Mass Spectrometry Databases: Difference between revisions
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== Introduction == | == Introduction == | ||
Library | 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.<br> | ||
The RKI databases of microbial MALDI-TOF mass spectra contain mass | 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 LC-MS¹ database is an ''in silico'' database | 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 == | == MALDI-TOF MS databases == | ||
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The different versions of RKI biosafety level 3 (BSL-3) MALDI-TOF MS database can be downloaded from the following locations: | 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 | 1. [https://doi.org/10.5281/zenodo.7702375 Zenodo database version 4] (20230306): | ||
Lasch P, Stämmler M & Schneider A, (2023). Version 4 ( | Lasch P, Stämmler M & Schneider A, (2023). Version 4 (20230306) of the | ||
MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly | MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly | ||
Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | ||
Zenodo. [https:// | Zenodo. [https://doi.org/10.5281/zenodo.7702375 https://doi.org/10.5281/zenodo.7702375] | ||
Version | Version Mar 06, 2023, creative commons CC BY-NC-SA 4.0 license | ||
2. Zenodo database version 3 (20181130): | 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 | Lasch P, Stämmler M & Schneider A, (2018). Version 3 (20181130) of the | ||
MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly | MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly | ||
Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | ||
Zenodo. [https://doi.org/10.5281/zenodo.1880975 https://doi.org/10.5281/zenodo.1880975] | Zenodo. [https://doi.org/10.5281/zenodo.1880975 https://doi.org/10.5281/zenodo.1880975] | ||
Version Nov 30, 2018, creative commons CC BY-NC 4.0 license | Version Nov 30, 2018, creative commons CC BY-NC-SA 4.0 license | ||
3. [https:// | 3. [https://wiki.microbe-ms.com/upload/3745_Zenodo_v1.pdf Zenodo database version 2] (20170523): | ||
Lasch P, Stämmler M & Schneider , (2017). Version 2 (20170523) of the | Lasch P, Stämmler 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 | ||
Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | Pathogenic Microorganisms from the Robert Koch-Institute (RKI). | ||
Zenodo. [http://doi.org/10.5281/zenodo.582602 http://doi.org/10.5281/zenodo.582602] | Zenodo. [http://doi.org/10.5281/zenodo.582602 http://doi.org/10.5281/zenodo.582602] | ||
Version May 23, 2017, creative commons CC BY-NC 4.0 license | Version May 23, 2017, creative commons CC BY-NC-SA 4.0 license | ||
4. [https:// | 4. [https://wiki.microbe-ms.com/upload/3280_Zenodo_v1.pdf Zenodo database version 1] (20161027): | ||
Lasch P, Stämmler M & Schneider A, (2016). A MALDI-TOF Mass Spectrometry | Lasch P, Stämmler 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 | ||
the Robert Koch-Institute (RKI). Zenodo. [http://doi.org/10.5281/zenodo.163517 http://doi.org/10.5281/zenodo.163517] | 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 4.0 license | Version October 27, 2016, creative commons CC BY-NC-SA 4.0 license | ||
== LC-MS¹ databases == | == LC-MS¹ databases == | ||
Line 45: | Line 45: | ||
Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹). | 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] | Zenodo. [https://doi.org/10.5281/zenodo.3573996 https://doi.org/10.5281/zenodo.3573996] | ||
Version December 13, 2019, creative commons CC BY-NC 4.0 license | 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]] | 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]] |
Latest revision as of 15:54, 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