Publications with MicrobeMS: Difference between revisions

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== Relevant publications ==     
== Publications in which MicrobeMS has been used or mentioned ==     
&nbsp;<br><ul>
&nbsp;<br><ol>


<li> [https://doi.org/10.5281/zenodo.7702375 Version 4 (20230306) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)]<br>
Lasch P, Stämmler M, Schneider A. <br>
Zenodo (Mar 06, '''2023''') doi:10.5281/zenodo.7702375</LI>&#160;


<li> [https://doi.org/10.1074/mcp.TIR120.002061 Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries]<br>
<li>Lasch, P., W. Beyer, A. Bosch, R. Borriss, et al.,<br>A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria. <br><i>Sci Data</i>, <b>2025</b>. 12(1): p. 187.<br>
Lasch P, Schneider A, Blumenscheit C, Doellinger J <br>
https://doi.org/10.1038/s41597-025-04504-z<br> &nbsp; <br></li>
Mol Cell Prot, '''2020''' 19(12), 2125-2139</LI>&#160;


<li> [https://doi.org/10.5281/zenodo.3573996 In silico Database for Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS&sup1;)]<br>
<li>Blumenscheit, C., Pfeifer, Y., Werner, G., John, C., Layer-Nicolaou, F., Schneider, A., Lasch, P., Doellinger, J., <br>Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics. <br><i>bioRxiv - biorxiv.org</i>, <b> Oct 28, 2024</b>.<br>
Lasch P, Schneider A, Blumenscheit C, Doellinger J <br>
https://doi.org/10.1101/2024.09.09.612008 .<br> &nbsp; <br></li>
Zenodo (December 13, '''2019''') doi: 10.5281/zenodo.3573996</LI>&#160;


<li> '''Preprint''': [https://doi.org/10.1101/870089 Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data]<br>
<li>Collins, T.J., Muste, C., Owens, K.G.<br>Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data. <br><i>J Am Soc Mass Spectrom</i>, <b>2024</b>. 35, 6, 1352–1362.<br>
Lasch P, Schneider A, Blumenscheit C, Doellinger J <br>
https://dx.doi.org/10.1021/jasms.4c00101.<br> &nbsp; <br></li>
bioRxiv (Dec 10, '''2019''') doi:10.1101/870089 </LI>&#160;


<li> [https://doi.org/10.5281/zenodo.1880975 Version 3 (20181130) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)]<br>
<li>Lasch, P., M. Stämmler, and A. Schneider,<br>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). <br><i>Zenodo</i>,<b> Mar 6, 2023.</b> <br>
Lasch P, Stämmler M, Schneider A. <br>
https://doi.org/10.5281/zenodo.7702374.<br> &nbsp; <br></li>
Zenodo (Nov 11, '''2018''') doi:10.5281/zenodo.1880975</LI>&#160;


<li> [https://www.ncbi.nlm.nih.gov/pubmed/29095137 Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils]<br>
<li>Yang Y.,<br>Chapter 3: MALDI-TOF Mass Fingerprinting for Rapid Identification of Bacteria: Data Analysis and Algorithm Development.<br><i> Detection and Analysis of Microorganisms by Mass Spectrometry: New Developments in Mass Spectrometry</i>,<b>06 Oct 2023</b><br>
P Martina, M Leguizamon, CI Prieto, SA Sousa, P Montanaro, WO Draghi, ...<br>
https://doi.org/10.1039/BK9781837670338-00045.<br> &nbsp; <br></li>
''International Journal of Systematic and Evolutionary Microbiology''.'''2017''' 68 (1), 14-20</LI>&#160;


<li> [http://doi.org/10.5281/zenodo.582602 Version 2 (20170523) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)]<br>
<li> Yin, M. M. Gao, Y. L., Zheng, C.H., Liu, J.X.,<br>NTBiRW: A Novel Neighbor Model based on Two-tier Bi-Random Walk for Predicting Potential Disease-related Microbes.<br><i> IEEE J Biomed Health Inform </i> 27(3),1644-1653). <b>07 Feb. 2023</b>.<br>
Lasch P, Stämmler M, Schneider A. <br>
https://doi.org/10.1109/JBHI.2022.3229473.<br> &nbsp; <br></li>
Zenodo (May 23, '''2017''') doi:10.5281/zenodo.582602</LI>&#160;


<li> [https://www.ncbi.nlm.nih.gov/pubmed/27053001 Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy]<br>
<li> Wang, L., Yang, X., Kuang, L., Zhang, Z., Zeng, B., Chen, Z.,<br>Graph Convolutional Neural Network with Multi-Layer Attention Mechanism for Predicting Potential Microbe-Disease Associations. <i> Current Bioinformatics.</i> 18(6):497-508(12). <b>2023</b>.<br>
R Dieckmann, JA Hammerl, H Hahmann, A Wicke, S Kleta, PW Dabrowski, ...<br>
https://doi.org/10.2174/1574893618666230316113621.<br> &nbsp; <br></li>
''Faraday Discussions''.'''2016''' 187, 353-375</LI>&#160;


<li> [http://doi.org/10.5281/zenodo.163517 Version 1 (20161027) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)]<br>
<li>Ramadan, A.A.,<br>Bacterial typing methods from past to present: A comprehensive overview. <br><i>Gene Reports</i>, <b>2022</b>. 29: p. 101675.<br>
Lasch P, Stämmler M, Schneider A. <br>
https://dx.doi.org/10.1016/j.genrep.2022.101675.<br> &nbsp; <br></li>
Zenodo (Oct 27, '''2016''') doi:10.5281/zenodo.163517</LI>&#160;


<li> [http://dx.doi.org/10.1016/j.trac.2016.04.013 Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of highly pathogenic bacteria]<br>
<li>Qiao, L.,<br>MALDI-TOF MS for pathogenic bacteria analysis. <br><i>International Journal of Mass Spectrometry</i>, <b>2022</b>. 482: p. 116935.<br>
Lasch P, Jacob D, Grunow R, Schwecke T, Doellinger J. <br>
https://dx.doi.org/10.1016/j.ijms.2022.116935.<br> &nbsp; <br></li>
''Trends Anal Chem''. '''2016'''. Part B, (Trends in CBRN Measurements for safety and security): 103–111. doi: 10.1016/j.trac.2016.04.013</LI>&#160;


<li> [http://dx.doi.org/10.1016/j.trac.2016.04.012 Inactivation techniques for MALDI-TOF MS analysis of highly pathogenic bacteria - A Critical Review]<br>
<li>Blumenscheit, C., Y. Pfeifer, G. Werner, C. John, et al.,<br>Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics. <br><i>Anal Chem</i>, <b>2021</b>. 93(44): p. 14599-14608.<br>
Lasch P, Grunow R, Antonation K, Weller S, Jacob D.<br>
https://www.ncbi.nlm.nih.gov/pubmed/34697938.<br> &nbsp; <br></li>
''Trends Anal Chem''. '''2016'''. 85, Part B, (Trends in CBRN Measurements for safety and security): 112–119. doi:10.1016/j.trac.2016.04.012</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/26042113 Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions]<br>
<li>Lasch, P., A. Schneider, C. Blumenscheit, and J. Doellinger,<br>Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS(1)) and in Silico Peptide Mass Libraries. <br><i>Mol Cell Proteomics</i>, <b>2020</b>. 19(12): p. 2125-2139.<br>
Sousa C, Botelho J, Grosso F, Silva L, Lopes J, Peixe L.<br>
https://www.ncbi.nlm.nih.gov/pubmed/32998977.<br> &nbsp; <br></li>
''Front Microbiol''. '''2015'''. 6:481. doi: 10.3389/fmicb.2015.00481.</LI>&#160;


<li> [https://link.springer.com/chapter/10.1007/978-3-319-26070-9_8 Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains]<br>
<li>Gittens, R.A., A. Almanza, K.L. Bennett, L.C. Mejia, et al.,<br>Proteomic fingerprinting of Neotropical hard tick species (Acari: Ixodidae) using a self-curated mass spectra reference library. <br><i>PLoS Negl Trop Dis</i>, <b>2020</b>. 14(10): p. e0008849.<br>
Lasch P, Jacob D, Klee SR, Werner G. <br>
https://www.ncbi.nlm.nih.gov/pubmed/33108372.<br> &nbsp; <br></li>
''In: Applications of Mass Spectrometry in Microbiology: From Strain Characterization to Rapid Screening for Antibiotic Resistance.'' Editors: Plamen A. Demirev and Todd R. Sandrin, Springer</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/26063856 Identification of Highly Pathogenic Microorganisms using MALDI-TOF Mass Spectrometry - Results of an Inter-Laboratory Ring Trial]<br>
<li>Baumeister, T.U.H., M. Vallet, F. Kaftan, L. Guillou, et al.,<br>Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry. <br><i>Metabolomics</i>, <b>2020</b>. 16(3): p. 28.<br>
Lasch P, Wahab T, Weil S, Pályi B, Tomaso H, Zange S, Granerud BK, Drevinek M, Kokotovic B, Wittwer M, Pflüger V, Di Caro A, Stämmler M, Grunow R, Jacob D.<br>
https://www.ncbi.nlm.nih.gov/pubmed/32090296.<br> &nbsp; <br></li>
''J Clin Microbiol''. '''2015'''. 53(8):2632-40. doi:10.1128/JCM.00813-15</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/24614010 Insufficient discriminatory power of MALDI-TOF mass spectrometry for typing of Enterococcus faecium and Staphylococcus aureus isolates]<br>
<li>Lasch, P., A. Schneider, C. Blumenscheit, and J. Doellinger,<br>Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data. <br><i>bioRxiv</i>, <b>2019</b>.<br>
Lasch P, Fleige C, Stämmler M, Layer F, Nübel U, Witte W, Werner G.<br>
https://doi.dx.org/10.1101/870089 .<br> &nbsp; <br></li>
''J Microbiol Methods''. '''2014'''. pii: S0167-7012(14)00055-4.</LI>&#160;


<li> [http://onlinelibrary.wiley.com/doi/10.1002/9783527638192.ch17/summary MALDI-TOF mass spectrometry for rapid identification of highly pathogenic microorganisms.]<br>
<li>Martina, P., M. Leguizamon, C.I. Prieto, S.A. Sousa, et al.,<br>Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils. <br><i>Int J Syst Evol Microbiol</i>, <b>2018</b>. 68(1): p. 14-20.<br>
Lasch P, Naumann D.<br>
https://www.ncbi.nlm.nih.gov/pubmed/29095137.<br> &nbsp; <br></li>
In: Proteomics, Glycomics and Antigenicity of BSL3 and BSL4 Agents. J. Stulik, R. Toman, P. Butaye, R.G. Ulrich (Eds). Wiley VCH. '''2011''', Weinheim, Germany.</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/20866090 Characterization of Yersinia using MALDI-TOF mass spectrometry and chemometrics.]<br>
<li>Lasch, P., M. Stämmler, and A. Schneider,<br>Version 3 (20181130) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI). <br><i>Zenodo</i>, <b>2018</b>. November 30, 2018.<br>
Lasch P, Drevinek M, Nattermann H, Grunow R, Stämmler M, Dieckmann R, Schwecke T, Naumann D. <br>
https://dx.doi.org/10.5281/zenodo.1880975.<br> &nbsp; <br></li>
''Anal Chem''. '''2010'''. 82(20):8464-75.</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/19767470 Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks.]<br>
<li>Yang, Y., Y. Lin, Z. Chen, T. Gong, et al.,<br>Bacterial Whole Cell Typing by Mass Spectra Pattern Matching with Bootstrapping Assessment. <br><i>Anal Chem</i>, <b>2017</b>. 89(22): p. 12556-12561.<br>
Lasch P, Beyer W, Nattermann H, Stämmler M, Siegbrecht E, Grunow R, Naumann D.<br>
https://www.ncbi.nlm.nih.gov/pubmed/29086558.<br> &nbsp; <br></li>
''Appl Environ Microbiol''. '''2009'''. 75(22):7229-42.</LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/19475140  Rapid identification of Burkholderia cepacia complex species including strains of the novel Taxon K, recovered from cystic fibrosis patients by intact cell MALDI-ToF mass spectrometry.]<br>
<li>Meyer, B., A. Rabenstein, and J. Kuever,<br>Mass Spectrometry: A Powerful Tool for the Identification of Wine-Related Bacteria and Yeasts. <br><i>Biology of Microorganisms on Grapes, in Must and in Wine</i>, <b>2017</b>: p. 659-701.<br>
Miñán A, Bosch A, Lasch P, Stämmler M, Serra DO, Degrossi J, Gatti B, Vay C, D'aquino M, Yantorno O, Naumann D.<br>
https://dx.doi.org/10.1007/978-3-319-60021-5_27.<br> &nbsp; <br></li>
''Analyst''. '''2009'''. 134(6):1138-48. </LI>&#160;


<li> [http://www.ncbi.nlm.nih.gov/pubmed/18290666 MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores.]<br>
<li>Lasch, P., M. Stämmler, and A. Schneider,<br>Version 2 (20170523) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI). <br><i>Zenodo</i>, <b>2017</b>. May 23, 2017.<br>
Lasch P, Nattermann H, Erhard M, Stämmler M, Grunow R, Bannert N, Appel B, Naumann D.<br>
http://dx.doi.org/10.5281/zenodo.582602.<br> &nbsp; <br></li>
''Anal Chem''. '''2008'''. 80(6):2026-34. </LI>&#160;


</ul>
<li>Lasch, P., M. Stämmler, and A. Schneider,<br>A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI). <br><i>Zenodo</i>, <b>2016</b>. Oct 27, 2017.<br>
http://dx.doi.org/10.5281/zenodo.163517.<br> &nbsp; <br></li>
 
<li>Lasch, P., D. Jacob, S.R. Klee, and G. Werner,<br>Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains. <br><i>In: Applications of Mass Spectrometry in Microbiology, Plamen Demirev, Todd R. Sandrin (Eds.)</i>, <b>2016</b>. Springer International Publishing: p. 203-234.<br>
http://dx.doi.org/10.1007/978-3-319-26070-9_8.<br> &nbsp; <br></li>
 
<li>Lasch, P., D. Jacob, R. Grunow, T. Schwecke, and J. Doellinger,<br>Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS for the identification of highly pathogenic bacteria. <br><i>TrAC Trends in Analytical Chemistry</i>, <b>2016</b>. 85, Part B(Trends in CBRN Measurements for safety and security): p. 103–111.<br>
http://dx.doi.org/10.1016/j.trac.2016.04.013.<br> &nbsp; <br></li>
 
<li>Lasch, P., R. Grunow, K. Antonation, S.A. Weller, and D. Jacob,<br>Inactivation Techniques for MALDI-TOF MS Analysis of Highly Pathogenic Bacteria - A Critical Review. <br><i>TrAC Trends in Analytical Chemistry</i>, <b>2016</b>. 85, Part B(Trends in CBRN Measurements for safety and security): p. 112–119.<br>
http://dx.doi.org/10.1016/j.trac.2016.04.012.<br> &nbsp; <br></li>
 
<li>Dieckmann, R., J.A. Hammerl, H. Hahmann, A. Wicke, et al.,<br>Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. <br><i>Faraday Discuss</i>, <b>2016</b>. 187: p. 353-75.<br>
http://www.ncbi.nlm.nih.gov/pubmed/27053001.<br> &nbsp; <br></li>
 
<li>Sousa, C., J. Botelho, F. Grosso, L. Silva, et al.,<br>Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions. <br><i>Front Microbiol</i>, <b>2015</b>. 6: p. 481.<br>
http://www.ncbi.nlm.nih.gov/pubmed/26042113.<br> &nbsp; <br></li>
 
<li>Smith, E.M., Z.N. Willis, M. Blakeley, F. Lovatt, et al.,<br>Bacterial species and their associations with acute and chronic mastitis in suckler ewes. <br><i>J Dairy Sci</i>, <b>2015</b>. 98(10): p. 7025-33.<br>
https://www.ncbi.nlm.nih.gov/pubmed/26277313.<br> &nbsp; <br></li>
 
<li>Lasch, P., T. Wahab, S. Weil, B. Palyi, et al.,<br>Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial. <br><i>J Clin Microbiol</i>, <b>2015</b>. 53(8): p. 2632-40.<br>
https://www.ncbi.nlm.nih.gov/pubmed/26063856.<br> &nbsp; <br></li>
 
<li>Lasch, P., C. Fleige, M. Stammler, F. Layer, et al.,<br>Insufficient discriminatory power of MALDI-TOF mass spectrometry for typing of Enterococcus faecium and Staphylococcus aureus isolates. <br><i>J Microbiol Methods</i>, <b>2014</b>. 100: p. 58-69.<br>
https://www.ncbi.nlm.nih.gov/pubmed/24614010.<br> &nbsp; <br></li>
 
<li>Lasch, P. and D. Naumann,<br>MALDI-TOF Mass Spectrometry for the Rapid Identification of Highly Pathogenic Microorganisms. <br><i>Proteomics, Glycomics and Antigenicity of BSL3 and BSL4 Agents, First Edition. Edited by Jiri Stulik, Rudolf Toman, Patrick Butaye, Robert G. Ulrich. 2011 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2011 by Wiley-VCH Verlag GmbH & Co. KGaA.</i>, <b>2011</b>: p. 219-212.<br>
http://dx.doi.org/10.1002/9783527638192.ch17.<br> &nbsp; <br></li>
 
<li>Lasch, P., M. Drevinek, H. Nattermann, R. Grunow, et al.,<br>Characterization of Yersinia using MALDI-TOF mass spectrometry and chemometrics. <br><i>Anal Chem</i>, <b>2010</b>. 82(20): p. 8464-75.<br>
http://www.ncbi.nlm.nih.gov/pubmed/20866090.<br> &nbsp; <br></li>
 
<li>Minan, A., A. Bosch, P. Lasch, M. Stammler, et al.,<br>Rapid identification of Burkholderia cepacia complex species including strains of the novel Taxon K, recovered from cystic fibrosis patients by intact cell MALDI-ToF mass spectrometry. <br><i>Analyst</i>, <b>2009</b>. 134(6): p. 1138-48.<br>
https://www.ncbi.nlm.nih.gov/pubmed/19475140.<br> &nbsp; <br></li>
 
<li>Lasch, P., W. Beyer, H. Nattermann, M. Stammler, et al.,<br>Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks. <br><i>Appl Environ Microbiol</i>, <b>2009</b>. 75(22): p. 7229-42.<br>
http://www.ncbi.nlm.nih.gov/pubmed/19767470.<br> &nbsp; <br></li>
 
<li>Lasch, P., H. Nattermann, M. Erhard, M. Stammler, et al.,<br>MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores. <br><i>Anal Chem</i>, <b>2008</b>. 80(6): p. 2026-34.<br>
https://www.ncbi.nlm.nih.gov/pubmed/18290666.<br> &nbsp; <br></li>
 
</ol>

Latest revision as of 17:42, 4 February 2025

Acknowledgements

MicrobeMS is a software project that has been developed by Peter Lasch at the Proteomics and Spectroscopy unit at the Robert Koch-Institute (Berlin/Germany). MicrobeMS is not open source but is provided for free, for testing or non-commercial use. Please send us references to any publications, presentations, or successful funding applications that make use of the MicrobeMS software, or MicrobeMS data sets (e-mail)).


We kindly ask users of MicrobeMS and MicrobeMS data sets to acknowledge us in their publications by citing the following publication:

Publications in which MicrobeMS has been used or mentioned

 

  1. Lasch, P., W. Beyer, A. Bosch, R. Borriss, et al.,
    A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria.
    Sci Data, 2025. 12(1): p. 187.
    https://doi.org/10.1038/s41597-025-04504-z
     
  2. Blumenscheit, C., Pfeifer, Y., Werner, G., John, C., Layer-Nicolaou, F., Schneider, A., Lasch, P., Doellinger, J.,
    Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics.
    bioRxiv - biorxiv.org, Oct 28, 2024.
    https://doi.org/10.1101/2024.09.09.612008 .
     
  3. Collins, T.J., Muste, C., Owens, K.G.
    Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data.
    J Am Soc Mass Spectrom, 2024. 35, 6, 1352–1362.
    https://dx.doi.org/10.1021/jasms.4c00101.
     
  4. Lasch, P., M. Stämmler, and A. Schneider,
    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).
    Zenodo, Mar 6, 2023.
    https://doi.org/10.5281/zenodo.7702374.
     
  5. Yang Y.,
    Chapter 3: MALDI-TOF Mass Fingerprinting for Rapid Identification of Bacteria: Data Analysis and Algorithm Development.
    Detection and Analysis of Microorganisms by Mass Spectrometry: New Developments in Mass Spectrometry,06 Oct 2023
    https://doi.org/10.1039/BK9781837670338-00045.
     
  6. Yin, M. M. Gao, Y. L., Zheng, C.H., Liu, J.X.,
    NTBiRW: A Novel Neighbor Model based on Two-tier Bi-Random Walk for Predicting Potential Disease-related Microbes.
    IEEE J Biomed Health Inform 27(3),1644-1653). 07 Feb. 2023.
    https://doi.org/10.1109/JBHI.2022.3229473.
     
  7. Wang, L., Yang, X., Kuang, L., Zhang, Z., Zeng, B., Chen, Z.,
    Graph Convolutional Neural Network with Multi-Layer Attention Mechanism for Predicting Potential Microbe-Disease Associations. Current Bioinformatics. 18(6):497-508(12). 2023.
    https://doi.org/10.2174/1574893618666230316113621.
     
  8. Ramadan, A.A.,
    Bacterial typing methods from past to present: A comprehensive overview.
    Gene Reports, 2022. 29: p. 101675.
    https://dx.doi.org/10.1016/j.genrep.2022.101675.
     
  9. Qiao, L.,
    MALDI-TOF MS for pathogenic bacteria analysis.
    International Journal of Mass Spectrometry, 2022. 482: p. 116935.
    https://dx.doi.org/10.1016/j.ijms.2022.116935.
     
  10. Blumenscheit, C., Y. Pfeifer, G. Werner, C. John, et al.,
    Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics.
    Anal Chem, 2021. 93(44): p. 14599-14608.
    https://www.ncbi.nlm.nih.gov/pubmed/34697938.
     
  11. Lasch, P., A. Schneider, C. Blumenscheit, and J. Doellinger,
    Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS(1)) and in Silico Peptide Mass Libraries.
    Mol Cell Proteomics, 2020. 19(12): p. 2125-2139.
    https://www.ncbi.nlm.nih.gov/pubmed/32998977.
     
  12. Gittens, R.A., A. Almanza, K.L. Bennett, L.C. Mejia, et al.,
    Proteomic fingerprinting of Neotropical hard tick species (Acari: Ixodidae) using a self-curated mass spectra reference library.
    PLoS Negl Trop Dis, 2020. 14(10): p. e0008849.
    https://www.ncbi.nlm.nih.gov/pubmed/33108372.
     
  13. Baumeister, T.U.H., M. Vallet, F. Kaftan, L. Guillou, et al.,
    Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry.
    Metabolomics, 2020. 16(3): p. 28.
    https://www.ncbi.nlm.nih.gov/pubmed/32090296.
     
  14. Lasch, P., A. Schneider, C. Blumenscheit, and J. Doellinger,
    Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data.
    bioRxiv, 2019.
    https://doi.dx.org/10.1101/870089 .
     
  15. Martina, P., M. Leguizamon, C.I. Prieto, S.A. Sousa, et al.,
    Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils.
    Int J Syst Evol Microbiol, 2018. 68(1): p. 14-20.
    https://www.ncbi.nlm.nih.gov/pubmed/29095137.
     
  16. Lasch, P., M. Stämmler, and A. Schneider,
    Version 3 (20181130) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI).
    Zenodo, 2018. November 30, 2018.
    https://dx.doi.org/10.5281/zenodo.1880975.
     
  17. Yang, Y., Y. Lin, Z. Chen, T. Gong, et al.,
    Bacterial Whole Cell Typing by Mass Spectra Pattern Matching with Bootstrapping Assessment.
    Anal Chem, 2017. 89(22): p. 12556-12561.
    https://www.ncbi.nlm.nih.gov/pubmed/29086558.
     
  18. Meyer, B., A. Rabenstein, and J. Kuever,
    Mass Spectrometry: A Powerful Tool for the Identification of Wine-Related Bacteria and Yeasts.
    Biology of Microorganisms on Grapes, in Must and in Wine, 2017: p. 659-701.
    https://dx.doi.org/10.1007/978-3-319-60021-5_27.
     
  19. Lasch, P., M. Stämmler, and A. Schneider,
    Version 2 (20170523) of the MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI).
    Zenodo, 2017. May 23, 2017.
    http://dx.doi.org/10.5281/zenodo.582602.
     
  20. Lasch, P., M. Stämmler, and A. Schneider,
    A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI).
    Zenodo, 2016. Oct 27, 2017.
    http://dx.doi.org/10.5281/zenodo.163517.
     
  21. Lasch, P., D. Jacob, S.R. Klee, and G. Werner,
    Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains.
    In: Applications of Mass Spectrometry in Microbiology, Plamen Demirev, Todd R. Sandrin (Eds.), 2016. Springer International Publishing: p. 203-234.
    http://dx.doi.org/10.1007/978-3-319-26070-9_8.
     
  22. Lasch, P., D. Jacob, R. Grunow, T. Schwecke, and J. Doellinger,
    Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS for the identification of highly pathogenic bacteria.
    TrAC Trends in Analytical Chemistry, 2016. 85, Part B(Trends in CBRN Measurements for safety and security): p. 103–111.
    http://dx.doi.org/10.1016/j.trac.2016.04.013.
     
  23. Lasch, P., R. Grunow, K. Antonation, S.A. Weller, and D. Jacob,
    Inactivation Techniques for MALDI-TOF MS Analysis of Highly Pathogenic Bacteria - A Critical Review.
    TrAC Trends in Analytical Chemistry, 2016. 85, Part B(Trends in CBRN Measurements for safety and security): p. 112–119.
    http://dx.doi.org/10.1016/j.trac.2016.04.012.
     
  24. Dieckmann, R., J.A. Hammerl, H. Hahmann, A. Wicke, et al.,
    Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy.
    Faraday Discuss, 2016. 187: p. 353-75.
    http://www.ncbi.nlm.nih.gov/pubmed/27053001.
     
  25. Sousa, C., J. Botelho, F. Grosso, L. Silva, et al.,
    Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions.
    Front Microbiol, 2015. 6: p. 481.
    http://www.ncbi.nlm.nih.gov/pubmed/26042113.
     
  26. Smith, E.M., Z.N. Willis, M. Blakeley, F. Lovatt, et al.,
    Bacterial species and their associations with acute and chronic mastitis in suckler ewes.
    J Dairy Sci, 2015. 98(10): p. 7025-33.
    https://www.ncbi.nlm.nih.gov/pubmed/26277313.
     
  27. Lasch, P., T. Wahab, S. Weil, B. Palyi, et al.,
    Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial.
    J Clin Microbiol, 2015. 53(8): p. 2632-40.
    https://www.ncbi.nlm.nih.gov/pubmed/26063856.
     
  28. Lasch, P., C. Fleige, M. Stammler, F. Layer, et al.,
    Insufficient discriminatory power of MALDI-TOF mass spectrometry for typing of Enterococcus faecium and Staphylococcus aureus isolates.
    J Microbiol Methods, 2014. 100: p. 58-69.
    https://www.ncbi.nlm.nih.gov/pubmed/24614010.
     
  29. Lasch, P. and D. Naumann,
    MALDI-TOF Mass Spectrometry for the Rapid Identification of Highly Pathogenic Microorganisms.
    Proteomics, Glycomics and Antigenicity of BSL3 and BSL4 Agents, First Edition. Edited by Jiri Stulik, Rudolf Toman, Patrick Butaye, Robert G. Ulrich. 2011 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2011 by Wiley-VCH Verlag GmbH & Co. KGaA., 2011: p. 219-212.
    http://dx.doi.org/10.1002/9783527638192.ch17.
     
  30. Lasch, P., M. Drevinek, H. Nattermann, R. Grunow, et al.,
    Characterization of Yersinia using MALDI-TOF mass spectrometry and chemometrics.
    Anal Chem, 2010. 82(20): p. 8464-75.
    http://www.ncbi.nlm.nih.gov/pubmed/20866090.
     
  31. Minan, A., A. Bosch, P. Lasch, M. Stammler, et al.,
    Rapid identification of Burkholderia cepacia complex species including strains of the novel Taxon K, recovered from cystic fibrosis patients by intact cell MALDI-ToF mass spectrometry.
    Analyst, 2009. 134(6): p. 1138-48.
    https://www.ncbi.nlm.nih.gov/pubmed/19475140.
     
  32. Lasch, P., W. Beyer, H. Nattermann, M. Stammler, et al.,
    Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks.
    Appl Environ Microbiol, 2009. 75(22): p. 7229-42.
    http://www.ncbi.nlm.nih.gov/pubmed/19767470.
     
  33. Lasch, P., H. Nattermann, M. Erhard, M. Stammler, et al.,
    MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores.
    Anal Chem, 2008. 80(6): p. 2026-34.
    https://www.ncbi.nlm.nih.gov/pubmed/18290666.
     
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