Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
16
datasets available to search
ShareScore release 0.9.0
Dataset results
16 results for “MALDI-TOF mass spectrometry”
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>
Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures - MALDI-ToF Mass Spectra
<p>Datasets in support of the <em>bioRxiv </em>submitted paper Doellinger et al. (<strong>2019</strong>) "<em>Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures"</em> - MALDI-ToF Mass Spectra.</p> <p>The experiment and sample description and spectra numbering is consistent with the publication. Mass spectral data files are provided as unprocessed raw data in the manufacturer's original data format (Bruker Daltonics). Data is compressed using the freely available 7zip software.</p> <p><strong>Content:</strong></p> <p><em><strong>Figure 1.zip</strong></em>: Cereulide detection in <em>B. cereus</em> samples cultivated using different cultivation media and different sample preparation, or cereulide extraction methods.</p> <p><em><strong>Figure 2.zip</strong></em>: Effectivity of cereulide extraction by different solvents from <em>B. cereus</em> F4810/72 colony material.</p> <p><em><strong>Figure 3.zip</strong></em>: MALDI LIFT-ToF /ToF MS spectrum of cereulide.</p> <p><em><strong>Figure 4.zip</strong></em>: Determination of the limit of detection (LOD) of cereulide by MALDI- and LDI-ToF</p> <p><em><strong>Table 1.zip</strong></em>: Analysis of cereulide in <em>B. cereus</em> strains by MALDI-ToF MS.</p> <p><em><strong>Fig.SI.01.zip: </strong></em> Ultraperformance Liquid Chromatography – Mass Spectrometry (UPLC-MS/MS) analysis of ethanolic washing solutions of <em>B. cereus</em> F4810/72.</p> <p><em><strong>Fig.SI.02.zip:</strong></em> A selection of MALDI-ToF and LDI-ToF technical replicate mass spectra obtained from a commercial cereulide standard.</p> <p><em><strong>Fig.SI.03.zip:</strong></em> Limit of detection (LOD) of cereulide determined by MALDI- and LDI-ToF MS of ethanol wash solutions from <em>B. cereus</em> ATCC 10987 spiked by a cereulide standard. </p> <p><em><strong>Fig.SI.04.zip:</strong></em> Direct cereulide detection by means of MALDI- (panels <strong>A</strong>-<strong>F</strong>) and LDI-ToF MS (panels <strong>G</strong>-<strong>M</strong>) in linear and reflectron measurement mode.</p>
MALDI-TOF Spectra for Zooarcheology by Mass Spectrometry (ZooMS) for Borić et al. (2021)
<p>This dataset contains MALDI-TOF spectral data in .mzML format for zooarcheology by mass spectrometry (ZooMS) samples referenced in Borić et al. (2021).</p> <p>Folder names correspond to the ZooMS sample names referenced in the article. Files in the same folder are technical replicates.</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 Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
<p>The spectra were provided as unprocessed raw data in the manufacturers data format (Bruker), as labelled two zip archives with SARS CoV 2 positives and negative, according to the reviewer's recommendation.</p> <p>This information belongs to the publication (in review in <em>Journal of Virological Methods</em>)<br> "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs"<br> All the information belongs to the National Reference Institute, INEI-ANLIS DR CARLOS G MALBRAN, BUENOS AIRES, ARGENTINA.</p>
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>
Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening
<p>Dataset relating to the publication:</p> <p>Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening</p> <p>by Luuk Nico van Oosten and Christian D. Klein</p> <p>Published in the Journal of Medicinal Chemistry, 2020</p> <p><strong>Important notice:</strong></p> <p><strong>The data are free to use for non-commercial, academic purposes, provided that the original source is<br> cited and the authors and the publication are credited in any derivative work.</strong></p> <p><strong>A patent application has been filed for the method described by van Oosten and Klein, which uses mass<br> spectrometry and machine learning to identify the pharmacological or other effects of compounds on cell<br> cultures and other biological systems.</strong></p> <p>Therefore, a license for the commercial use of the method must be negotiated by contacting either</p> <p>Anke Faller<br> Universität Heidelberg<br> Dezernat Forschung<br> Rechts- und Strukturfragen der Forschungsförderung<br> Seminarstraße 2, 69117 Heidelberg<br> Tel. +49 6221 54-12611<br> anke.faller(at)zuv.uni-heidelberg.de</p> <p>or</p> <p>Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de<br> Medicinal Chemistry<br> Institute of Pharmacy and Molecular Biotechnology IPMB<br> Heidelberg University, INF 364<br> D-69120 Heidelberg<br> Germany<br> Phone: ++49-6221-54-4875<br> FAX : ++49-6221-54-6430</p> <p> </p>
Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
Background: In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods: Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results: Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.
Microbiological Evaluation of Single Versus Multiple Visits Regeneration Using MALDI-TOF Mass Spectrometry
ClinicalTrials.gov study NCT04533074. IPD Sharing: Not stated. Countries: 1. Publications: 18.
Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
Open the record for dataset details and reuse information.
MALDI-TOF mass spectrometry profiling of bovine skim milk for subclinical mastitis detection
<p>MALDI-TOF spectra acquired from bovine milk collected from dairy cows in Piedmont (Italy)</p>
Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging
GEO Series GSE279139. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)
<p><strong>Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)</strong></p> <ul> <li>This data set originates from a collection of 41 clinical strains of <em>Mycobacterium abscessus complex</em> corresponding to 1001 mass spectra: <ul> <li>25 strains of <em>Mycobacterium abscessus</em> subsp. <em>abscessus</em> (633 mass spectra)</li> <li>9 strains of <em>Mycobacterium abscessus</em> subsp. <em>massiliense</em> (204 mass spectra)</li> <li>7 strains of <em>Mycobacterium abscessus</em> subsp. <em>bolletii </em>(164 mass spectra)</li> </ul> </li> </ul> <p> </p> <ul> <li>Each strain has been characterized using molecular method (DNA/DNA hydridation, using GenoType NTM-DR (Hain Lifescience, Nehren, Germany) according to the manufacturer's instructions for identification and analyzed by MALDI-TOF mass spectrometry according MycoEx protocol (Bruker<sup>®</sup>). The mass spectra spectra were obtained according to the following steps :</li> </ul> <p> </p> <ol> <li>Each of the 41 strains was cultured in aerobic atmosphere at 37°C for 7 ± 2 days on blood agar (COH, bioMerieux<sup>®</sup>). Then, one colony was extracted according to the MycoEx protocol (Bruker<sup>®</sup>). For each of the extracts, 8 technical replicates were realized and analyzed by MALDITOF MS (Bruker<sup>®</sup>). Dried spots were overlaid with 1µL of MALDI matrix (α-HCCA).</li> <li> <p>Data acquisition was performed using a Microflex LT (Bruker<sup>®</sup> Daltonics) mass spectrometer equipped with a N2 laser (λ =377 nm). Instrument parameters used were as follows: a masse range between 200-20000 Da, ion source 1: 20 kV, ion source 2: 18.5 kV, Iens: 8.45 kV, pulsed ion extraction: 330 ns, laser frequency: 20.0 Hz. Spectra were obtained after 500 shots. Each spot was analyzed three times. In total 24 spectra were obtained for each extraction.</p> </li> <li> <p>Spectra acquired for each isolate were visualized and analyzed using Flex Analysis software (Bruker<sup>®</sup> Daltonics), and spectra with low quality peaks were removed. A minimum of 15 spectra per extraction was necessary to validate the extraction.</p> </li> </ol> <p><strong>This database is only intended for medical research. Please contact: medecine-drv@sorbonne-universite.fr for data access.</strong></p> <p>After access agreement, the three following files will be available :</p> <ul> <li>The MABSC_spectra.zip file contains the MS peak list data in a Matlab compatible format.</li> <li>The MABSC_metadata.pdf file contains the molecular identifications of strains.</li> <li>The MABSC_notes.txt file contains informations concerning contains informations on the method of obtaining the data.</li> </ul>
Spectra from "Contribution of MALDI-TOF mass spectrometry and Machine Learning including Deep Learning techniques for the detection of virulence factors of Clostridioides difficile strains"
<p><strong>This database includes spectra from 201 <em>C. difficile </em> (CD) strains :</strong></p> <ul> <li>50 non-toxigenic strains (tcdA- tcdB-) (designated ToxA-B-) belonging to 19 different PR,</li> <li>151 toxigenic strains harbouring toxins A and B genes (ToxA+B+). Among the 151 ToxA+B+ strains, 46 corresponding to 8 different PR also harboured the binary toxin genes (ToxA+B+CDT+) and 105 (23 different PR) did not (ToxA+B+CDT-).</li> <li>Among the 46 ToxA+B+CDT+ strains, 22 belonged to the Hv strains i.e. PR 027 (n=13), PR 176 (n=5) and PR 181 (n=4) strains (ToxA+B+CDT+Hv) (Table S1). </li> </ul> <p><strong>Sample preparation.</strong> Each isolate stored at −80°C (Microbank; Pro-Lab Diagnostics) was thawed and cultivated on Columbia Blood Agar (CBA, bioMérieux) incubated in anaerobic atmosphere at 37°C for 48 hours. A subculture was performed in the same conditions. A chemical protein extraction was then carried out. Briefly, a single colony was suspended in 200 µl water and vortexed. After adding 900 µl ethanol, samples were vortexed and centrifuged at 13,000 × g for 2 minutes. The supernatant was removed, and the remaining ethanol was evaporated at room temperature. Next, 25 µl of 70% formic acid was added and mixed with the pellet, then 25 µl of acetonitrile was added. After centrifugation at 13,000 × g for 2 minutes, the supernatant was ready for analysis. <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><br> <strong>MALDI-TOF MS acquisition and analysis.</strong> Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics).</p> <p><br> <strong>A total of 4659 spectra were produced. </strong></p> <p><strong>Fore more details: please contact alexandre.godmer@aphp.fr</strong><br> </p>
Spectral database of Streptococcus pneumoniae, S. mitis and S. pseudopneumoniae (MALDI-TOF Mass Spectrometry)
<p>A total of 80 strains, including 60 <strong>pneumococca</strong>l strains, 8 <strong><em>S. pseudopneumoniae</em> </strong>strains, and 12 <strong><em>S. mitis</em></strong> strains, were molecularly characterized and obtained from the National Reference Center for Pneumococci for the creation of the database. Each strain was tested a minimum of 20 and a maximum of 24 times using MALDI-TOF MS.</p> <p><br> MALDI-TOF MS acquisition and analysis. Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics). <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><strong>A total of 1890 spectra were produced :</strong></p> <ul> <li><em>S. mitis</em> (n=264),</li> <li><em>S.pneumoniae</em> (n= 1434),</li> <li><em>S. pseudopneumoniae </em>(n=192)</li> </ul> <p><strong>Fore more details:</strong> please contact alexandre.godmer@aphp.fr</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.