Galaxy | Tool Preview

MSI Qualitycontrol (version
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
one column with m/z values, optional second column with names (m/z values can also be selected as name)
Will be added in both directions to input calibrant m/z
No: does not generate all plots but only the most informatives
Plot fold change of two m/zs
Plot fold change of two m/z 0
Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool uses Cardinal to read files and create a quality control report with descriptive plots for 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




Overview of the QC report plots

x-y images (pixel/spectra information)

Properties over spectra/pixels

Properties over m/z features

Intensity plots

Mass spectra and m/z accuracy