Bioinformatics Toolbox™

mzcdf2peaks - Convert mzCDF structure to peak list

Syntax

[Peaks, Times] = mzcdf2peaks(mzCDFStruct)

Arguments

mzCDFStruct

MATLAB structure containing information from a netCDF file, such as one created by the mzcdfread function. Its fields correspond to the variables and global attributes in a netCDF file. If a netCDF variable contains local attributes, an additional field is created, with the name of the field being the variable name appended with the _attributes string. The number and names of the fields will vary, depending on the mass spectrometer software, but typically there are mass_values and intensity_values fields.

Return Values

Peaks

Either of the following:

Two-column matrix, where the first column contains mass/charge (m/z) values and the second column contains ion intensity values.
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.

Times

Scalar of vector of retention times associated with a liquid chromatography/mass spectrometry (LC/MS) or gas chromatography/mass spectrometry (GC/MS) data set. If Times is a vector, the number of elements equals the number of peak lists contained in Peaks.

Description

[Peaks, Times] = mzcdf2peaks(mzCDFStruct) extracts peak information from mzCDFStruct, a MATLAB structure containing information from a netCDF file, such as one created by the mzcdfread function, and creates Peaks, a single matrix or a cell array of matrices containing mass/charge (m/z) values and ion intensity values, and Times, a scalar or vector of retention times associated with a liquid chromatography/mass spectrometry (LC/MS) or gas chromatography/mass spectrometry (GC/MS) data set.

mzCDFStruct contains fields that correspond to the variables and global attributes in a netCDF file. If a netCDF variable contains local attributes, an additional field is created, with the name of the field being the variable name appended with the _attributes string. The number and names of the fields will vary, depending on the mass spectrometer software, but typically there are mass_values and intensity_values fields.

Examples

In the following example, the file results.cdf is not provided.

Use the mzcdfread function to read a netCDF file into the MATLAB software as a structure. Then extract the peak information from the structure.

mzcdf_struct = mzcdfread('results.cdf');
[peaks,time] = mzcdf2peaks(mzcdf_struct)

peaks = 

    [7008x2 single]
    [7008x2 single]
    [7008x2 single]
    [7008x2 single]

time =

    8.3430
   12.6130
   16.8830
   21.1530

Create a color map containing a color for each peak list (retention time).
```
colors = hsv(numel(peaks));
```

Create a 3-D figure of the peaks and add labels to it.

figure
hold on

for i = 1:numel(peaks)
    t = repmat(time(i),size(peaks{i},1),1);
    plot3(t,peaks{i}(:,1),peaks{i}(:,2),'color',colors(i,:))
end

view(70,60)
xlabel('Time')
ylabel(mzcdf_struct.mass_axis_label)
zlabel(mzcdf_struct.intensity_axis_label)