Metabolomics tries to capture the temporal and spatial distribution of metabolites. Until recently only temporal distributions could be measured easily by performing time-course or flux experiments. The spatial resolution has to be captured by dissecting certain cell types using laser microtomes or manual dissection.

With the advent of Imaging Mass Spectrometry (mass spectral imaging) it is now possible to capture the spatial distribution of metabolites in much higher resolution. With other imaging techniques such as TEM or STM or force field microscopy it is possible to "see" single atoms, however the spatial resolution of imaging mass spectrometry is currently limited by the laser wavelength and sensitivity issues of the whole mass spectral setup and therefore much lower. The spatial area that can be covered in a reasonable time and the mass spectral resolution also depend on the scan-speed of the mass spectrometer. Either fast scanning TOF/TOF or hybrid QTof or Orbitrap high-resolution analyzers are useful for imaging experiments, but in principle any mass analyzer can be used.

The immense data volume of spatial and temporal information plus multi-stage mass spectrometric data make MS imaging a top candidate for cloud computing approaches. The immense computational infrastructure and computing power as well as complex software setups required for large scale MS imaging can thus be outsourced to portals such as OpenMSI.

Data formats:

  • imzML: Imaging Mass Spectrometry Markup Language [link]

MS Imaging Software:

  • MMSIT - MALDI MS Imaging Tool (MMSIT) Stoeckli/Novartis [link]
  • MITICS - Maldi MS Imaging software via [link]
  • BioMap - imaging software from Novartis [link]
  • ThermoFisher - ImageQuest software [link]
  • Bruker - flexImaging software [link]
  • TissueView - AB SCIEX/Danaher software [link]
  • Mirion - data analysis for MS imaging (only ref is ASMS poster)
  • MaldiVision - PremierBioSoft [LINK]

Imaging software:

  • Analyze (Mayo) the commercialized version can be purchased - [link]
  • SPM Imaging, a Matlab based imaging software (Wellcome Trust Centre for Neuroimaging) - [link]
  • NIH ImageJ, a general purpose image editing software [link]

Web portals and cloud computing:


A software overview from 2008 can be found in: MITICS (MALDI Imaging Team Imaging Computing System): A new open source mass spectrometry imaging software; (PDF)


Lipids, Lipids, all I see is Lipids. Explanation: membrane lipids are prominent ions in many MS imaging reports because the ionize nicely. The coverage has to be extended to the Thousands of other molecules in pathway databases such as KEGG.