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curve fitting to get overlapping peak areas

June 22, 2012 at 08:33 PM | categories: data analysis | 0 Comments

Contents
curve fitting to get overlapping peak areas
read in the data file
first we get the number of data points, and read up to the data
initialize the data vectors

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what_do_you_want.m
Peak finding in Raman spectroscopy
curve fitting to get overlapping peak
areas
Colors, 3D Plotting, and Data
Manipulation

now read in the data

Plot the data
correct for non-zero baseline
a fitting function for one peak
a fitting function for two peaks
Plot fitting function with an initial guess for each parameter
nonlinear fitting
now extract out the two peaks and integrate the areas
Compute relative amounts

curve fitting to get overlapping peak areas

John Kitchin
Today we examine an approach to fitting curves to overlapping peaks to deconvolute
them so we can estimate the area under each curve. You will need to download gc-data2.txt for this example. This file contains data from a gas chromatograph with two peaks
that overlap. We want the area under each peak to estimate the gas composition. You
will see how to read the text file in, parse it to get the data for plotting and analysis, and
then how to fit it.
functionmain

read in the data file

The data file is all text, and we have to read it in, and find lines that match certain
patterns to identify the regions that are data, then we read in the data lines.
clearall;closeall
datafile='gcdata2.txt';
fid=fopen(datafile);

first we get the number of data points, and read up to the data
i=0;
while1
line=fgetl(fid);
sm=strmatch('#ofPoints',line);
if~isempty(sm)
regex='#ofPoints(.*)';
[matchtokens]=regexp(line,regex,'match','tokens');
npoints=str2num(tokens{1}{1});
elseifstrcmp(line,'R.Time Intensity')
break
i=i+1
end
end
http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtogetoverlappingpeakareas/

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initialize the data vectors

t=zeros(1,npoints);
intensity=zeros(1,npoints);

now read in the data

forj=1:npoints
line=fgetl(fid);
[a]=textscan(line,'%f%d');
t(j)=a{1};
intensity(j)=a{2};
end
fclose(fid);

Plot the data

plot(t,intensity)
xlabel('Time(s)')
ylabel('Intensity(arb.units)')
xlim([46])

correct for non-zero baseline

intensity=intensity+352;
plot(t,intensity)
xlabel('Time(s)')
ylabel('Intensity(arb.units)')
xlim([46])

http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtogetoverlappingpeakareas/

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a fitting function for one peak

The peaks are asymmetric, decaying gaussian functions.
functionf=asym_peak(pars,t)
%fromAnal.Chem.1994,66,12941301
a0=pars(1);%peakarea
a1=pars(2);%elutiontime
a2=pars(3);%widthofgaussian
a3=pars(4);%exponentialdampingterm
f=a0/2/a3*exp(a2^2/2/a3^2+(a1t)/a3)...
.*(erf((ta1)/(sqrt(2)*a2)a2/sqrt(2)/a3)+1);
end

a fitting function for two peaks

to get two peaks, we simply add two peaks together.
functionf=two_peaks(pars,t)
a10=pars(1);%peakarea
a11=pars(2);%elutiontime
a12=pars(3);%widthofgaussian
a13=pars(4);%exponentialdampingterm
a20=pars(5);%peakarea
a21=pars(6);%elutiontime
a22=pars(7);%widthofgaussian
a23=pars(8);%exponentialdampingterm
p1=asym_peak([a10a11a12a13],t);
p2=asym_peak([a20a21a22a23],t);
f=p1+p2;
end

Plot fitting function with an initial guess for each parameter

the fit is not very good.
holdall;
parguess=[1500,4.85,0.05,0.05,5000,5.1,0.05,0.1];
plot(t,two_peaks(parguess,t),'g')
legend'rawdata''initialguess'

http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtogetoverlappingpeakareas/

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nonlinear fitting
now we use nonlinear fitting to get the parameters that best fit our data, and plot the fit
on the graph.
pars=nlinfit(t,intensity,@two_peaks,parguess)
plot(t,two_peaks(pars,t),'r')
legend'rawdata''initialguess''totalfit'
pars=
1.0e+03*
1.30520.00490.00010.00005.31620.00510.00000.0001

the fits are not perfect. The small peak is pretty good, but there is an unphysical tail on
the larger peak, and a small mismatch at the peak. There is not much to do about that, it
means the model peak we are using is not a good model for the peak. We will still
integrate the areas though.

now extract out the two peaks and integrate the areas
pars1=pars(1:4)
pars2=pars(5:8)

http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtogetoverlappingpeakareas/

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peak1=asym_peak(pars1,t);
peak2=asym_peak(pars2,t);
plot(t,peak1)
plot(t,peak2)
legend'rawdata''initialguess''totalfit''peak1''peak2';
area1=trapz(t,peak1)
area2=trapz(t,peak2)
pars1=
1.0e+03*
1.30520.00490.00010.0000
pars2=
1.0e+03*
5.31620.00510.00000.0001
area1=
1.3052e+03
area2=
5.3162e+03

Compute relative amounts

percent1=area1/(area1+area2)
percent2=area2/(area1+area2)
percent1=
0.1971
percent2=
0.8029

This sample was air, and the first peak is oxygen, and the second peak is nitrogen. we
http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtogetoverlappingpeakareas/

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come pretty close to the actual composition of air, although it is low on the oxygen
content. To do better, one would have to use a calibration curve.
end
%categories:dataanalysis
%post_id=1994;%deletethislinetoforcenewpost;
%permaLink=http://matlab.cheme.cmu.edu/2012/06/22/curvefittingtoget
overlappingpeakareas/;
Published with MATLAB 7.12

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