Published October 27, 2016 | Version v1
Dataset Open

A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)

  • 1. Robert Koch-Institute, Nordufer 20, D-13353 Berlin, GERMANY


(Version 20161027)

Edit #1 (May 23, 2017): New database version (v.2 - 20170523) - available: 10.5281/zenodo.582602

Edit #2 (Nov 30, 2018): New database version (v.3 - 20181130) - available: 10.5281/zenodo.1880975

Edit #3 (Mar 06, 2023): New database version (v.4 - 20230306) - available: 10.5281/zenodo.7702375


The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra contains mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Yersinia pestis, Burkholderia mallei, Burkholderia pseudomallei and Francisella tularensis as well as a selection of spectra from their close and more distant relatives. The RKI mass spectral database can be used as a reference for the diagnostics of BSL-3 bacteria using proprietary and free software packages for MALDI-TOF MS-based microbial identification. The database itself is distributed as a zip archive that contains the original mass spectra in its native data format (Bruker Daltonics). Please refer to the pdf file (161027-ZENODO-Metadata.pdf) to obtain information on the metadata of the spectra. Do not try to print this document (~1000 pages!)

The pkf-file (161027_zenodo_Peaklist_(30Peaks1,6).pkf ) contains so-called database spectra in a Matlab compatible format. The latter data file can be imported into MicrobeMS, a Matlab-based free-of-charge software solution developed at the RKI. MicrobeMS is available from

For the future it is intended to update the RKI database of MALDI-TOF mass spectra on a regular basis.

The author's grateful thanks are given to the following persons for providing microbial strains and species. Without their help this work would not be possible.

  • Wolfgang Beyer - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany
  • Guido Werner - Robert Koch-Institute, Nosocomial Pathogens and Antibiotic Resistances (FG13), Wernigerode, Germany
  • Alejandra Bosch - CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
  • Michal Drevinek - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic
  • Roland Grunow - Robert Koch-Institute, Highly Pathogenic Microorganisms (ZBS2), Berlin, Germany
  • Daniela Jacob - Robert Koch-Institute, Highly Pathogenic Microorganisms (ZBS2), Berlin, Germany
  • Silke Klee - Robert Koch-Institute, Highly Pathogenic Microorganisms (ZBS2), Berlin, Germany
  • Jörg Rau - Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany
  • Jens Jacob - Robert Koch-Institute, Hospital Hygiene, Infection Prevention and Control (FG14), Berlin, Germany
  • Martin Mielke - Robert Koch-Institute, Department 1 - Infectious Diseases, Berlin, Germany
  • Monika Ehling-Schulz - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria



License type for data base files (spectra): Creative Commons Attribution Non Commercial 4.0 International (CC-BY-NC): Licensees must credit the original authors by stating their names & the original work's title. Licensees may copy, distribute, display, and perform the work and make derivative works and remixes based on it only for non-commercial purposes.



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