msppresample - Resample signal with peaks while preserving peaks

Syntax

[X, Intensities] = msppresample(Peaks, N) msppresample(Peaks, N, ...'Range', RangeValue, ...) msppresample(Peaks, N, ...'FWHH', FWHHValue, ...) msppresample(Peaks, N, ...'ShowPlot', ShowPlotValue, ...)

Arguments

Peaks

Either of the following:

Two-column matrix, where the first column contains separation-unit values and the second column contains intensity values. The separation unit can quantify wavelength, frequency, distance, time, or m/z depending on the instrument that generates the signal data.
Cell array of peak lists, where each element is a two-column matrix of separation-unit values and intensity values, and each element corresponds to a signal or retention time.

Tip You can use the mzxml2peaks function or the mspeaks function to create the Peaks matrix or cell array.

N Integer specifying the number of equally spaced points (separation-unit values) in the resampled signal.

RangeValue 1-by-2 vector specifying the minimum and maximum separation-unit values for the output matrix Intensities. RangeValue must be within [min(inputSU) max(inputSU)], where inputSU is the concatenated separation-unit values from the input Peaks. 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 separation-unit values from the input Peaks. The default is a rough approximation of resolution observed in the input data, Peaks.

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.

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.

Return Values

`X`	Vector of equally spaced, common separation-unit 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 separation-unit range. Each row corresponds to a separation-unit 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`.

Description

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(Peaks, N) resamples Peaks, 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 separation-unit 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 separation-unit range. Each row corresponds to a separation-unit 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 separation-unit 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(Peaks, 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(Peaks, N, ...'Range', RangeValue, ...) specifies a separation-unit range for the output matrix Intensities using the minimum and maximum separation values specified in the 1-by-2 vector RangeValue. RangeValue must be within [min(inputSU) max(inputSU)], where inputSU is the concatenated separation-unit values from the input Peaks. Default is the full range [min(inputSU) max(inputSU)]

msppresample(Peaks, 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 separation-unit values from the input Peaks. The default is a rough approximation of resolution observed in the input data, Peaks.

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(Peaks, 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.

Examples

Load a MAT-file, 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 two-column 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(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(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(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(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')