Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal
This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
Input data
MSI data: 3 types of input data can be used:
- imzml file (upload imzml and ibd file via the "composite" function) Introduction to the imzml format
- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
- Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
Optional file with pixel coordinates and annotation:
Tabular file: One column with x values, one column with y values and one column with annotations
The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
Pixel with coordinates outside the coordinates of the input file are ignored
x_coord y_coord annotation 1 1 healthy 2 1 healthy 3 1 disease ... ...Optional tabular file with m/z values:
One column with numeric m/z values (without empty fields or letters)
The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
m/z features outside the m/z range of the input file are ignored
m/z 100.0 100.01 100.02 ... ...
Options
Choosing spectra
"All spectra": Plots average mass spectra (mean of all spectra)
"Single spectra": Returns a full mass spectrum plot for each input spectrum, which is defined by its x- and y-coordinates
- the annotation column is optional:
- without annotation column: plots a separate mass spectrum for every input spectrum
- with annotation column: plots average mass spectra for each annotation group in different colours
Choosing m/z axis
"Plot complete m/z range": Full m/z range is plotted
"zoomed in m/z range": Only a customized m/z range is plotted
- "Manual input": Provide the minimum and maximum m/z value to define the m/z axis of the plot
- "Tabular input": File with m/z values of interest. Needs manual choice of m/z values to subtract and add from the input m/z values to generate the m/z axis of the plot
Output