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Published March 6, 2023 | Version 4.1 (20230306); May 31, 2023: btmsp files modified
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Version 4.1 (20230306) of the MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)

Creators

  • 1. Robert Koch-Institute, ZBS 6

Description

(Version 20230306, btmsp files modified May 31, 2023)

Version 4.1 (20230306) of the RKI MALDI-ToF mass spectra database represents the third update of the original database (version 20161027, https://doi.org/10.5281/zenodo.163517). The RKI Database v.4.1 now contains a total of 11055 MALDI-ToF mass spectra from 1599 microbial strains of highly pathogenic (i.e. biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Brucella melitensis, Yersinia pestis, Burkholderia mallei / pseudomallei and Francisella tularensis as well as a selection of spectra of their close and distant relatives. The database can be used as a reference for the diagnosis of BSL-3 bacteria using proprietary and free software packages for MALDI-ToF MS-based microbial identification. The spectral data are provided as a zip archive (zenodo db 230306.zip) containing the original mass spectra in their native data format (Bruker Daltonics). Please refer to the pdf file (230306-ZENODO-Metadata.pdf) for information on cultivation conditions, sample preparation and details of the spectra acquisition. Please do not try to print this document (>1600 pages!).

Version 20230306 of the RKI database contains for the first time files in the btmsp format (e.g.  2023-May-23-Bacillus-RKI-Database-568.btmsp and others). These files were generated using the MALDI Biotyper software (Bruker Daltonics) and contain a total of 1599 main spectra (msp) from the BSL-3 database in the proprietary data format of the MALDI Biotyper software. *.btmsp files can be imported and used for identification with this software solution. Please refer to the manufacturer's manual for details on importing btmsp files. Note that the btmsp file available in database version 4 is broken and cannot be imported.

The pkf files (230306_ZENODO_30Peaks_0.75.pkf, 230306_ZENODO_45Peaks_0.75.pkf) represent two versions of the MS peak list data in a Matlab compatible format. The latter data can be imported into MicrobeMS, a free Matlab-based software solution developed at the RKI. MicrobeMS can be used for the identification of microorganisms by MALDI-ToF MS and is available at https://wiki-ms.microbe-ms.com.

The RKI mass spectrometry database is updated regularly.

The author would like to thank the following individuals for providing microbial strains and species or mass spectra thereof. Without their help, this work would not have been 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, Daniela Jacob, Silke Klee, Susann Dupke and Holger Scholz - 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
  • Herbert Tomaso – Friedrich-Löffler-Institut (FLI), Federal Research Institute for Animal Health, Jena, Germany
  • Gabriel Karner - Karner Düngerproduktion GmbH, Research & Development, Neulengbach, Austria
  • Rainer Borriss - Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
  • Le Thi Thanh Tam - Division of Plant Pathology and Phyto-Immunology, Plant Protection Research Institute, Hanoi, Socialist Republic of Vietnam
  • Xuewen Gao - College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing, People’s Republic of China

Notes

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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230306-ZENODO-Metadata.pdf

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Additional details

Related works

Is new version of
Dataset: 10.5281/zenodo.163517 (DOI)
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Dataset: 10.5281/zenodo.1880975 (DOI)

References

  • 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.
  • 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.
  • Wittwer M, Lasch P, .... , Jacob D, Grunow R. (2012) Applied Biosafety. 17(2): 59-63
  • Karger, A., Stock, R., ...., Tomaso, H. (2012) BMC Microbiol. 12, 229.
  • 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
  • Wu, H., Gu, Q., Xie, Y., ... , Gao, X. (2019) Environ. Microbiol. 0.
  • Tam, L. T. T., Jahne, J., Luong, P. T., Thao, ... , Borriss, R. (2020) Microbiol Resour Announc 9.