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MSI plot spectra (version 2.10.0.0)
Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)
Choose Yes if peak detection has already been done.
Choose no if your input is an Analyze7.5 or continuous imzML file
Will appear in the pdf output, if nothing given it will take the dataset name
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

Choosing m/z axis

Output