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5 results for “RKI”
rki
<p>COVID-19 data for Germany from 2020-03-02 to 2023-01-26, including tot_cases, tot_deaths</p> <p>Files:</p> <ul> <li>".pkl" Cache file backup</li> <li>Dataframe exported "PyCoa-DF.csv"</li> <li>Original database backup </li> </ul>
Version 4.2 (20230306) of the MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)
<p><em>(Version </em>20230306<em>, </em>btmsp files modified May 31, 2023, additional taxonomic information added Dec 27, 2024<em>) </em></p> <p>Version 4.2 (20230306) of the RKI MALDI-ToF mass spectra database represents the third update of the original database (version 20161027, <a href="http://doi.org/10.5281/zenodo.163517">https://doi.org/10.5281/zenodo.163517</a>). The RKI Database v.4.2 now contains a total of 11055 MALDI-ToF mass spectra from 1601 microbial strains of highly pathogenic (i.e. biosafety level 3, BSL-3) bacteria such as <em>Bacillus anthracis</em>, <em>Brucella melitensis</em>, <em>Yersinia pestis</em>, <em>Burkholderia mallei / pseudomallei</em> and <em>Francisella tularensis</em> 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 (<a href="https://zenodo.org/records/14562231/files/zenodo%20db%20230306.zip?download=1&preview=1">zenodo db 230306.zip</a>) containing the original mass spectra in their native data format (Bruker Daltonics). Please refer to the pdf file (<a href="https://zenodo.org/records/14562231/files/230306-ZENODO-Metadata.pdf?download=1&preview=1">230306-ZENODO-Metadata.pdf</a>) for information on cultivation conditions, sample preparation and details of the spectra acquisition. Please do not try to print this document (>1600 pages!).</p> <p>Version 20230306 of the RKI database contains for the first time files in the <em>btmsp</em> format (e.g. <a href="https://zenodo.org/records/14562231/files/2023-May-23-Bacillus-RKI-Database-568.btmsp?download=1&preview=1">2023-May-23-Bacillus-RKI-Database-568.btmsp </a> <a href="https://zenodo.org/api/files/35e90a0c-653d-4ba4-bf93-50b2bd80d073/2023-May-23-Bacillus-RKI-Database-570.btmsp"> </a>and others). These files were generated using the MALDI Biotyper software (Bruker Daltonics) and contain a total of 1601 main spectra (msp) from the BSL-3 database in the proprietary data format of the MALDI Biotyper software. *.<em>btmsp </em>files can be imported and used for identification with this software solution. Please refer to the manufacturer's manual for details on importing <em>btmsp </em>files. Note that the btmsp file available in database version 4 is broken and cannot be imported.</p> <p>The pkf files (<a href="https://zenodo.org/records/14562231/files/230306_ZENODO_30Peaks_0.75.pkf?download=1&preview=1">230306_ZENODO_30Peaks_0.75.pkf</a>, <a href="https://zenodo.org/records/14562231/files/230306_ZENODO_45Peaks_0.75.pkf?download=1&preview=1">230306_ZENODO_45Peaks_0.75.pkf</a>) 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 <a href="https://wiki-ms.microbe-ms.com">https://wiki-ms.microbe-ms.com</a>.</p> <p>The Excel file <a href="https://zenodo.org/records/14562231/files/Taxonomy%20information%20-%20RKI%20MALDI-ToF%20MS%20database%20of%20HPB%20at%20ZENODO%20v.4.xlsx?download=1&preview=1">Taxonomy information - RKI MALDI-ToF MS database of HPB at ZENODO v.4.xlsx</a> contains additional taxonomic information such as a detailed list of bacterial MALDI-ToF mass spectra (sheet #1), overviews on the number of spectra per strain, species or bacterial genus (sheet #2), numbers of strains per species, or genus (sheet #3), etc.</p> <p>The RKI mass spectrometry database is updated regularly.</p> <p>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.</p> <ul> <li><strong>Wolfgang Beyer</strong> - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany</li> <li><strong>Guido Werner</strong> - Robert Koch-Institute, Nosocomial Pathogens and Antibiotic Resistances (FG13), Wernigerode, Germany</li> <li><strong>Alejandra Bosch</strong> - CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina</li> <li><strong>Michal Drevinek</strong> - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic</li> <li><strong>Roland Grunow, Daniela Jacob, Silke Klee, Susann Dupke </strong>and <strong>Holger Scholz</strong> - Robert Koch-Institute, Highly Pathogenic Microorganisms (ZBS2), Berlin, Germany</li> <li><strong>Jörg Rau </strong>- Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany</li> <li><strong>Jens Jacob</strong> - Robert Koch-Institute, Hospital Hygiene, Infection Prevention and Control (FG14), Berlin, Germany</li> <li><strong>Martin Mielke</strong> - Robert Koch-Institute, Department 1 - Infectious Diseases, Berlin, Germany</li> <li><strong>Monika Ehling-Schulz</strong> - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria</li> <li><strong>Armand Paauw</strong> - Department of Medical Microbiology, CBRN protection, Universitair Medisch Centrum Utrecht, TNO, Rijswijk, The Netherlands</li> <li><strong>Herbert Tomaso</strong><strong> </strong>– Friedrich-Löffler-Institut (FLI), Federal Research Institute for Animal Health, Jena, Germany</li> <li><strong>Gabriel Karner</strong><strong> </strong>- Karner Düngerproduktion GmbH, Research & Development, Neulengbach, Austria</li> <li><strong>Rainer </strong><strong>Borriss</strong><strong> </strong>- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany</li> <li><strong>Le Thi Thanh Tam</strong><strong> </strong>- Division of Plant Pathology and Phyto-Immunology, Plant Protection Research Institute, Hanoi, Socialist Republic of Vietnam</li> <li><strong>Xuewen</strong><strong> Gao</strong><strong> </strong>- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing, People’s Republic of China</li> </ul> <p>For a detailed description of the database see: Lasch, P., Beyer, W., Bosch, A. <em>et al.</em> A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria. <em>Sci Data</em> <strong>12</strong>, 187 (2025). <a href="https://doi.org/10.1038/s41597-025-04504-z">https://doi.org/10.1038/s41597-025-04504-z</a></p>
Version 3 (20181130) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)
<p><em>(Version </em>20181130<em>) </em></p> <p><strong><em>Edit #1 (Mar 06, 2023): New database version (v.4.2 - 20230306) - available</em>: </strong><a href="https://zenodo.org/records/14562231">https://zenodo.org/records/14562231</a></p> <p>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 <em>Bacillus anthracis</em>, <em>Yersinia pestis</em>, <em>Burkholderia mallei</em>, <em>Burkholderia pseudomallei</em> and <em>Francisella tularensis</em> 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!)</p> <p>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 <a href="https://wiki-ms.microbe-ms.com">https://wiki-ms.microbe-ms.com</a>.</p> <p>The RKI mass spectral database will be updated on a regular basis.</p> <p>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.</p> <ul> <li><strong>Wolfgang Beyer</strong> - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany</li> <li><strong>Guido Werner</strong> - Robert Koch-Institute, <em>Nosocomial Pathogens and Antibiotic Resistances</em> (FG13), Wernigerode, Germany</li> <li><strong>Alejandra Bosch</strong> - <em>CINDEFI, CONICET-CCT</em> La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina</li> <li><strong>Michal Drevinek</strong> - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic</li> <li><strong>Roland Grunow</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Daniela Jacob</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Silke Klee</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Jörg Rau</strong> - Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany</li> <li><strong>Jens Jacob</strong> - Robert Koch-Institute, <em>Hospital Hygiene, Infection Prevention and Control </em>(FG14), Berlin, Germany</li> <li><strong>Martin Mielke</strong> - Robert Koch-Institute, <em>Department 1 - Infectious Diseases</em>, Berlin, Germany</li> <li><strong>Monika Ehling-Schulz</strong> - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria</li> <li><strong>Armand Paauw</strong> - Department of Medical Microbiology, CBRN protection, Universitair Medisch Centrum Utrecht, TNO, Rijswijk, The Netherlands</li> </ul>
A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)
<p><em>(Version 20161027) </em></p> <p><strong><em>Edit #1 (May 23, 2017): New database version (v.2 - 20170523) - available</em>: </strong> <a href="https://doi.org/10.5281/zenodo.582602">10.5281/zenodo.582602</a></p> <p><strong><em>Edit #2 (Nov 30, 2018): New database version (v.3 - 20181130) - available</em>: </strong> <a href="https://doi.org/10.5281/zenodo.1880975">10.5281/zenodo.1880975</a></p> <p><strong><em>Edit #3 (Mar 06, 2023): New database version (v.4.2 - 20230306) - available</em>: </strong> <a href="https://zenodo.org/records/14562231">10.5281/zenodo.7702375</a></p> <p> </p> <p>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 <em>Bacillus anthracis</em>, <em>Yersinia pestis</em>, <em>Burkholderia mallei</em>, <em>Burkholderia pseudomallei</em> and <em>Francisella tularensis</em> 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!)</p> <p>The pkf-file (161027_zenodo_Peaklist_(30Peaks1,6).pkf ) contains <em>so-called</em> 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 http://www.microbe-ms.com.</p> <p>For the future it is intended to update the RKI database of MALDI-TOF mass spectra on a regular basis.</p> <p>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.</p> <ul> <li>Wolfgang Beyer - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany</li> <li>Guido Werner - Robert Koch-Institute, <em> Nosocomial Pathogens and Antibiotic Resistances</em> (FG13), Wernigerode, Germany</li> <li>Alejandra Bosch - CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina</li> <li>Michal Drevinek - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic</li> <li>Roland Grunow - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li>Daniela Jacob - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li>Silke Klee - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li>Jörg Rau - Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany</li> <li>Jens Jacob - Robert Koch-Institute, <em>Hospital Hygiene, Infection Prevention and Control </em>(FG14), Berlin, Germany</li> <li>Martin Mielke - Robert Koch-Institute, <em>Department 1 - Infectious Diseases</em>, Berlin, Germany</li> <li>Monika Ehling-Schulz - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria</li> </ul> <p> </p>
Version 2 (20170523) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)
<p><em>(Version </em>20170523<em>) </em></p> <p><strong><em>Edit #1 (Nov 30, 2018): New database version (v.3 - 20181130) - available</em>: </strong> <a href="https://doi.org/10.5281/zenodo.1880975">10.5281/zenodo.1880975</a></p> <p><strong><em>Edit #2 (Mar 06, 2023): New database version (v.4.2 - 20230306) - available</em>: </strong> <a href="https://zenodo.org/records/14562231">10.5281/zenodo.7702375</a></p> <p>Version 2 (20170523) of the RKI’s MALDI-TOF mass spectral database is an update of the original database (version 20161027, https://doi.org/10.5281/zenodo.163517). The RKI database contains mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as <em>Bacillus anthracis</em>, <em>Yersinia pestis</em>, <em>Burkholderia mallei</em>, <em>Burkholderia pseudomallei</em> and <em>Francisella tularensis</em> 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 (170523-ZENODO-Metadata.pdf) to obtain information on the metadata of the spectra. Do not try to print this document (~1100 pages!)</p> <p>The pkf-file (170523_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.</p> <p>The RKI mass spectral database will be updated on a regular basis.</p> <p>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.</p> <ul> <li><strong>Wolfgang Beyer</strong> - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany</li> <li><strong>Guido Werner</strong> - Robert Koch-Institute, <em>Nosocomial Pathogens and Antibiotic Resistances</em> (FG13), Wernigerode, Germany</li> <li><strong>Alejandra Bosch</strong> - <em>CINDEFI, CONICET-CCT</em> La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina</li> <li><strong>Michal Drevinek</strong> - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic</li> <li><strong>Roland Grunow</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Daniela Jacob</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Silke Klee</strong> - Robert Koch-Institute, <em>Highly Pathogenic Microorganisms</em> (ZBS2), Berlin, Germany</li> <li><strong>Jörg Rau</strong> - Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany</li> <li><strong>Jens Jacob</strong> - Robert Koch-Institute, <em>Hospital Hygiene, Infection Prevention and Control </em>(FG14), Berlin, Germany</li> <li><strong>Martin Mielke</strong> - Robert Koch-Institute, <em>Department 1 - Infectious Diseases</em>, Berlin, Germany</li> <li><strong>Monika Ehling-Schulz</strong> - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria</li> <li><strong>Armand Paauw</strong> - Department of Medical Microbiology, CBRN protection, Universitair Medisch Centrum Utrecht, TNO, Rijswijk, The Netherlands</li> </ul>
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