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

This tool provides multiple tabular output options for mass spectrometry imaging data files.

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
     ...
     ...
    

Output options

• intensity matrix: m/z in rows, spectra in columns, filled with intensity values
• spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), median intensity, maximum intensity, highest m/z feature per spectrum, optional count of m/z per spectrum, optional spectrum annotation
• mz feature output: m/z in rows - for each m/z: name, m/z, mean, median, standard deviation (sd), standard error of the mean (sem), sum of all intensities per m/z, number of peaks (intensity > 0) per m/z
• summarized intensities: pixel annotations will be used to group spectra into annotation groups and calculate mean, median and sd of the intensities per group