File:Array-spec-avr.jpg and Mass Spectrometry Databases: Difference between pages
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== Introduction == | |||
Library-based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82 MicrobeMS can deal with experimental MALDI-TOF or LC-MS¹ mass spectra and the respective MS databases. <br> | |||
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'', ''Burkholderia mallei'', ''Burkholderia pseudomallei'' and ''Francisella tularensis'' as well as a selection of MALDI-TOF mass spectra from their close and more distant relatives. The RKI mass spectral databases 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 databases are distributed as zip archives and contain the original mass spectra in its native data format (Bruker Daltonics). MALDI-TOF MS Databases will be updated on a regular basis.<br> | |||
The LC-MS¹ database is an ''in silico'' database which has been compiled from Uni-Prot Knowledgebase (Uni-Prot/KB Swissprot and TrEMBL) resources, 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. [https://zenodo.org/record/7702375 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://zenodo.org/record/7702375 https://zenodo.org/record/7702375] | |||
Version Mar 06, 2023, creative commons CC BY-NC-SA 4.0 license | |||
2. [https://doi.org/10.5281/zenodo.1880975 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 https://doi.org/10.5281/zenodo.1880975] | |||
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): | |||
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 http://doi.org/10.5281/zenodo.582602] | |||
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): | |||
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 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, [https://doi.org/10.1101/870089 ''Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data]'', bioRxiv (Dec 10, '''2018'''), doi:10.1101/870089.<br> | |||
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 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|Identification analysis by means of LC-MS¹ and ''in silico'' databases]] |
Revision as of 15:12, 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 deal with experimental MALDI-TOF or LC-MS¹ mass spectra and the respective MS databases.
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Yersinia pestis, Burkholderia mallei, Burkholderia pseudomallei and Francisella tularensis as well as a selection of MALDI-TOF mass spectra from their close and more distant relatives. The RKI mass spectral databases 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 databases are distributed as zip archives and contain the original mass spectra in its native data format (Bruker Daltonics). MALDI-TOF MS Databases will be updated on a regular basis.
The LC-MS¹ database is an in silico database which has been compiled from Uni-Prot Knowledgebase (Uni-Prot/KB Swissprot and TrEMBL) resources, 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://zenodo.org/record/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
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