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)
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(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
(版本20230306，btmsp文件修改于2023年5月31日) RKI MALDI-飞行时间质谱数据库（Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Database, RKI MALDI-ToF MS Database）V4.1（20230306）是原始数据库（20161027版本，https://doi.org/10.5281/zenodo.163517）的第三次更新。本版数据库总计收录1599株高致病性细菌（生物安全等级3级，Biosafety Level 3, BSL-3）的11055条MALDI-ToF质谱数据，涵盖炭疽芽孢杆菌（Bacillus anthracis）、马耳他布鲁氏菌（Brucella melitensis）、鼠疫耶尔森菌（Yersinia pestis）、马鼻疽伯克霍尔德菌/类马鼻疽伯克霍尔德菌（Burkholderia mallei / pseudomallei）以及土拉弗朗西斯菌（Francisella tularensis），同时包含其近缘与远缘类群的部分质谱数据。本数据库可作为使用商用或开源软件开展基于MALDI-ToF MS的微生物鉴定的参考数据库。 质谱数据以压缩归档文件（zenodo db 230306.zip）形式提供，内含布鲁克·道尔顿公司（Bruker Daltonics）原生格式的原始质谱文件。有关培养条件、样品制备及质谱采集的详细信息，请参阅PDF文档（230306-ZENODO-Metadata.pdf）。请注意，请勿尝试打印该文档（页数超过1600页！）。 RKI数据库20230306版本首次提供btmsp格式文件（例如2023-May-23-Bacillus-RKI-Database-568.btmsp及其他同类文件）。此类文件由MALDI Biotyper软件（布鲁克·道尔顿公司）生成，总计包含该BSL-3数据库中的1599条主光谱（main spectra, MSP），采用MALDI Biotyper软件的专有数据格式。*.btmsp文件可导入该软件并用于微生物鉴定，详细导入操作请参阅厂商手册。请注意，数据库V4版本中的btmsp文件存在损坏，无法正常导入。 pkf文件（230306_ZENODO_30Peaks_0.75.pkf、230306_ZENODO_45Peaks_0.75.pkf）为两种版本的MS峰列表数据，采用Matlab兼容格式。此类数据可导入MicrobeMS——一款由罗伯特·科赫研究所（Robert Koch-Institute, RKI）开发的开源Matlab基微生物鉴定软件，可用于基于MALDI-ToF MS的微生物鉴定，获取地址为https://wiki-ms.microbe-ms.com。 RKI质谱数据库将定期更新。 作者谨向以下提供微生物菌株、菌种或其质谱数据的人员致以诚挚谢意。若无他们的协助，本工作无法完成： - 沃尔夫冈·拜尔（Wolfgang Beyer）——德国斯图加特霍恩海姆大学农业科学学院 - 圭多·沃纳（Guido Werner）——罗伯特·科赫研究所医院感染病原体与抗生素耐药性研究组（FG13），德国韦尔尼格罗德 - 亚历杭德拉·博施（Alejandra Bosch）——阿根廷布宜诺斯艾利斯省拉普拉塔国立大学理学院CONICET-CCT拉普拉塔中心CINDEFI研究所 - 米哈尔·德夫林内克（Michal Drevinek）——捷克共和国米林国家核、生物与化学防护研究所 - 罗兰·格鲁诺、丹妮拉·雅各布、西尔克·克莱、苏珊·杜普克与霍尔格·舒尔茨（Roland Grunow, Daniela Jacob, Silke Klee, Susann Dupke and Holger Scholz）——罗伯特·科赫研究所高致病性微生物研究部（ZBS2），德国柏林 - 约尔格·劳（Jörg Rau）——德国费尔巴赫斯图加特化学与兽医检测局 - 延斯·雅各布（Jens Jacob）——罗伯特·科赫研究所医院卫生、感染预防与控制研究组（FG14），德国柏林 - 马丁·米尔克（Martin Mielke）——罗伯特·科赫研究所传染病一科，德国柏林 - 莫妮卡·埃林-舒尔茨（Monika Ehling-Schulz）——奥地利维也纳兽医大学微生物研究所功能微生物学研究室 - 阿曼德·保乌（Armand Paauw）——荷兰乌得勒支大学医学中心医学微生物学系CBRN防护部，荷兰赖斯韦克TNO - 赫伯特·托马索（Herbert Tomaso）——德国耶拿联邦动物健康研究中心弗里德里希·勒夫勒研究所（Friedrich-Löffler-Institut, FLI） - 加布里埃尔·卡纳（Gabriel Karner）——奥地利纽伦巴赫卡纳肥料生产有限公司研发部 - 赖纳·博里斯（Rainer Borriss）——德国格雷夫斯瓦尔德海洋生物技术研究所（Institute of Marine Biotechnology e.V., IMaB） - 黎氏清谭（Le Thi Thanh Tam）——越南社会主义共和国河内植物保护研究所植物病理与植物免疫研究室 - 高学文（Xuewen Gao）——中国南京农业大学植物保护学院作物病虫害综合防治重点实验室
