Today, MALDI-ToF MS is an established technique to characterize and identify pathogenic bacteria. The technique is increasingly applied by clinical microbiological laboratories that use commercially available complete solutions, including spectra databases covering clinically relevant bacteria. Such databases are validated for clinical, or research applications, but are often less comprehensive concerning highly pathogenic bacteria (HPB). To improve MALDI-ToF MS diagnostics of HPB we initiated a program to develop protocols for reliable and MALDI-compatible microbial inactivation and to acquire mass spectra thereof many years ago. As a result of this project, databases covering HPB, closely related bacteria, and bacteria of clinical relevance have been made publicly available on platforms such as ZENODO. This publication in detail describes the most recent version of this database. The dataset contains a total of 11,055 spectra from altogether 1,601 microbial strains and 264 species and is primarily intended to improve the diagnosis of HPB. We hope that our MALDI-ToF MS data may also be a valuable resource for developing machine learning-based bacterial identification and classification methods.

Advisory Panel of the Medical Academy of the German Armed Forces Bundeswehr Institute of Microbiology Munich Germany

Chemisches und Veterinäruntersuchungsamt Stuttgart Fellbach Germany

CINDEFI UNLP CONICET CCT La Plata Facultad de Ciencias Exactas Universidad Nacional de La Plata La Plata Buenos Aires Argentina

College of Plant Protection Nanjing Agricultural University Key Laboratory of Integrated Management of Crop Diseases and Pests Nanjing People's Republic of China

Division of Plant Pathology and Phyto Immunology Plant Protection Research Institute Hanoi Vietnam

Friedrich Loeffler Institut Federal Research Institute for Animal Health Jena Germany

Functional Microbiology Institute of Microbiology University of Veterinary Medicine Vienna Austria

Institute of Marine Biotechnology e 5 Greifswald Germany

National Institute for Nuclear Chemical and Biological Protection Milin Czech Republic

Netherlands Organization for Applied Scientific Research TNO Department of CBRN Protection Rijswijk The Netherlands

Robert Koch Institute Nosocomial Pathogens and Antibiotic Resistances and National Reference Centre for Staphylococci and Enterococci Wernigerode Germany

Robert Koch Institute ZBS 2 Highly Pathogenic Microorganisms Berlin Germany

Robert Koch Institute ZBS 6 Proteomics and Spectroscopy Seestraße 10 Berlin D 13353 Germany

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