The "Modular Application Toolkit for Chromatography Mass-Spectrometry" is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.

Open Data Formats

  • supports chromatography and mass-spectral data from netcdf (ANDI-MS/-Chrom), mzXML, mzData and mzML formats
  • supports msp-format (Amdis, NIST MS Search, GMD-DB) database import for mass spectral search
  • mass-spectral data export in msp format
  • comma-separated-value (csv) data export for table-like data, e.g. alignments, peak tables etc.

Software Framework

  • generic framework for custom processing of chromatography-mass spectrometry data
  • efficient access to files of arbitrary size
  • easy to use level-of-abstraction application programming interface
  • creation of charts and plots for chromatograms, mass spectra, aligned and unaligned
  • academic and business friendly licensing (L-GPL v3 or EPL)


  • individual tasks can be executed concurrently
  • Mpaxs provides transparent parallel execution within the same virtual machine or within a distributed grid environment
  • convenience utilties for executing and collection of results from embarrassingly parallel tasks
  • simple integration with JAVA's Runnable and Callable classes


  • fast peak finder for chromatographic peaks
  • import of significant peaks as alignment anchors
  • multiple alignment and peak matching based on mass spectral similarities
  • clustering of chromatograms based on alignments


  • peak finder for comcodehensive GCxGC-MS and other multicolumn chromatography-MS
  • peak area integration based on 2D-TIC
  • multiple alignment and peak matching based on mass spectral similarities


  • Netbeans RCP based user interface to Maltcms, ChromA and ChromA4D
  • visual definition and editing of processing pipelines
  • visualizations of processing results, raw and processed data
Changed on 2014-10-17 by Nils Hoffmann