Software that enables MS imaging on Bruker instruments. CreateTarget creates a high-density raster; Analyze This! converts the spectra to Analyze 7.5 format for analysis in BioMap.

CreateTarget and Analyze This! are two tools that, in conjunction with BioMap for image analysis, are sufficient to perform MS imaging on Bruker MALDI-TOF(/TOF) instruments. The software was developed and tested on the Reflex IV MALDI-TOF and the Ultraflex II (MALDI-TOF/TOF). We are very keen to hear from users working with other instruments (Biflex, Autoflex etc) and to adapt our software for these platforms if necessary.

A full description of the software can be found in “Clerens S, Ceuppens R, Arckens  L (2006). CreateTarget and Analyze This!: new software assisting imaging mass spectrometry on Bruker Reflex IV and Ultraflex II instruments. Rapid Commun Mass Spectrom 20: 3061-3066.”

Supported instruments Bruker Reflex IV, Bruker Ultraflex II with Windows 2000 or XP (do not try to install on Windows NT)
Image format Analyze 7.5
Origin University of Leuven (Belgium)
Author Stefan Clerens
Download (1.9 MB) (1.7 MB)
Registration Online



CreateTarget creates a high density raster with the dimensions of the tissue section, and converts these parameters to a virtual target plate file (geometry file) that needs to be imported in FlexControl, the normal Bruker mass spectrometer control software.

This software then treats this high density raster as a MALDI target plate with thousands of samples on it. Thus, using the AutoXecute module it is easy to automatically acquire spectra for all the sample positions.

We advise to create a placeholder file (e.g. MSI.geo) on the computer running FlexControl, in the directory containing the standard geometry files. After one restart, FlexControl will find this new .geo file. From then on, simply overwrite this file with the file generated by CreateTarget – this eliminates the need for a restart with each new .geo file.


Following automated spectrum acquisition, the second program, Analyze This!, converts the array of spectra to an Analyze 7.5 image format that can be read by image analysis software.


This program read the spectra acquired in the MSI experiment, and converts them to Analyze 7.5 format, which can be imported in BioMap for image analysis.

The newest version (v 1.2.0) now supports any section shape (not necessarily rectangular), and includes support for spectrum folder nomenclature slightly different from that determined by CreateTarget.


Execute the installation file and follow the instructions.


A short how-to is included in both programs – click the About button on the program’s main window to view it. For more information, refer to the forum.