Mass Spectrometry Databases: Difference between revisions

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== Introduction ==
== Introduction ==


Library based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82, MicrobeMS can work with experimental MALDI-TOF or LC-MS;&sup1 mass spectra and their corresponding MS databases.
Library based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82, MicrobeMS can work with experimental MALDI-TOF or LC-MS&sup1; mass spectra and their corresponding MS databases.<br>
<br>
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectra of highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'', ''Burkholderia mallei'', ''Burkholderia pseudomallei'', ''Brucella melitensis'' and ''Francisella tularensis'' as well as a selection of MALDI-TOF mass spectra of their close and distant relatives. The RKI mass spectral databases 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 databases are distributed as zip archives and contain the original mass spectra in their native data format (Bruker Daltonics). The MALDI-TOF MS databases are updated on a regular basis.<br>
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectra of highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'', ''Burkholderia mallei'', ''Burkholderia pseudomallei'', ''Brucella melitensis'' and ''Francisella tularensis'' as well as a selection of MALDI-TOF mass spectra of their close and distant relatives. The RKI mass spectral databases 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 databases are distributed as zip archives and contain the original mass spectra in their native data format (Bruker Daltonics). The MALDI-TOF MS databases are updated on a regular basis.  
The LC-MS&sup1; database is an ''in silico'' database compiled from Uni-Prot Knowledgebase resources (Uni-Prot/KB Swissprot and TrEMBL), for details see below).
<br>
The LC-MS;&sup1 database is an ''in silico'' database compiled from Uni-Prot Knowledgebase resources (Uni-Prot/KB Swissprot and TrEMBL), for details see below).


== MALDI-TOF MS databases ==
== MALDI-TOF MS databases ==
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     Version Nov 30, 2018, creative commons CC BY-NC-SA 4.0 license
     Version Nov 30, 2018, creative commons CC BY-NC-SA 4.0 license


   3. [https://www.microbe-ms.com/microbe-ms/refdata/3745_Zenodo_v1.pdf Zenodo database version 2] (20170523):
   3. [https://wiki.microbe-ms.com/upload/3745_Zenodo_v1.pdf Zenodo database version 2] (20170523):
     Lasch P, St&auml;mmler M & Schneider , (2017). Version 2 (20170523) of the  
     Lasch P, St&auml;mmler M & Schneider , (2017). Version 2 (20170523) of the  
     MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
     MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
Line 34: Line 32:
     Version May 23, 2017, creative commons CC BY-NC-SA 4.0 license
     Version May 23, 2017, creative commons CC BY-NC-SA 4.0 license


   4. [https://www.microbe-ms.com/microbe-ms/refdata/3280_Zenodo_v1.pdf Zenodo database version 1] (20161027):
   4. [https://wiki.microbe-ms.com/upload/3280_Zenodo_v1.pdf Zenodo database version 1] (20161027):
     Lasch P, St&auml;mmler M & Schneider A, (2016). A MALDI-TOF Mass Spectrometry
     Lasch P, St&auml;mmler M & Schneider A, (2016). A MALDI-TOF Mass Spectrometry
     Database for Identification and Classification of Highly Pathogenic Microorganisms from  
     Database for Identification and Classification of Highly Pathogenic Microorganisms from  

Latest revision as of 14:54, 21 March 2023


Introduction

Library based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82, MicrobeMS can work with experimental MALDI-TOF or LC-MS¹ mass spectra and their corresponding MS databases.
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectra of highly pathogenic (biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Yersinia pestis, Burkholderia mallei, Burkholderia pseudomallei, Brucella melitensis and Francisella tularensis as well as a selection of MALDI-TOF mass spectra of their close and distant relatives. The RKI mass spectral databases 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 databases are distributed as zip archives and contain the original mass spectra in their native data format (Bruker Daltonics). The MALDI-TOF MS databases are updated on a regular basis.
The LC-MS¹ database is an in silico database compiled from Uni-Prot Knowledgebase resources (Uni-Prot/KB Swissprot and TrEMBL), for details see below).

MALDI-TOF MS databases

The different versions of RKI biosafety level 3 (BSL-3) MALDI-TOF MS database can be downloaded from the following locations:

 1. Zenodo database version 4 (20230306):
    Lasch P, Stämmler M & Schneider A, (2023). Version 4 (20230306) of the 
    MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
    Pathogenic Microorganisms from the Robert Koch-Institute (RKI). 
    Zenodo. https://doi.org/10.5281/zenodo.7702375
    Version Mar 06, 2023, creative commons CC BY-NC-SA 4.0 license
 2. Zenodo database version 3 (20181130):
    Lasch P, Stämmler M & Schneider A, (2018). 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. https://doi.org/10.5281/zenodo.1880975
    Version Nov 30, 2018, creative commons CC BY-NC-SA 4.0 license
 3. Zenodo database version 2 (20170523):
    Lasch P, Stämmler M & Schneider , (2017). 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. http://doi.org/10.5281/zenodo.582602
    Version May 23, 2017, creative commons CC BY-NC-SA 4.0 license
 4. Zenodo database version 1 (20161027):
    Lasch P, Stämmler M & Schneider A, (2016). A MALDI-TOF Mass Spectrometry
    Database for Identification and Classification of Highly Pathogenic Microorganisms from 
    the Robert Koch-Institute (RKI). Zenodo. http://doi.org/10.5281/zenodo.163517
    Version October 27, 2016, creative commons CC BY-NC-SA 4.0 license

LC-MS¹ databases

The original concept of microbial identification by means of MALDI-TOF MS of cultivated microbial cells and spectral distance-based comparison with entries of a microorganism spectra library has been adapted for LC-MS¹ microbial identification, see this preprint: Lasch P, Schneider A, Blumenscheit C and Doellinger J, Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data, bioRxiv (Dec 10, 2018), doi:10.1101/870089.

 1. Lasch P, Schneider A, Blumenscheit C, Doellinger J. (2019). In silico Database for 
    Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹). 
    Zenodo. https://doi.org/10.5281/zenodo.3573996
    Version December 13, 2019, creative commons CC BY-NC-SA 4.0 license

Details can be found here: Identification analysis by means of LC-MS¹ and in silico databases