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( ,
where inputSU is the concatenated separationunit
values from the input Peaklist . Default
is the full range [min( .  
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( ,
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. 
[
resamples X
, Intensities
]
= msppresample(Peaklist
, N
)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(
calls Peaklist
, N
,
... 'PropertyName
', PropertyValue
, ...)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:
specifies
a separationunit range for the output matrix
msppresample(Peaklist
, N
,
...'Range', RangeValue
, ...)Intensities
using
the minimum and maximum separation values specified in the 1by2
vector RangeValue
. RangeValue
must
be within [min(
,
where inputSU
) max(inputSU
)]inputSU
is the concatenated separationunit
values from the input Peaklist
. Default
is the full range [min(
inputSU
)
max(inputSU
)]
msppresample(
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 Peaklist
, N
,
...'FWHH', FWHHValue
,
...)median(diff(
,
where inputSU
))/2inputSU
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 
msppresample(
controls the display of a plot of an original
and resampled signal. Choices are Peaklist
, N
,
...'ShowPlot', ShowPlotValue
, ...)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