SampleAbundance = calc.Calculate(this.SpeciesAbundance);
}
public void CalculateSpeciesAbundanceByLinearRegression()
{
var mergedPeaks = MergeEnvelopes();
int maxLength = Math.Min(PeptideProfile.Count + 4, mergedPeaks.Count);
double[][] a = GetProfileMatrix(maxLength);
double[] x;
this.SpeciesAbundance = CalculateSpeciesAbundance(maxLength, a, mergedPeaks, out x);
double[] theoreticalIntensities = GetTheoreticalIntensities(maxLength, x);
double[] observedIntensities = GetObservedIntensities(maxLength, mergedPeaks);
double corr = StatisticsUtils.PearsonCorrelation(theoreticalIntensities, observedIntensities);
this.SpeciesAbundance.RegressionCorrelation = corr;
this.SpeciesAbundance.RegressionItems.Clear();
int pepCharge = GetCharge();
var gap = (Atom.O18.MonoMass - Atom.O.MonoMass) / pepCharge;
var gapC = (Atom.C13.MonoMass - Atom.C.MonoMass) / pepCharge;
double mzO16 = TheoreticalO16Mz;
double mzO181 = TheoreticalO16Mz + gap;
double mzO182 = mzO181 + gap;
double[] mzs = { mzO16, mzO16 + gapC, mzO181, mzO181 + gapC, mzO182, mzO182 + gapC };
for (int i = 0; i < maxLength && i < mzs.Length; i++)
{
var ri = new SpeciesRegressionItem();
ri.Mz = mzs[i];
ri.ObservedIntensity = observedIntensities[i];
ri.RegressionIntensity = theoreticalIntensities[i];
this.SpeciesAbundance.RegressionItems.Add(ri);
}
var calc = this.GetCalculator();
this.SampleAbundance = calc.Calculate(this.SpeciesAbundance);
}
/**
* the whole procedure contains two steps:
* first one is digestion at normal condition.
* second one is labelling at 18O water,the efficiency of this step is unknown.
* let's assume the abundance from O16 sample is x,
* the abundance from O18 labelled sample is y,
* the purity of O18 H2O is p,
* the efficiency of second step is k (here k must be less than or equal to p),
* then the final abundance of O16, Single O18, Double O18 have those formula:
* O16 = x + (1 - k) * (1 - k) * y
* O181 = 2 * k * (1 - k) * y
* O182 = k * k * y
*
* since it's very difficult to distinguish between extreme high O16 sample and extreme low labelling efficiency,
* we prefer extreme high o16 sample than extreme low labelling efficiency. So when labelling efficiency is lower than 0.2,
* we will consider it as full labelling efficiency (equals to purity of O18 water).
**/
#region ISampleAbundanceCalculator Members
public SampleAbundanceInfo Calculate(SpeciesAbundanceInfo speciesAbundance)
{
double o16 = speciesAbundance.O16;
double o18_1 = speciesAbundance.O181;
double o18_2 = speciesAbundance.O182;
//Console.Out.WriteLine("{0:0.00}\t{1:0.00}\t{2:0.00}", o16, o18_1, o18_2);
double k;
if (o18_2 == 0.0)
{
k = purityOfO18Water;
}
else
{
k = 2 / (2 + o18_1 / o18_2);
}
//Console.Out.WriteLine("k=" + k);
if (k > purityOfO18Water)
{
//consider k equals to p
k = purityOfO18Water;
}
else if (k <= MIN_LABELLING_EFFICIENCY)
{
if (o18_1 > o18_2)
{
Console.Out.WriteLine("k={0}; O16={1}; O181={2}; O182={3}", k, o16, o18_1, o18_2);
}
else
{
k = purityOfO18Water;
}
}
double x, y;
if (k == 1.0)
{
y = o18_1 + o18_2;
x = o16;
}
else
{
double y1 = o18_1 / (2 * k * (1 - k));
double y2 = o18_2 / (k * k);
y = Math.Max(y1, y2);
x = o16 - y * (1 - k) * (1 - k);
if (x < 0) // it cannot be fixed, just use simple formula
{
x = 0;
}
}
var result = new SampleAbundanceInfo();
result.O16 = x;
result.O18 = y;
result.LabellingEfficiency = k;
result.CalculateRatio();
return(result);
}