Dataset Open Access

Version 3 (20181130) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)

Lasch, Peter; Stämmler, Maren; Schneider, Andy

(Version 20181130)

Version 3 (20181130) of the RKI’s MALDI-TOF mass spectral database represents the second update of the original database (version 20161027, https://doi.org/10.5281/zenodo.163517). The RKI database v.3 contains altogether 6264 mass spectra from highly pathogenic (i.e. 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 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. Spectral data are distributed as a 7-zip archive that contains the original mass spectra in its native data format (Bruker Daltonics). Please refer to the pdf file (181130-ZENODO-Metadata.pdf) to obtain information on cultivation condition, sample preparation and details of spectra acquisition. Do not try to print this document (~1000 pages!)

The pkf-file (181130_ZENODO_Peaklist_30Peaks_1.6.pkf) contains the MS peak list data in a Matlab compatible format. The latter data file can be imported into MicrobeMS, a Matlab-based free-of-charge software solution developed at RKI. MicrobeMS is available from http://www.microbe-ms.com.

The RKI mass spectral database will be updated on a regular basis.

The author's grateful thanks are given to the following persons for providing microbial strains and species, or mass spectra. 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
  • Armand Paauw - Department of Medical Microbiology, CBRN protection, Universitair Medisch Centrum Utrecht, TNO, Rijswijk, The Netherlands
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.
Files (188.6 MB)
Name Size
181130-ZENODO-Metadata.pdf
md5:f6c22ea42d9b87cdee995cc7aa2ec2f6 		3.5 MB Download
181130_ZENODO_Peaklist_30Peaks_1.6.pkf
md5:bcd41a3a2dbdd1b81ecdf32d402fd8ba 		10.7 MB Download
zenodo db 181130.7z
md5:963e5dd210353cb6b033a65878c7513e 		174.4 MB Download

  • Lasch P, Nattermann H, ... Grunow R, Naumann D, Anal Chem. (2008) 80(6): 2026-34.

  • Miñán A, Bosch A, Lasch P, ... , Naumann, D. Analyst. (2009) 134(6):1138-48.

  • Lasch P , ... , Naumann D. Appl Environ Microbiol. (2009) 75(22):7229-42.

  • Lasch P, ... , Naumann D. Anal Chem. (2010) 82(20):8464-75.

  • Lasch P & Naumann D. In: Proteomics, Glycomics and Antigenicity of BSL3 and BSL4 Agents. Wiley VCH 2011, Weinheim.

  • Wittwer M, Lasch P, .... , Jacob D, Grunow R. (2012) Applied Biosafety. 17(2): 59-63

  • Lasch P, Fleige C, Stämmler M, Layer F, Nübel U, Witte W, Werner G, J. (2014) Microbiol. Methods 100. 58-69.

  • Lasch P, ...., Stämmler M, Grunow R, Jacob D. (2015). J Clin Microbiol 53(8): 2632-2640.

  • Dieckmann R, ... , Dabrowski PW, Nitsche A, Stämmler M, ... , Lasch P. (2015), Faraday Discuss., DOI: 10.1039/C5FD00165J

  • Lasch P, Jacob D, Klee SR, Werner G, (2016). Applications of Mass Spectrometry in Microbiology, Springer International Publishing, pp. 203-234.

  • Lasch P, Grunow R, ...., Jacob D (2016). MALDI-TOF MS for the Identification of HPB. Trends in Analytical Chemistry

  • Lasch P, Jacob D, Grunow R, .., Doellinger J. (2016). Inactivation Techniques for MALDI-TOF MS. Trends in Analytical Chemistry

  • Lista, F., Reubsaet, F. A., ..., Paauw, A. (2011). Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS. BMC Microbiol 11(1): 267.

2,077
2,136
views
downloads
All versions This version
Views 2,0772,076
Downloads 2,1362,134
Data volume 88.5 GB88.5 GB
Unique views 1,7531,752
Unique downloads 1,2661,264
More info on how stats are collected.
Indexed in
Publication date:
November 30, 2018
DOI:
10.5281/zenodo.1880975

Zenodo DOI Badge

DOI 

10.5281/zenodo.1880975

Markdown 

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1880975.svg)](https://doi.org/10.5281/zenodo.1880975)

reStructedText 

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1880975.svg
   :target: https://doi.org/10.5281/zenodo.1880975

HTML 

<a href="https://doi.org/10.5281/zenodo.1880975"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.1880975.svg" alt="DOI"></a>

Image URL 

https://zenodo.org/badge/DOI/10.5281/zenodo.1880975.svg

Target URL 

https://doi.org/10.5281/zenodo.1880975

Keyword(s):
MALDI TOF Mass Spectrometry Spectral Database Identification
Related identifiers:
Previous versions
License (for files):
Creative Commons Attribution 4.0 International

Versions

Version 1 10.5281/zenodo.1880975 Nov 30, 2018
Cite all versions? You can cite all versions by using the DOI 10.5281/zenodo.1880974. This DOI represents all versions, and will always resolve to the latest one. Read more.

Share

Cite as

Export