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A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)

Lasch, Peter; Stämmler, Maren; Schneider, Andy


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  <identifier identifierType="DOI">10.5281/zenodo.163517</identifier>
  <creators>
    <creator>
      <creatorName>Lasch, Peter</creatorName>
      <givenName>Peter</givenName>
      <familyName>Lasch</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6193-3144</nameIdentifier>
      <affiliation>Robert Koch-Institute, Nordufer 20, D-13353 Berlin, GERMANY</affiliation>
    </creator>
    <creator>
      <creatorName>Stämmler, Maren</creatorName>
      <givenName>Maren</givenName>
      <familyName>Stämmler</familyName>
      <affiliation>Robert Koch-Institute, Nordufer 20, D-13353 Berlin, GERMANY</affiliation>
    </creator>
    <creator>
      <creatorName>Schneider, Andy</creatorName>
      <givenName>Andy</givenName>
      <familyName>Schneider</familyName>
      <affiliation>Robert Koch-Institute, Nordufer 20, D-13353 Berlin, GERMANY</affiliation>
    </creator>
  </creators>
  <titles>
    <title>A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <subjects>
    <subject>MALDI TOF Mass Spectrometry, Highly Pathogenic Microorganisms, Spectral Database, Identification</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2016-10-27</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/163517</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1021/ac701822j</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1128/AEM.00857-09</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1021/ac101036s</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1039/b822669e</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1016/j.mimet.2014.02.015</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by-nc/4.0/legalcode">Creative Commons Attribution Non Commercial 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;em&gt;(Version&amp;nbsp;20161027) &lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&lt;em&gt;Edit #1 (May 23, 2017): New database version (v.2 - 20170523) - available&lt;/em&gt;: &lt;/strong&gt; &lt;a href="https://doi.org/10.5281/zenodo.582602"&gt;10.5281/zenodo.582602&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&lt;em&gt;Edit #2 (Nov 30, 2018): New database version (v.3 - 20181130) - available&lt;/em&gt;: &lt;/strong&gt; &lt;a href="https://doi.org/10.5281/zenodo.1880975"&gt;10.5281/zenodo.1880975&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;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 &lt;em&gt;Bacillus anthracis&lt;/em&gt;, &lt;em&gt;Yersinia pestis&lt;/em&gt;, &lt;em&gt;Burkholderia mallei&lt;/em&gt;, &lt;em&gt;Burkholderia pseudomallei&lt;/em&gt; and &lt;em&gt;Francisella tularensis&lt;/em&gt; 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!)&lt;/p&gt;

&lt;p&gt;The pkf-file (161027_zenodo_Peaklist_(30Peaks1,6).pkf ) contains &lt;em&gt;so-called&lt;/em&gt; 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.&lt;/p&gt;

&lt;p&gt;For the future it is intended to update the RKI database of MALDI-TOF mass spectra on a regular basis.&lt;/p&gt;

&lt;p&gt;The author&amp;#39;s grateful thanks are given to the following persons for providing microbial strains and species. Without their help this work would not be possible.&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Wolfgang Beyer - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany&lt;/li&gt;
	&lt;li&gt;Guido Werner - Robert Koch-Institute, &lt;em&gt; Nosocomial Pathogens and Antibiotic Resistances&lt;/em&gt; (FG13), Wernigerode, Germany&lt;/li&gt;
	&lt;li&gt;Alejandra Bosch - CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina&lt;/li&gt;
	&lt;li&gt;Michal Drevinek - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic&lt;/li&gt;
	&lt;li&gt;Roland Grunow - Robert Koch-Institute, &lt;em&gt;Highly Pathogenic Microorganisms&lt;/em&gt; (ZBS2), Berlin, Germany&lt;/li&gt;
	&lt;li&gt;Daniela Jacob - Robert Koch-Institute, &lt;em&gt;Highly Pathogenic Microorganisms&lt;/em&gt; (ZBS2), Berlin, Germany&lt;/li&gt;
	&lt;li&gt;Silke Klee - Robert Koch-Institute, &lt;em&gt;Highly Pathogenic Microorganisms&lt;/em&gt; (ZBS2), Berlin, Germany&lt;/li&gt;
	&lt;li&gt;J&amp;ouml;rg Rau - Chemisches und Veterin&amp;auml;runtersuchungsamt Stuttgart, Fellbach, Germany&lt;/li&gt;
	&lt;li&gt;Jens Jacob - Robert Koch-Institute, &lt;em&gt;Hospital Hygiene, Infection Prevention and Control &lt;/em&gt;(FG14), Berlin, Germany&lt;/li&gt;
	&lt;li&gt;Martin Mielke - Robert Koch-Institute, &lt;em&gt;Department 1 - Infectious Diseases&lt;/em&gt;, Berlin, Germany&lt;/li&gt;
	&lt;li&gt;Monika Ehling-Schulz - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
    <description descriptionType="Other">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 &amp; 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.</description>
  </descriptions>
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