How to calculate the peak areas of every single peak from the mass spectrum?

Hi, I am wondering any toolboxs or codes could be used to calculate the peak areas of every single peak from the txt file or fig file. I know how to integrate the peak area in the excel using the txt file, but have to find the tails from the baseline manually. The picture showed how peak area was identified. I also attached a txt file from the mass spectrum. For the output, the centroid mass and peak area of every peak will be needed.

Answer 1

[A. Sawas]

The function findpeaks can find the peak values and locations.

data = importdata('Example.txt');
plot(data);
[pks,loc] = findpeaks(data);
findpeaks(data); %Use findpeaks without output arguments to display the peaks

Then you can find the boundaries around that peaks in order to find the area.

for k = 1:length(loc)
   i = loc(k);
   while i > 1 && data(i-1) <= data(i)
       i = i - 1;
   end
   b_min(k) = i;

   i = loc(k);
   while i < length(data) && data(i+1) <= data(i)
       i = i + 1;
   end
   b_max(k) = i;
end

%b_min: minimum boundary
%b_max: maximum boundary

To find the area under the first peak:

A = trapz(data([b_min(1):b_max(1)]));

You can find the area under all the peaks then the one with maxium area as follows:

for k=1:length(b_min)
    A(k) = trapz(X([b_min(k):b_max(k)]),Y([b_min(k):b_max(k)]));
end
[max_area, i] = max(A); 
max_peak = loc(i);

[Maggie Chen]

Thank you for the codes! When I ran the script, it showed

Error using findpeaks

Too many output arguments.

Do you have any idea how to fix it? Thank you!

[A. Sawas]

What version of Matlab you are using?

[Maggie Chen]

I am using Matlab R2016b.

[A. Sawas]

findpeaks with two output arguments is defined in 2016b and it should work flawlessly.

[pks,locs] = findpeaks(data) additionally returns the indices at which the peaks occur.

Can you post exactly the line where you are calling it ?

[A. Sawas]

There might be another function with the same name but has a different signature than the one provided in Matlab's signal processing toolbox.

Please print the output of the following command:

which findpeaks

[Maggie Chen]

I think it is because I named the script findpeaks. After I changed the name to findpeakareas and ran the script, the output is here.

[A. Sawas]

Ok, so now the problem is with the input data. Since your data is in two columns format the first being the X and second is Y. You need to add this line and replace data in the remainng code with Y

X = data(:,1);
Y = data(:,2);
[pks,loc] = findpeaks(Y);
% the rest of the code after changing data to Y

[Maggie Chen]

Thanks! No errors this time! I got a figure as output. Could the output be saved as txt file? Also I believe the Y in the output is the peak height not the peak area of the individual peak and the X is not the X value at the peak centroid.

Thank you so much for help!

[Jawaher Seddiq]

I tried this but getting an error can you check please

[Maria Basile]

@A. Sawas hi!

I know it's been a while since your comment (sorry for my bad english), but I'm trying to use your code below and it works pretty well until locs indices are non integers, that is my situation. I can't figure out how to fix it, because even if I change "while i>1" with "while i>0" then the indices of data will be a non integer and I'll get an error. I'm new at this type of analysis.. could you help me, please?

for k = 1:length(loc)

i = loc(k);

while i > 1 && data(i-1) <= data(i)

i = i - 1;

end

b_min(k) = i;

i = loc(k);

while i < length(data) && data(i+1) <= data(i)

i = i + 1;

end

b_max(k) = i;

end

%b_min: minimum boundary

%b_max: maximum boundary