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:
TipYou can use the 
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 .TipTo ensure that the resolution of the peaks is preserved, set 
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 . 
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.
msppresample
is useful to prepare a set of
signals for imaging functions such as msheatmap
and
preprocessing functions such as msbackadj
and msnorm
.
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:
msppresample(
specifies
a separationunit range for the output matrix 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
.
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(
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