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Resample signal with peaks while preserving peaks
[X, Intensities]
= msppresample(Peaklist, N)
msppresample(Peaklist, N,
...'Range', RangeValue, ...)
msppresample(Peaklist, N,
...'FWHH', FWHHValue,
...)
msppresample(Peaklist, N,
...'ShowPlot', ShowPlotValue, ...)
Peaklist  Either of the following:
 
N  Integer specifying the number of equally spaced points (separationunit values) in the resampled signal.  
RangeValue  1by2 vector specifying the minimum and maximum separationunit values for the output matrix Intensities. RangeValue must be within [min(inputSU) max(inputSU)], where inputSU is the concatenated separationunit values from the input Peaklist. Default is the full range [min(inputSU) max(inputSU)].  
FWHHValue  Value that specifies the full width at half height (FWHH) in separation units. The FWHH is used to convert each peak to a Gaussian shaped curve. Default is median(diff(inputSU))/2, where inputSU is the concatenated separationunit values from the input Peaklist. The default is a rough approximation of resolution observed in the input data, Peaklist.  
ShowPlotValue  Controls the display of a plot of an
original and resampled signal. Choices are true, false,
or I, an integer specifying the index of
a signal in Intensities. If you set to true,
the first signal in Intensities is plotted.
Default is:

X  Vector of equally spaced, common separationunit values for a set of signals with peaks. The number of elements in the vector equals N, or the number of rows in matrix Intensities. 
Intensities  Matrix of reconstructed intensity values for a set of peaks that share the same separationunit range. Each row corresponds to a separationunit value, and each column corresponds to either a set of signals with peaks or a retention time. The number of rows equals N, or the number of elements in vector X. 
Tip Use the following syntaxes with data from any separation technique that produces signal data, such as spectroscopy, NMR, electrophoresis, chromatography, or mass spectrometry. 
[X, Intensities] = msppresample(Peaklist, N) resamples Peaklist, a peak list, by converting centroided peaks to a semicontinuous, raw signal that preserves peak information. The resampled signal has N equally spaced points. Output X is a vector of N elements specifying the equally spaced, common separationunit values for the set of signals with peaks. Output Intensities is a matrix of reconstructed intensity values for a set of peaks that share the same separationunit range. Each row corresponds to a separationunit value, and each column corresponds to either a set of signals with peaks or a retention time. The number of rows equals N.
msppresample uses a Gaussian kernel to reconstruct the signal. The intensity at any given separationunit value is taken from the maximum intensity of any contributing (overlapping) peaks.
Tip msppresample is useful to prepare a set of signals for imaging functions such as msheatmap and preprocessing functions such as msbackadj and msnorm. 
msppresample(Peaklist, N, ... 'PropertyName', PropertyValue, ...) calls msppresample with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:
msppresample(Peaklist, N,
...'Range', RangeValue, ...) specifies
a separationunit range for the output matrix Intensities using
the minimum and maximum separation values specified in the 1by2
vector RangeValue. RangeValue must
be within [min(inputSU) max(inputSU)],
where inputSU is the concatenated separationunit
values from the input Peaklist. Default
is the full range [min(inputSU)
max(inputSU)]
msppresample(Peaklist, N, ...'FWHH', FWHHValue, ...) sets the full width at half height (FWHH) in separation units. The FWHH is used to convert each peak to a Gaussian shaped curve. Default is median(diff(inputSU))/2, where inputSU is the concatenated separationunit values from the input Peaklist. The default is a rough approximation of resolution observed in the input data, Peaklist.
Tip To ensure that the resolution of the peaks is preserved, set FWHHValue to half the distance between the two peaks of interest that are closest to each other. 
msppresample(Peaklist, N, ...'ShowPlot', ShowPlotValue, ...) controls the display of a plot of an original and resampled signal. Choices are true, false, or I, an integer specifying the index of a signal in Intensities. If you set to true, the first signal in Intensities is plotted. Default is:
false — When return values are specified.
true — When return values are not specified.
Load a MATfile, included with the Bioinformatics Toolbox™ software, that contains liquid chromatography/mass spectrometry (LC/MS) data variables. It includes peaks, a cell array of peak lists, where each element is a twocolumn matrix of m/z values and ion intensity values, and each element corresponds to a spectrum or retention time.
load lcmsdata
Resample the data, specifying 5000 m/z values in the resampled signal. Then create a heat map of the LC/MS data.
[MZ,Y] = msppresample(ms_peaks,5000); msheatmap(MZ,ret_time,log(Y))
Plot the reconstructed profile spectra between two retention times.
figure t1 = 3370; t2 = 3390; h = find(ret_time>t1 & ret_time<t2); [MZ,Y] = msppresample(ms_peaks(h),10000); plot3(repmat(MZ,1,numel(h)),repmat(ret_time(h)',10000,1),Y) xlabel('Mass/Charge (M/Z)') ylabel('Retention Time') zlabel('Relative Intensity')
Resample the data to plot the Total Ion Chromatogram (TIC).
figure [MZ,Y] = msppresample(ms_peaks,5000); plot(ret_time,sum(Y)) title('Total Ion Chromatogram (TIC)') xlabel('Retention Time') ylabel('Relative Intensity')
Resample the data to plot the Extracted Ion Chromatogram (XIC) in the 450 to 500 m/z range.
figure [MZ,Y] = msppresample(ms_peaks,5000,'Range',[450 500]); plot(ret_time,sum(Y)) title('Extracted Ion Chromatogram (XIC) from 450 to 500 M/Z') xlabel('Retention Time') ylabel('Relative Intensity')
msdotplot  mspalign  mspeaks  msresample  mzcdf2peaks  mzcdfread  mzxml2peaks  mzxmlread