Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool provides provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.

Input 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" data (with variable name "msidata", saved as .RData)

Options:

• pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible)
• m/z feature filtering: can use a tabular file containing m/z of interest or by defining a range for the m/z values (! numeric input will be rounded to 2 digits before matching to m/z!)
• m/z feature removing: perturbing m/z such as matrix contaminants can be removed by specifying their m/z in a tabular file and optionally set a window (window in ppm or m/z in which peaks should be removed)

Output:

• imzML file filtered for pixels and/or m/z
• optional: pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z
• optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)

Tip:

• It is recommended to use the filtering tool only for m/z which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool "Join two files on column allowing a small difference" should be used to find corresponding m/z values, which can then be used for filtering.